Starting phenix.real_space_refine on Fri Mar 6 01:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lg5_23311/03_2026/7lg5_23311_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lg5_23311/03_2026/7lg5_23311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lg5_23311/03_2026/7lg5_23311_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lg5_23311/03_2026/7lg5_23311_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lg5_23311/03_2026/7lg5_23311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lg5_23311/03_2026/7lg5_23311.map" } resolution = 2.63 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= 0.004 sd= 0.041 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 24 5.49 5 Mg 12 5.21 5 S 96 5.16 5 C 16828 2.51 5 N 4696 2.21 5 O 5232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 26888 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6657 Classifications: {'peptide': 871} Link IDs: {'PTRANS': 40, 'TRANS': 830} Chain breaks: 1 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 3, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B, C, D Time building chain proxies: 7.18, per 1000 atoms: 0.27 Number of scatterers: 26888 At special positions: 0 Unit cell: (135.945, 147.915, 144.495, 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 96 16.00 P 24 15.00 Mg 12 11.99 O 5232 8.00 N 4696 7.00 C 16828 6.00 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6320 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 28 sheets defined 38.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.622A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.524A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 245 through 254 removed outlier: 5.188A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 405 through 408 removed outlier: 4.077A pdb=" N ILE A 408 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 423 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.716A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.881A pdb=" N VAL A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.575A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.865A pdb=" N ALA A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 630 Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 680 through 682 No H-bonds generated for 'chain 'A' and resid 680 through 682' Processing helix chain 'A' and resid 690 through 707 Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 781 through 790 Processing helix chain 'A' and resid 810 through 824 removed outlier: 3.551A pdb=" N ASP A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 removed outlier: 3.881A pdb=" N ILE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.622A pdb=" N ASP B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.525A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 217 Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 245 through 254 removed outlier: 5.188A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.078A pdb=" N ILE B 408 " --> pdb=" O THR B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 423 Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 472 through 480 removed outlier: 3.716A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 511 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.882A pdb=" N VAL B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 594 through 607 removed outlier: 3.576A pdb=" N LYS B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.865A pdb=" N ALA B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 630 Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 690 through 707 Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 781 through 790 Processing helix chain 'B' and resid 810 through 824 removed outlier: 3.550A pdb=" N ASP B 814 " --> pdb=" O GLY B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 868 removed outlier: 3.880A pdb=" N ILE B 866 " --> pdb=" O ALA B 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.623A pdb=" N ASP C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.525A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 210 through 217 Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 245 through 254 removed outlier: 5.188A pdb=" N ASN C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.077A pdb=" N ILE C 408 " --> pdb=" O THR C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 409 through 423 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'C' and resid 472 through 480 removed outlier: 3.715A pdb=" N MET C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 511 Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.881A pdb=" N VAL C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 Processing helix chain 'C' and resid 594 through 607 removed outlier: 3.576A pdb=" N LYS C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.864A pdb=" N ALA C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 630 Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 690 through 707 Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 750 through 762 Processing helix chain 'C' and resid 781 through 790 Processing helix chain 'C' and resid 810 through 824 removed outlier: 3.550A pdb=" N ASP C 814 " --> pdb=" O GLY C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 868 removed outlier: 3.881A pdb=" N ILE C 866 " --> pdb=" O ALA C 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.623A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.524A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 219 through 229 Processing helix chain 'D' and resid 245 through 254 removed outlier: 5.188A pdb=" N ASN D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 405 through 408 removed outlier: 4.077A pdb=" N ILE D 408 " --> pdb=" O THR D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 409 through 423 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 472 through 480 removed outlier: 3.716A pdb=" N MET D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 511 Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.881A pdb=" N VAL D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.575A pdb=" N LYS D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.865A pdb=" N ALA D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 630 Processing helix chain 'D' and resid 644 through 652 Processing helix chain 'D' and resid 680 through 682 No H-bonds generated for 'chain 'D' and resid 680 through 682' Processing helix chain 'D' and resid 690 through 707 Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'D' and resid 781 through 790 Processing helix chain 'D' and resid 810 through 824 removed outlier: 3.551A pdb=" N ASP D 814 " --> pdb=" O GLY D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 868 removed outlier: 3.881A pdb=" N ILE D 866 " --> pdb=" O ALA D 862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.720A pdb=" N ARG A 26 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 6 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 24 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR A 8 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 22 " --> pdb=" O THR A 8 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 109 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 275 removed outlier: 5.314A pdb=" N ILE A 273 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 260 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 258 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 4.351A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 534 removed outlier: 6.608A pdb=" N ILE A 525 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 490 " --> pdb=" O CYS A 574 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP A 575 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 616 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A 577 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN A 618 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N VAL A 579 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 635 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER A 639 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 667 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU A 669 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 795 through 796 removed outlier: 6.609A pdb=" N GLY A 769 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS A 741 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 854 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 743 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 10 removed outlier: 6.721A pdb=" N ARG B 26 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR B 6 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 24 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 22 " --> pdb=" O THR B 8 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 109 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'B' and resid 272 through 275 removed outlier: 5.314A pdb=" N ILE B 273 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE B 260 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 258 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.351A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB4, first strand: chain 'B' and resid 530 through 534 removed outlier: 6.609A pdb=" N ILE B 525 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 490 " --> pdb=" O CYS B 574 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 575 " --> pdb=" O TYR B 614 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL B 616 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY B 577 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN B 618 " --> pdb=" O GLY B 577 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N VAL B 579 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 635 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER B 639 " --> pdb=" O TYR B 660 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 677 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 667 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG B 675 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 669 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR B 673 " --> pdb=" O GLU B 669 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 795 through 796 removed outlier: 6.609A pdb=" N GLY B 769 " --> pdb=" O VAL B 853 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS B 741 " --> pdb=" O VAL B 852 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 854 " --> pdb=" O HIS B 741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 743 " --> pdb=" O VAL B 854 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 10 removed outlier: 6.721A pdb=" N ARG C 26 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 6 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 24 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR C 8 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 22 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL C 109 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'C' and resid 272 through 275 removed outlier: 5.314A pdb=" N ILE C 273 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE C 260 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 258 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 400 through 403 removed outlier: 4.351A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AC2, first strand: chain 'C' and resid 530 through 534 removed outlier: 6.608A pdb=" N ILE C 525 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 490 " --> pdb=" O CYS C 574 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP C 575 " --> pdb=" O TYR C 614 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL C 616 " --> pdb=" O ASP C 575 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY C 577 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASN C 618 " --> pdb=" O GLY C 577 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N VAL C 579 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL C 635 " --> pdb=" O ILE C 656 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 639 " --> pdb=" O TYR C 660 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 677 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 667 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG C 675 " --> pdb=" O ILE C 667 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU C 669 " --> pdb=" O THR C 673 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR C 673 " --> pdb=" O GLU C 669 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 795 through 796 removed outlier: 6.608A pdb=" N GLY C 769 " --> pdb=" O VAL C 853 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS C 741 " --> pdb=" O VAL C 852 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL C 854 " --> pdb=" O HIS C 741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 743 " --> pdb=" O VAL C 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 2 through 10 removed outlier: 6.720A pdb=" N ARG D 26 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR D 6 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL D 24 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR D 8 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 22 " --> pdb=" O THR D 8 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL D 109 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'D' and resid 272 through 275 removed outlier: 5.314A pdb=" N ILE D 273 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 260 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 258 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 400 through 403 removed outlier: 4.350A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AC9, first strand: chain 'D' and resid 530 through 534 removed outlier: 6.608A pdb=" N ILE D 525 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE D 490 " --> pdb=" O CYS D 574 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP D 575 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL D 616 " --> pdb=" O ASP D 575 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY D 577 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN D 618 " --> pdb=" O GLY D 577 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N VAL D 579 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL D 635 " --> pdb=" O ILE D 656 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER D 639 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 677 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE D 667 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG D 675 " --> pdb=" O ILE D 667 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU D 669 " --> pdb=" O THR D 673 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR D 673 " --> pdb=" O GLU D 669 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 795 through 796 removed outlier: 6.609A pdb=" N GLY D 769 " --> pdb=" O VAL D 853 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N HIS D 741 " --> pdb=" O VAL D 852 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL D 854 " --> pdb=" O HIS D 741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU D 743 " --> pdb=" O VAL D 854 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3108 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: 5.67 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4677 1.29 - 1.43: 6547 1.43 - 1.57: 15732 1.57 - 1.70: 220 1.70 - 1.84: 168 Bond restraints: 27344 Sorted by residual: bond pdb=" C PRO C 481 " pdb=" O PRO C 481 " ideal model delta sigma weight residual 1.240 1.156 0.084 1.12e-02 7.97e+03 5.66e+01 bond pdb=" C PRO B 481 " pdb=" O PRO B 481 " ideal model delta sigma weight residual 1.240 1.156 0.084 1.12e-02 7.97e+03 5.63e+01 bond pdb=" C PRO A 481 " pdb=" O PRO A 481 " ideal model delta sigma weight residual 1.240 1.156 0.084 1.12e-02 7.97e+03 5.63e+01 bond pdb=" C PRO D 481 " pdb=" O PRO D 481 " ideal model delta sigma weight residual 1.240 1.157 0.084 1.12e-02 7.97e+03 5.59e+01 bond pdb=" NE ARG A 35 " pdb=" CZ ARG A 35 " ideal model delta sigma weight residual 1.326 1.384 -0.058 1.10e-02 8.26e+03 2.82e+01 ... (remaining 27339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 34383 3.22 - 6.44: 2535 6.44 - 9.66: 259 9.66 - 12.88: 19 12.88 - 16.10: 16 Bond angle restraints: 37212 Sorted by residual: angle pdb=" N LEU A 843 " pdb=" CA LEU A 843 " pdb=" C LEU A 843 " ideal model delta sigma weight residual 113.50 97.40 16.10 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N LEU B 843 " pdb=" CA LEU B 843 " pdb=" C LEU B 843 " ideal model delta sigma weight residual 113.50 97.40 16.10 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N LEU C 843 " pdb=" CA LEU C 843 " pdb=" C LEU C 843 " ideal model delta sigma weight residual 113.50 97.41 16.09 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N LEU D 843 " pdb=" CA LEU D 843 " pdb=" C LEU D 843 " ideal model delta sigma weight residual 113.50 97.43 16.07 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N GLY D 78 " pdb=" CA GLY D 78 " pdb=" C GLY D 78 " ideal model delta sigma weight residual 112.82 97.67 15.15 1.38e+00 5.25e-01 1.21e+02 ... (remaining 37207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15943 17.99 - 35.98: 437 35.98 - 53.97: 156 53.97 - 71.95: 60 71.95 - 89.94: 28 Dihedral angle restraints: 16624 sinusoidal: 6712 harmonic: 9912 Sorted by residual: dihedral pdb=" C LEU C 425 " pdb=" N LEU C 425 " pdb=" CA LEU C 425 " pdb=" CB LEU C 425 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU D 425 " pdb=" N LEU D 425 " pdb=" CA LEU D 425 " pdb=" CB LEU D 425 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU A 425 " pdb=" N LEU A 425 " pdb=" CA LEU A 425 " pdb=" CB LEU A 425 " ideal model delta harmonic sigma weight residual -122.60 -112.31 -10.29 0 2.50e+00 1.60e-01 1.69e+01 ... (remaining 16621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2994 0.092 - 0.183: 1013 0.183 - 0.275: 249 0.275 - 0.366: 32 0.366 - 0.457: 12 Chirality restraints: 4300 Sorted by residual: chirality pdb=" CA PRO B 481 " pdb=" N PRO B 481 " pdb=" C PRO B 481 " pdb=" CB PRO B 481 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA PRO C 481 " pdb=" N PRO C 481 " pdb=" C PRO C 481 " pdb=" CB PRO C 481 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA PRO A 481 " pdb=" N PRO A 481 " pdb=" C PRO A 481 " pdb=" CB PRO A 481 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.45 2.00e-01 2.50e+01 5.16e+00 ... (remaining 4297 not shown) Planarity restraints: 4840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 780 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C SER D 780 " -0.067 2.00e-02 2.50e+03 pdb=" O SER D 780 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP D 781 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 780 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C SER A 780 " -0.067 2.00e-02 2.50e+03 pdb=" O SER A 780 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP A 781 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 780 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.50e+01 pdb=" C SER B 780 " 0.067 2.00e-02 2.50e+03 pdb=" O SER B 780 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 781 " -0.022 2.00e-02 2.50e+03 ... (remaining 4837 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 28 2.39 - 3.02: 15249 3.02 - 3.65: 37505 3.65 - 4.27: 62070 4.27 - 4.90: 99995 Nonbonded interactions: 214847 Sorted by model distance: nonbonded pdb=" OE2 GLU B 558 " pdb="MG MG B 903 " model vdw 1.766 2.170 nonbonded pdb=" OE2 GLU A 558 " pdb="MG MG A 903 " model vdw 1.766 2.170 nonbonded pdb=" OE2 GLU C 558 " pdb="MG MG C 903 " model vdw 1.766 2.170 nonbonded pdb=" OE2 GLU D 558 " pdb="MG MG D 903 " model vdw 1.766 2.170 nonbonded pdb=" OG1 THR D 500 " pdb="MG MG D 903 " model vdw 1.982 2.170 ... (remaining 214842 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 6.720 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: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 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 : 0.018 0.131 27344 Z= 0.990 Angle : 1.830 16.100 37212 Z= 1.245 Chirality : 0.098 0.457 4300 Planarity : 0.009 0.071 4840 Dihedral : 11.601 89.942 10304 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.13 % 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: -0.64 (0.13), residues: 3468 helix: -1.08 (0.13), residues: 1272 sheet: 1.47 (0.21), residues: 548 loop : -0.42 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 177 TYR 0.038 0.007 TYR C 285 PHE 0.034 0.006 PHE C 768 TRP 0.014 0.005 TRP A 763 HIS 0.019 0.003 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.01849 (27344) covalent geometry : angle 1.83019 (37212) hydrogen bonds : bond 0.20810 ( 1112) hydrogen bonds : angle 6.91742 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 CYS cc_start: 0.8489 (m) cc_final: 0.8176 (p) REVERT: A 243 PHE cc_start: 0.6625 (m-10) cc_final: 0.6393 (m-80) REVERT: B 133 CYS cc_start: 0.8491 (m) cc_final: 0.8171 (p) REVERT: B 243 PHE cc_start: 0.6484 (m-10) cc_final: 0.6246 (m-80) REVERT: C 133 CYS cc_start: 0.8534 (m) cc_final: 0.8212 (p) REVERT: C 243 PHE cc_start: 0.6699 (m-10) cc_final: 0.6482 (m-80) REVERT: D 133 CYS cc_start: 0.8467 (m) cc_final: 0.8154 (p) REVERT: D 243 PHE cc_start: 0.6685 (m-10) cc_final: 0.6458 (m-80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.6503 time to fit residues: 158.5834 Evaluate side-chains 106 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 HIS B 353 HIS B 740 HIS C 740 HIS D 740 HIS D 748 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.099739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.063507 restraints weight = 75861.000| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.60 r_work: 0.3011 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27344 Z= 0.139 Angle : 0.639 8.243 37212 Z= 0.347 Chirality : 0.047 0.198 4300 Planarity : 0.005 0.066 4840 Dihedral : 9.476 86.997 4072 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.74 % Allowed : 4.60 % Favored : 94.66 % 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: 0.00 (0.14), residues: 3468 helix: 0.14 (0.14), residues: 1308 sheet: 1.24 (0.23), residues: 532 loop : -0.44 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 754 TYR 0.015 0.002 TYR B 63 PHE 0.008 0.001 PHE D 638 TRP 0.034 0.002 TRP C 278 HIS 0.010 0.001 HIS B 83 Details of bonding type rmsd covalent geometry : bond 0.00287 (27344) covalent geometry : angle 0.63940 (37212) hydrogen bonds : bond 0.04647 ( 1112) hydrogen bonds : angle 5.12717 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 MET cc_start: 0.9014 (ptm) cc_final: 0.8659 (pp-130) REVERT: A 669 GLU cc_start: 0.8632 (tt0) cc_final: 0.8396 (tp30) REVERT: B 370 MET cc_start: 0.9013 (ptm) cc_final: 0.8670 (pp-130) REVERT: B 669 GLU cc_start: 0.8630 (tt0) cc_final: 0.8390 (tp30) REVERT: C 353 HIS cc_start: 0.8766 (m90) cc_final: 0.8401 (m170) REVERT: C 669 GLU cc_start: 0.8592 (tt0) cc_final: 0.8362 (tp30) REVERT: D 353 HIS cc_start: 0.8746 (m90) cc_final: 0.8362 (m170) REVERT: D 669 GLU cc_start: 0.8591 (tt0) cc_final: 0.8362 (tp30) REVERT: D 684 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8964 (ptm) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 0.5990 time to fit residues: 104.7920 Evaluate side-chains 124 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 243 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 302 optimal weight: 0.8980 chunk 314 optimal weight: 0.2980 chunk 114 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 284 optimal weight: 0.4980 chunk 247 optimal weight: 10.0000 chunk 321 optimal weight: 0.0270 chunk 129 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 HIS A 840 ASN B 353 HIS B 748 HIS B 840 ASN C 748 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.098533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062238 restraints weight = 75710.704| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.64 r_work: 0.2983 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27344 Z= 0.104 Angle : 0.549 8.474 37212 Z= 0.294 Chirality : 0.044 0.190 4300 Planarity : 0.004 0.051 4840 Dihedral : 8.563 83.206 4072 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.91 % Allowed : 5.93 % Favored : 93.15 % 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: 0.29 (0.14), residues: 3468 helix: 0.70 (0.15), residues: 1320 sheet: 1.31 (0.23), residues: 504 loop : -0.53 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 805 TYR 0.012 0.001 TYR B 285 PHE 0.011 0.001 PHE C 692 TRP 0.038 0.002 TRP D 278 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00213 (27344) covalent geometry : angle 0.54855 (37212) hydrogen bonds : bond 0.03922 ( 1112) hydrogen bonds : angle 4.57257 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 793 PHE cc_start: 0.8268 (m-80) cc_final: 0.7701 (m-80) REVERT: B 669 GLU cc_start: 0.8642 (tt0) cc_final: 0.8354 (tp30) REVERT: B 793 PHE cc_start: 0.8231 (m-80) cc_final: 0.7670 (m-80) REVERT: C 353 HIS cc_start: 0.8757 (m90) cc_final: 0.8382 (m170) REVERT: C 793 PHE cc_start: 0.8183 (m-80) cc_final: 0.7614 (m-80) REVERT: D 793 PHE cc_start: 0.8269 (m-80) cc_final: 0.7728 (m-80) outliers start: 26 outliers final: 12 residues processed: 141 average time/residue: 0.5593 time to fit residues: 94.1448 Evaluate side-chains 117 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 226 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 206 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 249 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN B 353 HIS B 840 ASN C 741 HIS C 840 ASN D 741 HIS D 840 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.091639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054644 restraints weight = 74980.749| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.62 r_work: 0.2798 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27344 Z= 0.189 Angle : 0.610 11.447 37212 Z= 0.326 Chirality : 0.047 0.206 4300 Planarity : 0.004 0.036 4840 Dihedral : 8.857 85.134 4072 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.62 % Allowed : 6.04 % Favored : 92.35 % 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: 0.01 (0.14), residues: 3468 helix: 0.61 (0.15), residues: 1344 sheet: 1.23 (0.23), residues: 496 loop : -0.87 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 754 TYR 0.015 0.002 TYR B 519 PHE 0.013 0.001 PHE D 457 TRP 0.070 0.003 TRP C 278 HIS 0.005 0.001 HIS A 586 Details of bonding type rmsd covalent geometry : bond 0.00449 (27344) covalent geometry : angle 0.61018 (37212) hydrogen bonds : bond 0.05602 ( 1112) hydrogen bonds : angle 4.77293 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 113 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.6977 (p) REVERT: B 75 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6781 (p) REVERT: C 75 THR cc_start: 0.7234 (OUTLIER) cc_final: 0.6956 (p) REVERT: D 75 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6996 (p) REVERT: D 767 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6545 (ppt170) outliers start: 46 outliers final: 17 residues processed: 142 average time/residue: 0.5976 time to fit residues: 99.6887 Evaluate side-chains 123 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 767 ARG Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Chi-restraints excluded: chain D residue 866 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 24 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 317 optimal weight: 0.0870 chunk 289 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 246 optimal weight: 10.0000 chunk 60 optimal weight: 0.0020 chunk 233 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 overall best weight: 1.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 HIS C 840 ASN D 840 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.092904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056219 restraints weight = 74946.464| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.64 r_work: 0.2837 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27344 Z= 0.116 Angle : 0.529 10.123 37212 Z= 0.279 Chirality : 0.044 0.193 4300 Planarity : 0.004 0.037 4840 Dihedral : 8.292 82.755 4072 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.79 % Allowed : 5.72 % Favored : 92.49 % 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: 0.31 (0.15), residues: 3468 helix: 0.97 (0.15), residues: 1320 sheet: 1.14 (0.22), residues: 520 loop : -0.72 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 754 TYR 0.011 0.001 TYR A 519 PHE 0.009 0.001 PHE D 692 TRP 0.037 0.002 TRP B 278 HIS 0.003 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00261 (27344) covalent geometry : angle 0.52940 (37212) hydrogen bonds : bond 0.03770 ( 1112) hydrogen bonds : angle 4.40678 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 110 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6880 (p) REVERT: A 94 MET cc_start: 0.7611 (mtt) cc_final: 0.7032 (mtt) REVERT: C 75 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6833 (p) REVERT: D 75 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6875 (p) outliers start: 51 outliers final: 20 residues processed: 150 average time/residue: 0.5223 time to fit residues: 94.5162 Evaluate side-chains 126 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 740 HIS Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 740 HIS Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 529 GLU Chi-restraints excluded: chain C residue 740 HIS Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 529 GLU Chi-restraints excluded: chain D residue 740 HIS Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 94 optimal weight: 0.7980 chunk 304 optimal weight: 0.0170 chunk 224 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 169 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 HIS B 840 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.092985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056256 restraints weight = 75013.957| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.66 r_work: 0.2841 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27344 Z= 0.106 Angle : 0.517 10.917 37212 Z= 0.270 Chirality : 0.044 0.198 4300 Planarity : 0.004 0.036 4840 Dihedral : 8.019 81.229 4072 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.47 % Allowed : 5.83 % Favored : 92.70 % 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: 0.33 (0.15), residues: 3468 helix: 1.05 (0.15), residues: 1328 sheet: 1.02 (0.22), residues: 528 loop : -0.74 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 754 TYR 0.011 0.001 TYR B 519 PHE 0.008 0.001 PHE D 692 TRP 0.032 0.002 TRP A 278 HIS 0.003 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00232 (27344) covalent geometry : angle 0.51660 (37212) hydrogen bonds : bond 0.03574 ( 1112) hydrogen bonds : angle 4.29353 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.6879 (p) REVERT: A 94 MET cc_start: 0.7625 (mtt) cc_final: 0.7060 (mtt) REVERT: B 75 THR cc_start: 0.7064 (OUTLIER) cc_final: 0.6730 (p) REVERT: B 94 MET cc_start: 0.7620 (mtt) cc_final: 0.7049 (mtt) REVERT: C 75 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6756 (p) REVERT: C 278 TRP cc_start: 0.8783 (OUTLIER) cc_final: 0.8363 (t60) REVERT: D 75 THR cc_start: 0.7126 (OUTLIER) cc_final: 0.6813 (p) REVERT: D 767 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6653 (ppt170) outliers start: 42 outliers final: 16 residues processed: 140 average time/residue: 0.5350 time to fit residues: 89.9941 Evaluate side-chains 120 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 767 ARG Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 228 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 HIS B 353 HIS B 741 HIS B 840 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.090368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053455 restraints weight = 74759.737| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.65 r_work: 0.2767 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 27344 Z= 0.199 Angle : 0.588 11.594 37212 Z= 0.310 Chirality : 0.046 0.231 4300 Planarity : 0.004 0.037 4840 Dihedral : 8.607 86.457 4072 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.33 % Allowed : 6.36 % Favored : 92.31 % 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: 0.04 (0.14), residues: 3468 helix: 0.88 (0.15), residues: 1348 sheet: 0.79 (0.22), residues: 528 loop : -0.98 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 653 TYR 0.014 0.001 TYR A 519 PHE 0.009 0.001 PHE A 457 TRP 0.016 0.002 TRP A 278 HIS 0.003 0.001 HIS C 586 Details of bonding type rmsd covalent geometry : bond 0.00474 (27344) covalent geometry : angle 0.58757 (37212) hydrogen bonds : bond 0.05247 ( 1112) hydrogen bonds : angle 4.57887 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7678 (mtt) cc_final: 0.7186 (mtt) REVERT: B 75 THR cc_start: 0.7196 (OUTLIER) cc_final: 0.6839 (p) REVERT: B 94 MET cc_start: 0.7668 (mtt) cc_final: 0.7178 (mtt) REVERT: C 689 MET cc_start: 0.8462 (mpp) cc_final: 0.7855 (pmm) REVERT: D 94 MET cc_start: 0.7675 (mtt) cc_final: 0.7173 (mtt) REVERT: D 767 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6836 (ppt170) outliers start: 38 outliers final: 17 residues processed: 132 average time/residue: 0.5702 time to fit residues: 89.6570 Evaluate side-chains 118 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 767 ARG Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 166 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.092018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055403 restraints weight = 74926.149| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.65 r_work: 0.2817 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27344 Z= 0.104 Angle : 0.524 12.566 37212 Z= 0.272 Chirality : 0.044 0.182 4300 Planarity : 0.004 0.038 4840 Dihedral : 8.106 84.627 4072 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.19 % Allowed : 6.78 % Favored : 92.03 % 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: 0.32 (0.15), residues: 3468 helix: 1.17 (0.15), residues: 1320 sheet: 0.90 (0.22), residues: 524 loop : -0.81 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 861 TYR 0.010 0.001 TYR A 519 PHE 0.008 0.001 PHE C 638 TRP 0.021 0.001 TRP A 278 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00225 (27344) covalent geometry : angle 0.52370 (37212) hydrogen bonds : bond 0.03562 ( 1112) hydrogen bonds : angle 4.27299 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6829 (p) REVERT: A 94 MET cc_start: 0.7650 (mtt) cc_final: 0.7159 (mtt) REVERT: B 75 THR cc_start: 0.7145 (OUTLIER) cc_final: 0.6846 (p) REVERT: B 94 MET cc_start: 0.7627 (mtt) cc_final: 0.7146 (mtt) REVERT: C 75 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6791 (p) REVERT: C 278 TRP cc_start: 0.8847 (OUTLIER) cc_final: 0.8554 (t60) REVERT: D 75 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6812 (p) REVERT: D 94 MET cc_start: 0.7628 (mtt) cc_final: 0.7095 (mtt) REVERT: D 767 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6811 (ppt170) outliers start: 34 outliers final: 21 residues processed: 127 average time/residue: 0.5983 time to fit residues: 89.9706 Evaluate side-chains 126 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 182 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 278 TRP Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 767 ARG Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 240 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 339 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.090778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054029 restraints weight = 74910.789| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.63 r_work: 0.2784 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27344 Z= 0.158 Angle : 0.553 13.455 37212 Z= 0.288 Chirality : 0.045 0.182 4300 Planarity : 0.004 0.037 4840 Dihedral : 8.322 88.028 4072 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.19 % Allowed : 7.06 % Favored : 91.75 % 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: 0.29 (0.15), residues: 3468 helix: 1.15 (0.15), residues: 1316 sheet: 0.83 (0.22), residues: 524 loop : -0.82 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 861 TYR 0.014 0.001 TYR D 519 PHE 0.007 0.001 PHE D 638 TRP 0.015 0.001 TRP A 278 HIS 0.002 0.001 HIS B 586 Details of bonding type rmsd covalent geometry : bond 0.00376 (27344) covalent geometry : angle 0.55330 (37212) hydrogen bonds : bond 0.04548 ( 1112) hydrogen bonds : angle 4.38451 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.6983 (p) REVERT: A 94 MET cc_start: 0.7679 (mtt) cc_final: 0.7225 (mtt) REVERT: B 75 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6917 (p) REVERT: B 94 MET cc_start: 0.7651 (mtt) cc_final: 0.7212 (mtt) REVERT: C 75 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6926 (p) REVERT: D 75 THR cc_start: 0.7235 (OUTLIER) cc_final: 0.6916 (p) REVERT: D 94 MET cc_start: 0.7673 (mtt) cc_final: 0.7202 (mtt) REVERT: D 767 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6873 (ppt170) outliers start: 34 outliers final: 22 residues processed: 129 average time/residue: 0.5561 time to fit residues: 86.1196 Evaluate side-chains 127 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 546 ILE Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 767 ARG Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 49 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 170 optimal weight: 0.2980 chunk 199 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.092116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056061 restraints weight = 74468.103| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.55 r_work: 0.2832 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27344 Z= 0.097 Angle : 0.521 14.059 37212 Z= 0.267 Chirality : 0.044 0.177 4300 Planarity : 0.004 0.038 4840 Dihedral : 7.924 86.920 4072 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.95 % Allowed : 7.51 % Favored : 91.54 % 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: 0.47 (0.15), residues: 3468 helix: 1.33 (0.15), residues: 1308 sheet: 0.86 (0.22), residues: 528 loop : -0.70 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 861 TYR 0.010 0.001 TYR C 519 PHE 0.007 0.001 PHE A 638 TRP 0.020 0.001 TRP A 278 HIS 0.002 0.000 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00209 (27344) covalent geometry : angle 0.52082 (37212) hydrogen bonds : bond 0.03319 ( 1112) hydrogen bonds : angle 4.18308 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6936 Ramachandran restraints generated. 3468 Oldfield, 0 Emsley, 3468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 75 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6831 (p) REVERT: A 94 MET cc_start: 0.7710 (mtt) cc_final: 0.7259 (mtt) REVERT: B 75 THR cc_start: 0.6979 (OUTLIER) cc_final: 0.6722 (p) REVERT: B 94 MET cc_start: 0.7696 (mtt) cc_final: 0.7220 (mtt) REVERT: C 75 THR cc_start: 0.7062 (OUTLIER) cc_final: 0.6777 (p) REVERT: D 75 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6787 (p) REVERT: D 94 MET cc_start: 0.7670 (mtt) cc_final: 0.7191 (mtt) REVERT: D 767 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6951 (ppt170) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.5507 time to fit residues: 83.0973 Evaluate side-chains 123 residues out of total 2848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 768 PHE Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 767 ARG Chi-restraints excluded: chain D residue 768 PHE Chi-restraints excluded: chain D residue 836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 302 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 313 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 309 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.092537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056129 restraints weight = 74757.848| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.64 r_work: 0.2844 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27344 Z= 0.094 Angle : 0.511 13.686 37212 Z= 0.260 Chirality : 0.044 0.172 4300 Planarity : 0.004 0.037 4840 Dihedral : 7.534 85.088 4072 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.88 % Allowed : 7.51 % Favored : 91.61 % 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: 0.50 (0.15), residues: 3468 helix: 1.32 (0.15), residues: 1328 sheet: 0.85 (0.22), residues: 528 loop : -0.67 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 861 TYR 0.011 0.001 TYR C 519 PHE 0.013 0.001 PHE C 692 TRP 0.017 0.001 TRP A 278 HIS 0.002 0.000 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00202 (27344) covalent geometry : angle 0.51076 (37212) hydrogen bonds : bond 0.03175 ( 1112) hydrogen bonds : angle 4.09464 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9937.40 seconds wall clock time: 169 minutes 6.49 seconds (10146.49 seconds total)