Starting phenix.real_space_refine on Thu Mar 5 22:06:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stn_25434/03_2026/7stn_25434_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stn_25434/03_2026/7stn_25434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7stn_25434/03_2026/7stn_25434_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stn_25434/03_2026/7stn_25434_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7stn_25434/03_2026/7stn_25434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stn_25434/03_2026/7stn_25434.map" } resolution = 3.19 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 8480 2.51 5 N 2062 2.21 5 O 2326 1.98 5 H 12256 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 231 Unusual residues: {'3PE': 5, 'BGI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'3PE': 3, 'BGI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Time building chain proxies: 4.99, per 1000 atoms: 0.20 Number of scatterers: 25188 At special positions: 0 Unit cell: (135, 76.68, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 O 2326 8.00 N 2062 7.00 C 8480 6.00 H 12256 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.0 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 60.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.663A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.704A pdb=" N GLY A 245 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.872A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.588A pdb=" N TYR A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.533A pdb=" N LEU A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.661A pdb=" N LYS A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 370 through 380 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.569A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 451 " --> pdb=" O TRP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.537A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.857A pdb=" N ASP A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 3.531A pdb=" N TYR A 511 " --> pdb=" O ASN A 507 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.574A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.002A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.826A pdb=" N GLU A 603 " --> pdb=" O TYR A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 613 removed outlier: 3.937A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 661 removed outlier: 4.138A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.545A pdb=" N THR A 667 " --> pdb=" O LYS A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 694 Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.600A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 745 Processing helix chain 'A' and resid 750 through 787 removed outlier: 3.969A pdb=" N TYR A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 787 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 Processing helix chain 'A' and resid 798 through 822 removed outlier: 4.092A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 3.547A pdb=" N SER A 831 " --> pdb=" O HIS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 removed outlier: 3.561A pdb=" N TYR A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) Proline residue: A 840 - end of helix removed outlier: 3.842A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 904 Processing helix chain 'A' and resid 917 through 946 removed outlier: 4.296A pdb=" N TYR A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 3.987A pdb=" N ASN A 951 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 1002 removed outlier: 3.887A pdb=" N ASN A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.663A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.704A pdb=" N GLY B 245 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.872A pdb=" N PHE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.588A pdb=" N TYR B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 removed outlier: 3.533A pdb=" N LEU B 326 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.661A pdb=" N LYS B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.570A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 451 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 removed outlier: 3.537A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.857A pdb=" N ASP B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 3.531A pdb=" N TYR B 511 " --> pdb=" O ASN B 507 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.575A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 550' Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.002A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.826A pdb=" N GLU B 603 " --> pdb=" O TYR B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 613 removed outlier: 3.936A pdb=" N CYS B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 609 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 removed outlier: 4.139A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.544A pdb=" N THR B 667 " --> pdb=" O LYS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 694 Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.600A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 745 Processing helix chain 'B' and resid 750 through 787 removed outlier: 3.969A pdb=" N TYR B 754 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 798 through 822 removed outlier: 4.093A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 removed outlier: 3.546A pdb=" N SER B 831 " --> pdb=" O HIS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 853 removed outlier: 3.562A pdb=" N TYR B 835 " --> pdb=" O SER B 831 " (cutoff:3.500A) Proline residue: B 840 - end of helix removed outlier: 3.842A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 904 Processing helix chain 'B' and resid 917 through 946 removed outlier: 4.296A pdb=" N TYR B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 removed outlier: 3.987A pdb=" N ASN B 951 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 1002 removed outlier: 3.887A pdb=" N ASN B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.816A pdb=" N LYS B 874 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 391 " --> pdb=" O ALA B 873 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU B 875 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 357 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU A 431 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 359 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 433 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 361 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 435 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 363 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG A 622 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 491 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N CYS A 624 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY A 493 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER A 626 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ILE A 495 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ARG A 628 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N THR A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU A 630 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.188A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 240 removed outlier: 3.816A pdb=" N LYS A 874 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE B 357 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU B 431 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 359 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS B 433 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 361 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 435 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER B 363 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ARG B 622 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 491 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N CYS B 624 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY B 493 " --> pdb=" O CYS B 624 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER B 626 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N ILE B 495 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ARG B 628 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N THR B 497 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU B 630 " --> pdb=" O THR B 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.187A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2085 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: 6.19 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12232 1.03 - 1.23: 46 1.23 - 1.42: 5654 1.42 - 1.61: 7460 1.61 - 1.81: 106 Bond restraints: 25498 Sorted by residual: bond pdb=" C28 BGI B1202 " pdb=" N27 BGI B1202 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C28 BGI A1202 " pdb=" N27 BGI A1202 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C28 BGI A1202 " pdb=" N22 BGI A1202 " ideal model delta sigma weight residual 1.382 1.515 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C28 BGI B1202 " pdb=" N22 BGI B1202 " ideal model delta sigma weight residual 1.382 1.514 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C13 BGI B1202 " pdb=" N15 BGI B1202 " ideal model delta sigma weight residual 1.343 1.472 -0.129 2.00e-02 2.50e+03 4.19e+01 ... (remaining 25493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 45356 2.88 - 5.76: 237 5.76 - 8.64: 49 8.64 - 11.52: 2 11.52 - 14.40: 8 Bond angle restraints: 45652 Sorted by residual: angle pdb=" O12 3PE A1203 " pdb=" P 3PE A1203 " pdb=" O14 3PE A1203 " ideal model delta sigma weight residual 123.79 109.39 14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE B1203 " pdb=" P 3PE B1203 " pdb=" O14 3PE B1203 " ideal model delta sigma weight residual 123.79 109.42 14.37 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE A1206 " pdb=" P 3PE A1206 " pdb=" O14 3PE A1206 " ideal model delta sigma weight residual 123.79 109.44 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.47 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 3PE B1204 " pdb=" P 3PE B1204 " pdb=" O14 3PE B1204 " ideal model delta sigma weight residual 123.79 109.48 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 45647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11595 17.84 - 35.69: 448 35.69 - 53.53: 195 53.53 - 71.38: 50 71.38 - 89.22: 14 Dihedral angle restraints: 12302 sinusoidal: 6540 harmonic: 5762 Sorted by residual: dihedral pdb=" N TYR B 699 " pdb=" CA TYR B 699 " pdb=" CB TYR B 699 " pdb=" CG TYR B 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.31 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" N TYR A 699 " pdb=" CA TYR A 699 " pdb=" CB TYR A 699 " pdb=" CG TYR A 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.28 54.28 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB ARG A 645 " pdb=" CG ARG A 645 " pdb=" CD ARG A 645 " pdb=" NE ARG A 645 " ideal model delta sinusoidal sigma weight residual 60.00 111.47 -51.47 3 1.50e+01 4.44e-03 9.02e+00 ... (remaining 12299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1896 0.099 - 0.199: 74 0.199 - 0.298: 2 0.298 - 0.398: 0 0.398 - 0.497: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C19 BGI A1202 " pdb=" C18 BGI A1202 " pdb=" C20 BGI A1202 " pdb=" O30 BGI A1202 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C19 BGI B1202 " pdb=" C18 BGI B1202 " pdb=" C20 BGI B1202 " pdb=" O30 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C18 BGI B1202 " pdb=" C17 BGI B1202 " pdb=" C19 BGI B1202 " pdb=" O31 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1971 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 945 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" N GLU B 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU B 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU B 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 945 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" N GLU A 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU A 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU A 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 943 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" N VAL A 944 " -0.030 2.00e-02 2.50e+03 pdb=" CA VAL A 944 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL A 944 " 0.013 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1055 2.21 - 2.80: 50880 2.80 - 3.40: 67180 3.40 - 4.00: 87425 4.00 - 4.60: 139624 Nonbonded interactions: 346164 Sorted by model distance: nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.608 2.450 nonbonded pdb=" O VAL B 665 " pdb=" HG SER B 668 " model vdw 1.670 2.450 nonbonded pdb=" O VAL A 665 " pdb=" HG SER A 668 " model vdw 1.671 2.450 nonbonded pdb=" OE1 GLN A 834 " pdb=" H GLN A 834 " model vdw 1.681 2.450 ... (remaining 346159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 135 through 1204) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.310 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.450 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 : 0.006 0.147 13242 Z= 0.328 Angle : 0.776 14.398 17896 Z= 0.323 Chirality : 0.042 0.497 1974 Planarity : 0.002 0.030 2214 Dihedral : 11.717 89.221 4922 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.15 % Allowed : 1.67 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.30 (0.22), residues: 1564 helix: 3.01 (0.17), residues: 828 sheet: 1.12 (0.45), residues: 140 loop : -0.60 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 926 TYR 0.007 0.001 TYR B 731 PHE 0.008 0.001 PHE B 984 TRP 0.010 0.001 TRP A 933 HIS 0.002 0.000 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00648 (13242) covalent geometry : angle 0.77560 (17896) hydrogen bonds : bond 0.13029 ( 723) hydrogen bonds : angle 4.93569 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.495 Fit side-chains REVERT: A 699 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: B 699 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7592 (m-80) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.2852 time to fit residues: 56.1171 Evaluate side-chains 63 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089943 restraints weight = 53761.715| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.74 r_work: 0.3036 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13242 Z= 0.160 Angle : 0.467 5.189 17896 Z= 0.253 Chirality : 0.039 0.161 1974 Planarity : 0.003 0.037 2214 Dihedral : 11.155 92.495 2110 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.83 % Allowed : 4.77 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.22), residues: 1564 helix: 2.78 (0.18), residues: 858 sheet: 1.10 (0.45), residues: 140 loop : -0.64 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 281 TYR 0.007 0.001 TYR B 842 PHE 0.012 0.001 PHE B 984 TRP 0.010 0.001 TRP A 933 HIS 0.002 0.001 HIS B 400 Details of bonding type rmsd covalent geometry : bond 0.00365 (13242) covalent geometry : angle 0.46668 (17896) hydrogen bonds : bond 0.05383 ( 723) hydrogen bonds : angle 4.30266 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.675 Fit side-chains REVERT: A 147 ASP cc_start: 0.5731 (OUTLIER) cc_final: 0.5505 (p0) REVERT: A 699 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: A 800 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: B 699 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 800 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7448 (tt0) outliers start: 11 outliers final: 3 residues processed: 73 average time/residue: 0.2348 time to fit residues: 25.4329 Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 95 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088327 restraints weight = 53535.625| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.48 r_work: 0.2976 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13242 Z= 0.170 Angle : 0.452 5.071 17896 Z= 0.245 Chirality : 0.039 0.151 1974 Planarity : 0.003 0.034 2214 Dihedral : 10.810 89.898 2110 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.68 % Allowed : 5.30 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.15 (0.22), residues: 1564 helix: 2.73 (0.17), residues: 852 sheet: 1.12 (0.45), residues: 140 loop : -0.58 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 281 TYR 0.010 0.001 TYR B 404 PHE 0.014 0.001 PHE B 984 TRP 0.010 0.001 TRP A 933 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00389 (13242) covalent geometry : angle 0.45241 (17896) hydrogen bonds : bond 0.05517 ( 723) hydrogen bonds : angle 4.18758 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.618 Fit side-chains REVERT: A 699 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: B 699 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8030 (m-80) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.2208 time to fit residues: 19.5805 Evaluate side-chains 59 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.088241 restraints weight = 53437.481| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.45 r_work: 0.2976 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13242 Z= 0.148 Angle : 0.430 5.002 17896 Z= 0.234 Chirality : 0.038 0.158 1974 Planarity : 0.003 0.030 2214 Dihedral : 10.419 89.260 2110 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.83 % Allowed : 5.61 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.21), residues: 1564 helix: 2.75 (0.17), residues: 850 sheet: 1.11 (0.44), residues: 140 loop : -0.49 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 372 TYR 0.007 0.001 TYR B 842 PHE 0.012 0.001 PHE B 984 TRP 0.009 0.001 TRP B 933 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00343 (13242) covalent geometry : angle 0.42963 (17896) hydrogen bonds : bond 0.05171 ( 723) hydrogen bonds : angle 4.06351 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.585 Fit side-chains REVERT: A 377 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8246 (mm) REVERT: A 699 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: A 800 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: B 699 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: B 800 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7617 (tt0) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.2326 time to fit residues: 20.8811 Evaluate side-chains 63 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086828 restraints weight = 53547.756| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.49 r_work: 0.2955 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13242 Z= 0.167 Angle : 0.442 5.090 17896 Z= 0.242 Chirality : 0.038 0.155 1974 Planarity : 0.003 0.032 2214 Dihedral : 10.575 88.178 2110 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.91 % Allowed : 5.61 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.08 (0.21), residues: 1564 helix: 2.72 (0.17), residues: 836 sheet: 1.08 (0.45), residues: 130 loop : -0.55 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 644 TYR 0.009 0.001 TYR A 404 PHE 0.014 0.001 PHE A 984 TRP 0.009 0.001 TRP B 933 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00390 (13242) covalent geometry : angle 0.44162 (17896) hydrogen bonds : bond 0.05409 ( 723) hydrogen bonds : angle 4.08538 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.687 Fit side-chains REVERT: A 699 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: A 800 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: B 699 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: B 800 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7644 (tt0) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.2506 time to fit residues: 23.7199 Evaluate side-chains 64 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 797 GLN B 598 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.122110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.084709 restraints weight = 53500.259| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.46 r_work: 0.2963 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13242 Z= 0.192 Angle : 0.464 5.136 17896 Z= 0.255 Chirality : 0.039 0.154 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.959 87.329 2110 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.98 % Allowed : 6.14 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.89 (0.21), residues: 1564 helix: 2.58 (0.17), residues: 836 sheet: 0.62 (0.44), residues: 130 loop : -0.56 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.010 0.001 TYR B 404 PHE 0.015 0.001 PHE B 541 TRP 0.009 0.002 TRP B 693 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00449 (13242) covalent geometry : angle 0.46437 (17896) hydrogen bonds : bond 0.05709 ( 723) hydrogen bonds : angle 4.15403 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.562 Fit side-chains REVERT: A 377 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 699 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: A 800 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: B 699 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: B 800 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7557 (tt0) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.2768 time to fit residues: 25.1958 Evaluate side-chains 66 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087105 restraints weight = 52995.048| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.45 r_work: 0.2980 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13242 Z= 0.133 Angle : 0.424 4.931 17896 Z= 0.232 Chirality : 0.038 0.135 1974 Planarity : 0.003 0.051 2214 Dihedral : 10.674 86.293 2110 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.98 % Allowed : 5.98 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.95 (0.21), residues: 1564 helix: 2.64 (0.18), residues: 846 sheet: 0.59 (0.44), residues: 130 loop : -0.61 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 154 TYR 0.008 0.001 TYR B 684 PHE 0.011 0.001 PHE B 984 TRP 0.009 0.001 TRP A 976 HIS 0.001 0.000 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00304 (13242) covalent geometry : angle 0.42387 (17896) hydrogen bonds : bond 0.05182 ( 723) hydrogen bonds : angle 4.02470 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.592 Fit side-chains REVERT: A 377 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 699 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: A 800 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: B 699 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: B 800 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7525 (tt0) outliers start: 13 outliers final: 8 residues processed: 61 average time/residue: 0.2733 time to fit residues: 23.8710 Evaluate side-chains 65 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 58 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 797 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084541 restraints weight = 53666.246| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.55 r_work: 0.2917 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13242 Z= 0.255 Angle : 0.503 5.326 17896 Z= 0.277 Chirality : 0.041 0.140 1974 Planarity : 0.004 0.035 2214 Dihedral : 11.256 85.378 2110 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.83 % Allowed : 6.36 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.66 (0.21), residues: 1564 helix: 2.44 (0.17), residues: 834 sheet: 0.22 (0.42), residues: 130 loop : -0.65 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 644 TYR 0.011 0.002 TYR B 815 PHE 0.019 0.002 PHE A 541 TRP 0.011 0.002 TRP B 693 HIS 0.004 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00599 (13242) covalent geometry : angle 0.50257 (17896) hydrogen bonds : bond 0.06171 ( 723) hydrogen bonds : angle 4.24301 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.644 Fit side-chains REVERT: A 377 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 699 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: B 699 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8029 (m-80) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.2790 time to fit residues: 24.2527 Evaluate side-chains 64 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 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 = 0.3662 r_free = 0.3662 target = 0.121969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086256 restraints weight = 53556.075| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.54 r_work: 0.2944 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13242 Z= 0.152 Angle : 0.441 5.377 17896 Z= 0.242 Chirality : 0.038 0.136 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.812 85.303 2110 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.98 % Allowed : 6.44 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.83 (0.21), residues: 1564 helix: 2.62 (0.17), residues: 832 sheet: 0.22 (0.43), residues: 130 loop : -0.61 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 366 TYR 0.009 0.001 TYR B 684 PHE 0.013 0.001 PHE A 984 TRP 0.008 0.001 TRP B 933 HIS 0.002 0.000 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00350 (13242) covalent geometry : angle 0.44088 (17896) hydrogen bonds : bond 0.05441 ( 723) hydrogen bonds : angle 4.09567 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.545 Fit side-chains REVERT: A 377 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7995 (mm) REVERT: A 699 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: A 800 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: B 699 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7950 (m-80) REVERT: B 800 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: B 882 ASP cc_start: 0.6279 (t0) cc_final: 0.5731 (p0) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.2663 time to fit residues: 24.5526 Evaluate side-chains 68 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 102 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 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 = 0.3638 r_free = 0.3638 target = 0.120111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084757 restraints weight = 53819.581| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.49 r_work: 0.2913 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13242 Z= 0.252 Angle : 0.503 5.304 17896 Z= 0.277 Chirality : 0.040 0.140 1974 Planarity : 0.004 0.035 2214 Dihedral : 11.238 84.874 2110 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.83 % Allowed : 6.74 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.55 (0.21), residues: 1564 helix: 2.36 (0.17), residues: 834 sheet: 0.00 (0.42), residues: 130 loop : -0.68 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 366 TYR 0.010 0.001 TYR B 404 PHE 0.017 0.002 PHE A 984 TRP 0.011 0.002 TRP B 693 HIS 0.004 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00596 (13242) covalent geometry : angle 0.50334 (17896) hydrogen bonds : bond 0.06195 ( 723) hydrogen bonds : angle 4.25374 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.586 Fit side-chains REVERT: A 699 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: A 882 ASP cc_start: 0.6324 (t0) cc_final: 0.5915 (p0) REVERT: B 699 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: B 882 ASP cc_start: 0.6325 (t0) cc_final: 0.5870 (p0) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.2755 time to fit residues: 24.8808 Evaluate side-chains 65 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 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 = 0.3656 r_free = 0.3656 target = 0.121464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.085921 restraints weight = 53233.531| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.76 r_work: 0.2948 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13242 Z= 0.164 Angle : 0.450 5.688 17896 Z= 0.247 Chirality : 0.038 0.136 1974 Planarity : 0.003 0.034 2214 Dihedral : 10.844 84.257 2110 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.83 % Allowed : 6.74 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.72 (0.21), residues: 1564 helix: 2.55 (0.17), residues: 832 sheet: 0.02 (0.43), residues: 130 loop : -0.66 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 372 TYR 0.009 0.001 TYR B 684 PHE 0.013 0.001 PHE A 984 TRP 0.009 0.001 TRP B 933 HIS 0.002 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00380 (13242) covalent geometry : angle 0.45033 (17896) hydrogen bonds : bond 0.05540 ( 723) hydrogen bonds : angle 4.12394 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5768.53 seconds wall clock time: 98 minutes 19.94 seconds (5899.94 seconds total)