Starting phenix.real_space_refine on Thu Mar 5 10:50:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wac_32381/03_2026/7wac_32381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wac_32381/03_2026/7wac_32381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wac_32381/03_2026/7wac_32381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wac_32381/03_2026/7wac_32381.map" model { file = "/net/cci-nas-00/data/ceres_data/7wac_32381/03_2026/7wac_32381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wac_32381/03_2026/7wac_32381.cif" } resolution = 2.91 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= -0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 13920 2.51 5 N 3844 2.21 5 O 4180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Time building chain proxies: 4.84, per 1000 atoms: 0.22 Number of scatterers: 22016 At special positions: 0 Unit cell: (145.2, 141.68, 104.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 4180 8.00 N 3844 7.00 C 13920 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: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 42.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.881A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.804A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.697A pdb=" N GLN A 198 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.421A pdb=" N ASP A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N ALA A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.934A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 345 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 424 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 498 through 513 removed outlier: 3.529A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.515A pdb=" N ALA A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.513A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 608 removed outlier: 3.832A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 690 through 707 removed outlier: 4.099A pdb=" N ILE A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 76 through 91 removed outlier: 3.882A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 3.805A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.696A pdb=" N GLN B 198 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 244 through 254 removed outlier: 4.422A pdb=" N ASP B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.735A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.933A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 424 Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 498 through 513 removed outlier: 3.530A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.515A pdb=" N ALA B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.514A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 3.832A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 644 through 653 Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 690 through 707 removed outlier: 4.099A pdb=" N ILE B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 695 " --> pdb=" O PRO B 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 696 " --> pdb=" O PHE B 692 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 721 Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 76 through 91 removed outlier: 3.882A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.804A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.697A pdb=" N GLN C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 244 through 254 removed outlier: 4.420A pdb=" N ASP C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.734A pdb=" N ALA C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 removed outlier: 4.932A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 345 " --> pdb=" O GLU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 424 Processing helix chain 'C' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 498 through 513 removed outlier: 3.529A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.515A pdb=" N ALA C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.513A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.832A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 690 through 707 removed outlier: 4.100A pdb=" N ILE C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA C 695 " --> pdb=" O PRO C 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 696 " --> pdb=" O PHE C 692 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 76 through 91 removed outlier: 3.882A pdb=" N VAL D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 140 removed outlier: 3.805A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.697A pdb=" N GLN D 198 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 244 through 254 removed outlier: 4.422A pdb=" N ASP D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.734A pdb=" N ALA D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 4.933A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 345 " --> pdb=" O GLU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 4.198A pdb=" N GLY D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 424 Processing helix chain 'D' and resid 457 through 462 removed outlier: 3.564A pdb=" N ALA D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 498 through 513 removed outlier: 3.530A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.514A pdb=" N ALA D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.514A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 608 removed outlier: 3.831A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 644 through 653 Processing helix chain 'D' and resid 682 through 686 Processing helix chain 'D' and resid 690 through 707 removed outlier: 4.099A pdb=" N ILE D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 695 " --> pdb=" O PRO D 691 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN D 696 " --> pdb=" O PHE D 692 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 6.376A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (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 237 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 313 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 319 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 429 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 451 " --> pdb=" O GLY A 429 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP A 431 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 533 removed outlier: 5.603A pdb=" N LEU A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 527 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 490 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE A 578 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 492 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU A 575 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 634 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 613 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA A 636 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA A 615 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE A 638 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 617 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.376A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 237 through 240 Processing sheet with id=AB1, first strand: chain 'B' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 313 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 319 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY B 429 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 451 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 431 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB3, first strand: chain 'B' and resid 530 through 533 removed outlier: 5.604A pdb=" N LEU B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE B 527 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 490 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 578 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 492 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU B 575 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 634 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY B 613 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 636 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA B 615 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE B 638 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 617 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 9 removed outlier: 6.376A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AB7, first strand: chain 'C' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 313 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 319 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY C 429 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 451 " --> pdb=" O GLY C 429 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP C 431 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AB9, first strand: chain 'C' and resid 530 through 533 removed outlier: 5.604A pdb=" N LEU C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE C 527 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 490 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 578 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER C 492 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU C 575 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN C 634 " --> pdb=" O PRO C 611 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 613 " --> pdb=" O GLN C 634 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA C 636 " --> pdb=" O GLY C 613 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA C 615 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE C 638 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 617 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 2 through 9 removed outlier: 6.375A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'D' and resid 237 through 240 Processing sheet with id=AC4, first strand: chain 'D' and resid 400 through 403 removed outlier: 5.110A pdb=" N VAL D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 313 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 319 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY D 429 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL D 451 " --> pdb=" O GLY D 429 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP D 431 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 327 through 328 Processing sheet with id=AC6, first strand: chain 'D' and resid 530 through 533 removed outlier: 5.602A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 490 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE D 578 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER D 492 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLU D 575 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN D 634 " --> pdb=" O PRO D 611 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY D 613 " --> pdb=" O GLN D 634 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA D 636 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA D 615 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE D 638 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 617 " --> pdb=" O PHE D 638 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7408 1.34 - 1.46: 3843 1.46 - 1.58: 11005 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 22376 Sorted by residual: bond pdb=" CG1 ILE D 211 " pdb=" CD1 ILE D 211 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG1 ILE B 211 " pdb=" CD1 ILE B 211 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CG1 ILE C 211 " pdb=" CD1 ILE C 211 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.41e+00 bond pdb=" CG1 ILE A 211 " pdb=" CD1 ILE A 211 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 bond pdb=" CA MET D 627 " pdb=" C MET D 627 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.80e-02 3.09e+03 6.80e-01 ... (remaining 22371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 29634 1.37 - 2.75: 575 2.75 - 4.12: 110 4.12 - 5.49: 13 5.49 - 6.87: 12 Bond angle restraints: 30344 Sorted by residual: angle pdb=" C CYS C 59 " pdb=" N SER C 60 " pdb=" CA SER C 60 " ideal model delta sigma weight residual 120.58 124.20 -3.62 1.32e+00 5.74e-01 7.51e+00 angle pdb=" C CYS D 59 " pdb=" N SER D 60 " pdb=" CA SER D 60 " ideal model delta sigma weight residual 120.58 124.17 -3.59 1.32e+00 5.74e-01 7.41e+00 angle pdb=" C CYS B 59 " pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta sigma weight residual 120.58 124.17 -3.59 1.32e+00 5.74e-01 7.39e+00 angle pdb=" C CYS A 59 " pdb=" N SER A 60 " pdb=" CA SER A 60 " ideal model delta sigma weight residual 120.58 124.16 -3.58 1.32e+00 5.74e-01 7.35e+00 angle pdb=" N THR A 204 " pdb=" CA THR A 204 " pdb=" C THR A 204 " ideal model delta sigma weight residual 114.64 110.84 3.80 1.52e+00 4.33e-01 6.24e+00 ... (remaining 30339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 12367 17.46 - 34.91: 873 34.91 - 52.37: 184 52.37 - 69.82: 20 69.82 - 87.28: 40 Dihedral angle restraints: 13484 sinusoidal: 5300 harmonic: 8184 Sorted by residual: dihedral pdb=" CG ARG C 236 " pdb=" CD ARG C 236 " pdb=" NE ARG C 236 " pdb=" CZ ARG C 236 " ideal model delta sinusoidal sigma weight residual -180.00 -135.64 -44.36 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 236 " pdb=" CD ARG A 236 " pdb=" NE ARG A 236 " pdb=" CZ ARG A 236 " ideal model delta sinusoidal sigma weight residual -180.00 -135.65 -44.35 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG B 236 " pdb=" CD ARG B 236 " pdb=" NE ARG B 236 " pdb=" CZ ARG B 236 " ideal model delta sinusoidal sigma weight residual 180.00 -135.65 -44.35 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 13481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2437 0.036 - 0.073: 743 0.073 - 0.109: 293 0.109 - 0.146: 87 0.146 - 0.182: 8 Chirality restraints: 3568 Sorted by residual: chirality pdb=" CA ILE A 260 " pdb=" N ILE A 260 " pdb=" C ILE A 260 " pdb=" CB ILE A 260 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA ILE C 260 " pdb=" N ILE C 260 " pdb=" C ILE C 260 " pdb=" CB ILE C 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 3565 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 60 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO A 61 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 60 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO C 61 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 60 " 0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 61 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " 0.023 5.00e-02 4.00e+02 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2794 2.76 - 3.29: 20604 3.29 - 3.83: 35024 3.83 - 4.36: 39433 4.36 - 4.90: 72178 Nonbonded interactions: 170033 Sorted by model distance: nonbonded pdb=" OG1 THR D 335 " pdb=" O ILE D 377 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 335 " pdb=" O ILE A 377 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR B 335 " pdb=" O ILE B 377 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR C 335 " pdb=" O ILE C 377 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG B 301 " pdb=" O TYR B 302 " model vdw 2.277 3.120 ... (remaining 170028 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: 0.470 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.080 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.002 0.047 22376 Z= 0.121 Angle : 0.511 6.868 30344 Z= 0.285 Chirality : 0.044 0.182 3568 Planarity : 0.003 0.040 3912 Dihedral : 13.361 87.275 8276 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.53 (0.15), residues: 2884 helix: 1.76 (0.16), residues: 1072 sheet: 0.71 (0.22), residues: 520 loop : -1.03 (0.16), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 309 TYR 0.009 0.001 TYR C 519 PHE 0.007 0.001 PHE A 243 TRP 0.008 0.001 TRP D 15 HIS 0.003 0.000 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00247 (22376) covalent geometry : angle 0.51055 (30344) hydrogen bonds : bond 0.14451 ( 1020) hydrogen bonds : angle 4.92318 ( 2868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.758 Fit side-chains REVERT: A 160 GLN cc_start: 0.9119 (tt0) cc_final: 0.8723 (tm-30) REVERT: A 300 GLU cc_start: 0.7201 (pm20) cc_final: 0.6958 (pm20) REVERT: B 160 GLN cc_start: 0.9145 (tt0) cc_final: 0.8725 (tm-30) REVERT: C 160 GLN cc_start: 0.9136 (tt0) cc_final: 0.8737 (tm-30) REVERT: D 32 LEU cc_start: 0.8854 (mp) cc_final: 0.8313 (tt) REVERT: D 252 TYR cc_start: 0.8625 (t80) cc_final: 0.8425 (t80) REVERT: D 300 GLU cc_start: 0.7295 (pm20) cc_final: 0.6990 (pm20) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.5880 time to fit residues: 105.9421 Evaluate side-chains 111 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 247 GLN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 247 GLN B 344 ASN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN C 247 GLN C 344 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN D 247 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.125596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.071570 restraints weight = 43270.082| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.72 r_work: 0.2588 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 22376 Z= 0.296 Angle : 0.589 9.336 30344 Z= 0.315 Chirality : 0.048 0.179 3568 Planarity : 0.004 0.033 3912 Dihedral : 4.205 17.463 3124 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.19 % Allowed : 4.94 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2884 helix: 1.73 (0.16), residues: 1132 sheet: 0.52 (0.21), residues: 520 loop : -1.10 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 102 TYR 0.012 0.001 TYR A 519 PHE 0.013 0.002 PHE D 43 TRP 0.013 0.001 TRP D 278 HIS 0.005 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00708 (22376) covalent geometry : angle 0.58892 (30344) hydrogen bonds : bond 0.04875 ( 1020) hydrogen bonds : angle 4.28746 ( 2868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.851 Fit side-chains REVERT: A 160 GLN cc_start: 0.9138 (tt0) cc_final: 0.8868 (tm-30) REVERT: B 160 GLN cc_start: 0.9155 (tt0) cc_final: 0.8866 (tm-30) REVERT: C 160 GLN cc_start: 0.9137 (tt0) cc_final: 0.8874 (tm-30) REVERT: D 160 GLN cc_start: 0.9134 (tt0) cc_final: 0.8759 (tm-30) REVERT: D 300 GLU cc_start: 0.7522 (pm20) cc_final: 0.7170 (pm20) outliers start: 28 outliers final: 15 residues processed: 129 average time/residue: 0.5406 time to fit residues: 81.5202 Evaluate side-chains 117 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 534 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 179 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 258 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 6 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.129721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.075970 restraints weight = 42609.467| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.74 r_work: 0.2686 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22376 Z= 0.085 Angle : 0.462 7.655 30344 Z= 0.242 Chirality : 0.043 0.188 3568 Planarity : 0.003 0.033 3912 Dihedral : 3.769 15.908 3124 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.24 % Allowed : 6.56 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.66 (0.15), residues: 2884 helix: 1.94 (0.16), residues: 1132 sheet: 0.50 (0.21), residues: 516 loop : -1.05 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.009 0.001 TYR A 519 PHE 0.011 0.001 PHE A 43 TRP 0.011 0.001 TRP D 278 HIS 0.002 0.000 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00176 (22376) covalent geometry : angle 0.46150 (30344) hydrogen bonds : bond 0.02905 ( 1020) hydrogen bonds : angle 3.83523 ( 2868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.847 Fit side-chains REVERT: B 160 GLN cc_start: 0.9171 (tt0) cc_final: 0.8873 (tm-30) REVERT: C 160 GLN cc_start: 0.9163 (tt0) cc_final: 0.8890 (tm-30) REVERT: D 138 ASP cc_start: 0.8183 (m-30) cc_final: 0.7590 (t0) REVERT: D 160 GLN cc_start: 0.9133 (tt0) cc_final: 0.8761 (tm-30) outliers start: 29 outliers final: 13 residues processed: 125 average time/residue: 0.5483 time to fit residues: 80.1208 Evaluate side-chains 114 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 207 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 110 optimal weight: 50.0000 chunk 254 optimal weight: 50.0000 chunk 231 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.072804 restraints weight = 42802.188| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.73 r_work: 0.2614 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22376 Z= 0.180 Angle : 0.509 8.568 30344 Z= 0.268 Chirality : 0.045 0.188 3568 Planarity : 0.003 0.031 3912 Dihedral : 3.896 16.087 3124 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.94 % Allowed : 9.33 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.15), residues: 2884 helix: 1.91 (0.16), residues: 1140 sheet: 0.47 (0.21), residues: 516 loop : -1.11 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 301 TYR 0.010 0.001 TYR B 519 PHE 0.008 0.001 PHE B 480 TRP 0.008 0.001 TRP D 278 HIS 0.002 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00430 (22376) covalent geometry : angle 0.50892 (30344) hydrogen bonds : bond 0.03952 ( 1020) hydrogen bonds : angle 4.00119 ( 2868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.869 Fit side-chains REVERT: B 160 GLN cc_start: 0.9167 (tt0) cc_final: 0.8861 (tm-30) REVERT: C 160 GLN cc_start: 0.9155 (tt0) cc_final: 0.8880 (tm-30) REVERT: D 138 ASP cc_start: 0.8262 (m-30) cc_final: 0.7687 (t0) REVERT: D 160 GLN cc_start: 0.9159 (tt0) cc_final: 0.8790 (tm-30) outliers start: 22 outliers final: 11 residues processed: 118 average time/residue: 0.5197 time to fit residues: 72.1582 Evaluate side-chains 111 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 50.0000 chunk 118 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 134 optimal weight: 0.0370 chunk 57 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.126256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.071032 restraints weight = 43122.165| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.82 r_work: 0.2592 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22376 Z= 0.209 Angle : 0.514 8.495 30344 Z= 0.273 Chirality : 0.045 0.185 3568 Planarity : 0.003 0.032 3912 Dihedral : 3.987 16.868 3124 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.45 % Allowed : 9.88 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.60 (0.15), residues: 2884 helix: 2.01 (0.16), residues: 1116 sheet: 0.38 (0.21), residues: 512 loop : -1.11 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 301 TYR 0.010 0.001 TYR D 14 PHE 0.008 0.001 PHE A 43 TRP 0.007 0.001 TRP A 278 HIS 0.002 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00499 (22376) covalent geometry : angle 0.51351 (30344) hydrogen bonds : bond 0.04031 ( 1020) hydrogen bonds : angle 4.00974 ( 2868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.897 Fit side-chains REVERT: A 160 GLN cc_start: 0.9172 (tt0) cc_final: 0.8889 (tm-30) REVERT: B 160 GLN cc_start: 0.9177 (tt0) cc_final: 0.8868 (tm-30) REVERT: C 160 GLN cc_start: 0.9168 (tt0) cc_final: 0.8868 (tm-30) REVERT: D 160 GLN cc_start: 0.9177 (tt0) cc_final: 0.8804 (tm-30) outliers start: 34 outliers final: 16 residues processed: 123 average time/residue: 0.5297 time to fit residues: 76.7674 Evaluate side-chains 110 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 459 MET Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 201 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.073643 restraints weight = 43130.238| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.87 r_work: 0.2647 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22376 Z= 0.100 Angle : 0.466 7.842 30344 Z= 0.245 Chirality : 0.044 0.193 3568 Planarity : 0.003 0.030 3912 Dihedral : 3.712 15.918 3124 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.89 % Allowed : 11.12 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.74 (0.15), residues: 2884 helix: 2.17 (0.16), residues: 1116 sheet: 0.47 (0.21), residues: 512 loop : -1.09 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 301 TYR 0.009 0.001 TYR B 519 PHE 0.010 0.001 PHE A 243 TRP 0.012 0.001 TRP B 278 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00225 (22376) covalent geometry : angle 0.46625 (30344) hydrogen bonds : bond 0.02948 ( 1020) hydrogen bonds : angle 3.76940 ( 2868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.791 Fit side-chains REVERT: A 160 GLN cc_start: 0.9185 (tt0) cc_final: 0.8888 (tm-30) REVERT: B 160 GLN cc_start: 0.9194 (tt0) cc_final: 0.8883 (tm-30) REVERT: C 160 GLN cc_start: 0.9180 (tt0) cc_final: 0.8877 (tm-30) REVERT: D 138 ASP cc_start: 0.8307 (m-30) cc_final: 0.7717 (OUTLIER) outliers start: 21 outliers final: 16 residues processed: 118 average time/residue: 0.5551 time to fit residues: 76.2961 Evaluate side-chains 107 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 82 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 284 optimal weight: 0.0020 chunk 38 optimal weight: 7.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.126793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072625 restraints weight = 42846.539| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.74 r_work: 0.2606 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22376 Z= 0.167 Angle : 0.489 6.934 30344 Z= 0.260 Chirality : 0.045 0.192 3568 Planarity : 0.003 0.031 3912 Dihedral : 3.810 16.213 3124 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.02 % Allowed : 11.88 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.72 (0.15), residues: 2884 helix: 2.16 (0.16), residues: 1116 sheet: 0.42 (0.22), residues: 512 loop : -1.08 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 70 TYR 0.010 0.001 TYR D 519 PHE 0.007 0.001 PHE A 43 TRP 0.011 0.001 TRP A 278 HIS 0.002 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00396 (22376) covalent geometry : angle 0.48916 (30344) hydrogen bonds : bond 0.03671 ( 1020) hydrogen bonds : angle 3.87503 ( 2868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.771 Fit side-chains REVERT: A 160 GLN cc_start: 0.9187 (tt0) cc_final: 0.8891 (tm-30) REVERT: B 160 GLN cc_start: 0.9195 (tt0) cc_final: 0.8873 (tm-30) REVERT: C 160 GLN cc_start: 0.9185 (tt0) cc_final: 0.8888 (tm-30) REVERT: D 260 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8722 (pp) outliers start: 24 outliers final: 16 residues processed: 115 average time/residue: 0.5099 time to fit residues: 69.1129 Evaluate side-chains 109 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 3 optimal weight: 30.0000 chunk 251 optimal weight: 50.0000 chunk 52 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 150 optimal weight: 30.0000 chunk 107 optimal weight: 50.0000 chunk 229 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.124956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.070363 restraints weight = 42943.566| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.75 r_work: 0.2567 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 22376 Z= 0.280 Angle : 0.570 8.803 30344 Z= 0.301 Chirality : 0.047 0.174 3568 Planarity : 0.004 0.033 3912 Dihedral : 4.141 17.691 3124 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.24 % Allowed : 12.31 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.58 (0.15), residues: 2884 helix: 1.99 (0.16), residues: 1112 sheet: 0.37 (0.22), residues: 512 loop : -1.10 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 70 TYR 0.013 0.001 TYR D 14 PHE 0.009 0.002 PHE A 43 TRP 0.009 0.001 TRP B 278 HIS 0.003 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00670 (22376) covalent geometry : angle 0.57029 (30344) hydrogen bonds : bond 0.04594 ( 1020) hydrogen bonds : angle 4.15468 ( 2868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.834 Fit side-chains REVERT: A 160 GLN cc_start: 0.9118 (tt0) cc_final: 0.8839 (tm-30) REVERT: A 278 TRP cc_start: 0.8766 (OUTLIER) cc_final: 0.8452 (t60) REVERT: B 160 GLN cc_start: 0.9119 (tt0) cc_final: 0.8830 (tm-30) REVERT: B 278 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.8413 (t60) REVERT: C 160 GLN cc_start: 0.9118 (tt0) cc_final: 0.8838 (tm-30) outliers start: 29 outliers final: 15 residues processed: 115 average time/residue: 0.5026 time to fit residues: 67.8945 Evaluate side-chains 108 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 586 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 586 HIS Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 534 THR Chi-restraints excluded: chain D residue 586 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 150 optimal weight: 30.0000 chunk 193 optimal weight: 0.4980 chunk 271 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.073325 restraints weight = 42801.798| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.74 r_work: 0.2638 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22376 Z= 0.123 Angle : 0.477 8.143 30344 Z= 0.251 Chirality : 0.044 0.197 3568 Planarity : 0.003 0.032 3912 Dihedral : 3.795 16.292 3124 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.85 % Allowed : 12.95 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.74 (0.15), residues: 2884 helix: 2.16 (0.16), residues: 1116 sheet: 0.34 (0.22), residues: 512 loop : -1.01 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 70 TYR 0.016 0.001 TYR B 252 PHE 0.007 0.001 PHE B 638 TRP 0.010 0.001 TRP D 278 HIS 0.002 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00286 (22376) covalent geometry : angle 0.47711 (30344) hydrogen bonds : bond 0.03141 ( 1020) hydrogen bonds : angle 3.83027 ( 2868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.880 Fit side-chains REVERT: A 160 GLN cc_start: 0.9147 (tt0) cc_final: 0.8849 (tm-30) REVERT: B 160 GLN cc_start: 0.9151 (tt0) cc_final: 0.8844 (tm-30) REVERT: C 160 GLN cc_start: 0.9143 (tt0) cc_final: 0.8842 (tm-30) outliers start: 20 outliers final: 9 residues processed: 108 average time/residue: 0.5067 time to fit residues: 64.5075 Evaluate side-chains 97 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 29 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 217 optimal weight: 0.5980 chunk 210 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 253 optimal weight: 0.4980 chunk 7 optimal weight: 50.0000 chunk 158 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.073077 restraints weight = 43571.037| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.88 r_work: 0.2650 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22376 Z= 0.099 Angle : 0.459 8.724 30344 Z= 0.240 Chirality : 0.044 0.193 3568 Planarity : 0.003 0.031 3912 Dihedral : 3.620 15.454 3124 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.43 % Allowed : 13.59 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.87 (0.15), residues: 2884 helix: 2.26 (0.16), residues: 1116 sheet: 0.46 (0.22), residues: 508 loop : -0.95 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 70 TYR 0.018 0.001 TYR B 252 PHE 0.007 0.001 PHE B 638 TRP 0.018 0.001 TRP B 278 HIS 0.002 0.001 HIS C 327 Details of bonding type rmsd covalent geometry : bond 0.00223 (22376) covalent geometry : angle 0.45856 (30344) hydrogen bonds : bond 0.02865 ( 1020) hydrogen bonds : angle 3.68316 ( 2868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.847 Fit side-chains REVERT: A 160 GLN cc_start: 0.9150 (tt0) cc_final: 0.8884 (tm-30) REVERT: B 160 GLN cc_start: 0.9162 (tt0) cc_final: 0.8861 (tm-30) REVERT: B 243 PHE cc_start: 0.8415 (m-80) cc_final: 0.8189 (t80) REVERT: B 300 GLU cc_start: 0.8917 (pt0) cc_final: 0.8600 (pp20) REVERT: C 160 GLN cc_start: 0.9154 (tt0) cc_final: 0.8864 (tm-30) REVERT: D 300 GLU cc_start: 0.9007 (pt0) cc_final: 0.8590 (pp20) outliers start: 10 outliers final: 10 residues processed: 98 average time/residue: 0.5357 time to fit residues: 61.8252 Evaluate side-chains 96 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 251 optimal weight: 0.1980 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 208 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.073670 restraints weight = 43456.259| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.86 r_work: 0.2660 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22376 Z= 0.093 Angle : 0.444 8.169 30344 Z= 0.232 Chirality : 0.043 0.179 3568 Planarity : 0.003 0.031 3912 Dihedral : 3.515 15.157 3124 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.51 % Allowed : 13.50 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.94 (0.16), residues: 2884 helix: 2.33 (0.16), residues: 1116 sheet: 0.44 (0.22), residues: 508 loop : -0.89 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 70 TYR 0.020 0.001 TYR B 252 PHE 0.007 0.001 PHE B 638 TRP 0.015 0.001 TRP B 278 HIS 0.002 0.000 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00209 (22376) covalent geometry : angle 0.44387 (30344) hydrogen bonds : bond 0.02767 ( 1020) hydrogen bonds : angle 3.60275 ( 2868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6324.61 seconds wall clock time: 108 minutes 27.80 seconds (6507.80 seconds total)