Starting phenix.real_space_refine on Wed Jun 18 21:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wac_32381/06_2025/7wac_32381.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wac_32381/06_2025/7wac_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_32381/06_2025/7wac_32381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wac_32381/06_2025/7wac_32381.map" model { file = "/net/cci-nas-00/data/ceres_data/7wac_32381/06_2025/7wac_32381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wac_32381/06_2025/7wac_32381.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.24, per 1000 atoms: 0.60 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: 7.30 Conformation dependent library (CDL) restraints added in 3.1 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: 2.65 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: 9.25 Time building geometry restraints manager: 8.75 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 10.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.170 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:50.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (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 TRP 0.008 0.001 TRP D 15 HIS 0.003 0.000 HIS A 79 PHE 0.007 0.001 PHE A 243 TYR 0.009 0.001 TYR C 519 ARG 0.002 0.000 ARG C 309 Details of bonding type rmsd hydrogen bonds : bond 0.14451 ( 1020) hydrogen bonds : angle 4.92318 ( 2868) covalent geometry : bond 0.00247 (22376) covalent geometry : angle 0.51055 (30344) *********************** 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 : 3.737 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: 1.6447 time to fit residues: 299.8844 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 : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 overall best weight: 6.9588 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.126099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.072098 restraints weight = 42952.767| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.71 r_work: 0.2596 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 22376 Z= 0.250 Angle : 0.566 9.283 30344 Z= 0.302 Chirality : 0.047 0.179 3568 Planarity : 0.004 0.035 3912 Dihedral : 4.178 17.163 3124 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.41 % Allowed : 4.81 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 2884 helix: 1.74 (0.16), residues: 1132 sheet: 0.52 (0.21), residues: 520 loop : -1.09 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 278 HIS 0.004 0.001 HIS D 650 PHE 0.010 0.001 PHE A 480 TYR 0.012 0.001 TYR A 519 ARG 0.008 0.000 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 1020) hydrogen bonds : angle 4.21021 ( 2868) covalent geometry : bond 0.00596 (22376) covalent geometry : angle 0.56649 (30344) *********************** 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 144 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 2.638 Fit side-chains REVERT: A 160 GLN cc_start: 0.9137 (tt0) cc_final: 0.8878 (tm-30) REVERT: B 160 GLN cc_start: 0.9157 (tt0) cc_final: 0.8880 (tm-30) REVERT: C 160 GLN cc_start: 0.9138 (tt0) cc_final: 0.8877 (tm-30) REVERT: D 160 GLN cc_start: 0.9127 (tt0) cc_final: 0.8769 (tm-30) REVERT: D 300 GLU cc_start: 0.7527 (pm20) cc_final: 0.7180 (pm20) outliers start: 33 outliers final: 17 residues processed: 129 average time/residue: 1.1577 time to fit residues: 176.1560 Evaluate side-chains 121 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 2.644 ------------------------------------------------------------------------------- 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 133 CYS 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 133 CYS 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 133 CYS 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 197 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 245 optimal weight: 50.0000 chunk 274 optimal weight: 0.4980 chunk 201 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 249 optimal weight: 30.0000 chunk 37 optimal weight: 0.0270 overall best weight: 1.4040 ------------------------------------------------------------------------------- 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 = 0.129649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.074854 restraints weight = 42734.109| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.83 r_work: 0.2676 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 22376 Z= 0.088 Angle : 0.457 7.767 30344 Z= 0.240 Chirality : 0.043 0.198 3568 Planarity : 0.003 0.034 3912 Dihedral : 3.744 15.713 3124 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.24 % Allowed : 6.94 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2884 helix: 1.99 (0.16), residues: 1132 sheet: 0.52 (0.21), residues: 516 loop : -1.03 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 278 HIS 0.002 0.000 HIS D 650 PHE 0.008 0.001 PHE B 43 TYR 0.009 0.001 TYR A 519 ARG 0.005 0.000 ARG D 102 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 1020) hydrogen bonds : angle 3.81385 ( 2868) covalent geometry : bond 0.00188 (22376) covalent geometry : angle 0.45714 (30344) *********************** 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 : 2.445 Fit side-chains REVERT: A 160 GLN cc_start: 0.9164 (tt0) cc_final: 0.8901 (tm-30) REVERT: B 160 GLN cc_start: 0.9175 (tt0) cc_final: 0.8873 (tm-30) REVERT: C 160 GLN cc_start: 0.9166 (tt0) cc_final: 0.8896 (tm-30) REVERT: D 138 ASP cc_start: 0.8198 (m-30) cc_final: 0.7592 (t0) REVERT: D 160 GLN cc_start: 0.9146 (tt0) cc_final: 0.8774 (tm-30) outliers start: 29 outliers final: 13 residues processed: 125 average time/residue: 1.2217 time to fit residues: 178.2494 Evaluate side-chains 113 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 459 MET 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 656 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 108 optimal weight: 50.0000 chunk 18 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 101 optimal weight: 40.0000 chunk 192 optimal weight: 0.1980 chunk 262 optimal weight: 10.0000 chunk 39 optimal weight: 50.0000 chunk 269 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 46 optimal weight: 0.2980 overall best weight: 5.2986 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.126571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.072419 restraints weight = 43069.798| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.74 r_work: 0.2610 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22376 Z= 0.195 Angle : 0.519 8.602 30344 Z= 0.273 Chirality : 0.045 0.189 3568 Planarity : 0.003 0.030 3912 Dihedral : 3.933 16.244 3124 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.89 % Allowed : 9.20 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 2884 helix: 1.90 (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 TRP 0.008 0.001 TRP D 278 HIS 0.002 0.001 HIS D 650 PHE 0.007 0.001 PHE C 480 TYR 0.010 0.001 TYR D 519 ARG 0.006 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1020) hydrogen bonds : angle 4.02764 ( 2868) covalent geometry : bond 0.00465 (22376) covalent geometry : angle 0.51877 (30344) *********************** 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 123 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 2.540 Fit side-chains REVERT: A 160 GLN cc_start: 0.9168 (tt0) cc_final: 0.8897 (tm-30) REVERT: B 160 GLN cc_start: 0.9180 (tt0) cc_final: 0.8873 (tm-30) REVERT: C 160 GLN cc_start: 0.9165 (tt0) cc_final: 0.8891 (tm-30) REVERT: D 138 ASP cc_start: 0.8266 (m-30) cc_final: 0.7676 (t0) REVERT: D 160 GLN cc_start: 0.9166 (tt0) cc_final: 0.8796 (tm-30) outliers start: 21 outliers final: 11 residues processed: 118 average time/residue: 1.1991 time to fit residues: 167.0205 Evaluate side-chains 108 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 459 MET Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS 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 656 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 144 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 chunk 225 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 281 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.127426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.073423 restraints weight = 42783.735| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.73 r_work: 0.2622 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1910 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= 0.146 Angle : 0.478 8.436 30344 Z= 0.252 Chirality : 0.044 0.183 3568 Planarity : 0.003 0.030 3912 Dihedral : 3.813 16.274 3124 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.02 % Allowed : 10.14 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2884 helix: 1.99 (0.16), residues: 1140 sheet: 0.44 (0.21), residues: 516 loop : -1.10 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.002 0.001 HIS D 650 PHE 0.007 0.001 PHE C 638 TYR 0.009 0.001 TYR C 519 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 1020) hydrogen bonds : angle 3.87934 ( 2868) covalent geometry : bond 0.00344 (22376) covalent geometry : angle 0.47826 (30344) *********************** 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 127 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 2.512 Fit side-chains REVERT: A 160 GLN cc_start: 0.9183 (tt0) cc_final: 0.8881 (tm-30) REVERT: B 160 GLN cc_start: 0.9194 (tt0) cc_final: 0.8876 (tm-30) REVERT: C 160 GLN cc_start: 0.9187 (tt0) cc_final: 0.8883 (tm-30) REVERT: D 138 ASP cc_start: 0.8281 (m-30) cc_final: 0.7690 (OUTLIER) REVERT: D 160 GLN cc_start: 0.9182 (tt0) cc_final: 0.8798 (tm-30) outliers start: 24 outliers final: 16 residues processed: 120 average time/residue: 1.1544 time to fit residues: 162.9915 Evaluate side-chains 108 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 286 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 39 optimal weight: 50.0000 chunk 246 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 281 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 160 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.125570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.069793 restraints weight = 43507.074| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.88 r_work: 0.2571 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 22376 Z= 0.252 Angle : 0.546 7.822 30344 Z= 0.289 Chirality : 0.046 0.193 3568 Planarity : 0.003 0.033 3912 Dihedral : 4.068 17.122 3124 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 10.99 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 2884 helix: 2.02 (0.16), residues: 1112 sheet: 0.39 (0.22), residues: 512 loop : -1.12 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.003 0.001 HIS C 650 PHE 0.008 0.001 PHE B 43 TYR 0.011 0.001 TYR D 14 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1020) hydrogen bonds : angle 4.10122 ( 2868) covalent geometry : bond 0.00602 (22376) covalent geometry : angle 0.54621 (30344) *********************** 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: 31 poor density : 94 time to evaluate : 2.560 Fit side-chains REVERT: A 40 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6675 (tp) REVERT: A 160 GLN cc_start: 0.9167 (tt0) cc_final: 0.8875 (tm-30) REVERT: B 160 GLN cc_start: 0.9164 (tt0) cc_final: 0.8840 (tm-30) REVERT: B 278 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.8425 (t60) REVERT: C 70 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7657 (tpp80) REVERT: C 160 GLN cc_start: 0.9161 (tt0) cc_final: 0.8864 (tm-30) outliers start: 31 outliers final: 12 residues processed: 120 average time/residue: 1.1421 time to fit residues: 162.1732 Evaluate side-chains 109 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE 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 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 C residue 70 ARG Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS 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 656 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 0.0020 chunk 149 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.128069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.074122 restraints weight = 42790.113| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.74 r_work: 0.2643 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22376 Z= 0.107 Angle : 0.468 7.830 30344 Z= 0.247 Chirality : 0.044 0.197 3568 Planarity : 0.003 0.031 3912 Dihedral : 3.735 16.029 3124 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.72 % Allowed : 11.88 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2884 helix: 2.16 (0.16), residues: 1116 sheet: 0.43 (0.22), residues: 508 loop : -1.05 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 278 HIS 0.002 0.000 HIS A 327 PHE 0.008 0.001 PHE B 638 TYR 0.009 0.001 TYR A 519 ARG 0.005 0.000 ARG A 301 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 1020) hydrogen bonds : angle 3.79796 ( 2868) covalent geometry : bond 0.00242 (22376) covalent geometry : angle 0.46806 (30344) *********************** 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 119 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 2.762 Fit side-chains REVERT: A 40 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6678 (tp) REVERT: A 160 GLN cc_start: 0.9182 (tt0) cc_final: 0.8872 (tm-30) REVERT: B 160 GLN cc_start: 0.9187 (tt0) cc_final: 0.8857 (tm-30) REVERT: C 160 GLN cc_start: 0.9186 (tt0) cc_final: 0.8872 (tm-30) REVERT: D 260 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8730 (pp) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 1.2486 time to fit residues: 165.8144 Evaluate side-chains 105 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE 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 B residue 114 ILE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 CYS 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 81 optimal weight: 0.9980 chunk 242 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 254 optimal weight: 40.0000 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.126908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.071832 restraints weight = 43177.610| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.82 r_work: 0.2614 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22376 Z= 0.154 Angle : 0.493 8.456 30344 Z= 0.259 Chirality : 0.044 0.180 3568 Planarity : 0.003 0.032 3912 Dihedral : 3.780 16.141 3124 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.85 % Allowed : 12.10 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 2884 helix: 2.18 (0.16), residues: 1116 sheet: 0.37 (0.22), residues: 512 loop : -1.05 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 278 HIS 0.002 0.001 HIS D 57 PHE 0.007 0.001 PHE D 480 TYR 0.009 0.001 TYR C 519 ARG 0.007 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1020) hydrogen bonds : angle 3.87978 ( 2868) covalent geometry : bond 0.00364 (22376) covalent geometry : angle 0.49262 (30344) *********************** 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 111 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 2.422 Fit side-chains REVERT: A 40 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6646 (tp) REVERT: A 160 GLN cc_start: 0.9181 (tt0) cc_final: 0.8891 (tm-30) REVERT: B 160 GLN cc_start: 0.9181 (tt0) cc_final: 0.8857 (tm-30) REVERT: C 160 GLN cc_start: 0.9175 (tt0) cc_final: 0.8877 (tm-30) outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 1.1488 time to fit residues: 146.2692 Evaluate side-chains 103 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE 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 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 Chi-restraints excluded: chain D residue 656 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 14 optimal weight: 30.0000 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 111 optimal weight: 40.0000 chunk 4 optimal weight: 10.0000 chunk 167 optimal weight: 0.0270 chunk 138 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 3.9644 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.126824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.072053 restraints weight = 43165.193| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.81 r_work: 0.2617 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22376 Z= 0.151 Angle : 0.485 8.036 30344 Z= 0.256 Chirality : 0.044 0.199 3568 Planarity : 0.003 0.033 3912 Dihedral : 3.783 19.122 3124 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.98 % Allowed : 12.44 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 2884 helix: 2.18 (0.16), residues: 1116 sheet: 0.35 (0.22), residues: 512 loop : -1.00 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 278 HIS 0.002 0.001 HIS D 327 PHE 0.006 0.001 PHE B 638 TYR 0.010 0.001 TYR D 519 ARG 0.006 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1020) hydrogen bonds : angle 3.87201 ( 2868) covalent geometry : bond 0.00356 (22376) covalent geometry : angle 0.48477 (30344) *********************** 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 117 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 2.632 Fit side-chains REVERT: A 40 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6662 (tp) REVERT: A 160 GLN cc_start: 0.9156 (tt0) cc_final: 0.8856 (tm-30) REVERT: B 160 GLN cc_start: 0.9165 (tt0) cc_final: 0.8851 (tm-30) REVERT: C 160 GLN cc_start: 0.9159 (tt0) cc_final: 0.8869 (tm-30) REVERT: C 300 GLU cc_start: 0.9024 (pt0) cc_final: 0.8490 (pp20) outliers start: 23 outliers final: 14 residues processed: 113 average time/residue: 1.1277 time to fit residues: 151.0019 Evaluate side-chains 109 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE 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 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 656 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 12 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 142 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 260 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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** A 460 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.074153 restraints weight = 43163.407| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.79 r_work: 0.2654 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2314 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= 0.101 Angle : 0.462 8.556 30344 Z= 0.242 Chirality : 0.044 0.209 3568 Planarity : 0.003 0.031 3912 Dihedral : 3.627 17.948 3124 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.68 % Allowed : 13.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.16), residues: 2884 helix: 2.25 (0.16), residues: 1116 sheet: 0.34 (0.22), residues: 512 loop : -0.94 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 278 HIS 0.002 0.001 HIS D 327 PHE 0.007 0.001 PHE C 638 TYR 0.019 0.001 TYR C 252 ARG 0.006 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 1020) hydrogen bonds : angle 3.73426 ( 2868) covalent geometry : bond 0.00230 (22376) covalent geometry : angle 0.46205 (30344) ********************** 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 111 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 2.635 Fit side-chains REVERT: A 160 GLN cc_start: 0.9176 (tt0) cc_final: 0.8873 (tm-30) REVERT: B 160 GLN cc_start: 0.9180 (tt0) cc_final: 0.8871 (tm-30) REVERT: C 160 GLN cc_start: 0.9182 (tt0) cc_final: 0.8873 (tm-30) REVERT: C 300 GLU cc_start: 0.8932 (pt0) cc_final: 0.8106 (pm20) REVERT: D 278 TRP cc_start: 0.8722 (OUTLIER) cc_final: 0.8335 (t60) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 1.1840 time to fit residues: 150.1960 Evaluate side-chains 97 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 2.567 ------------------------------------------------------------------------------- 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 299 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 278 TRP 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 231 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 262 optimal weight: 0.0980 chunk 214 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 = 0.3832 r_free = 0.3832 target = 0.127168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.073412 restraints weight = 42909.887| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.72 r_work: 0.2629 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22376 Z= 0.141 Angle : 0.474 8.704 30344 Z= 0.249 Chirality : 0.044 0.183 3568 Planarity : 0.003 0.032 3912 Dihedral : 3.700 17.136 3124 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.51 % Allowed : 13.37 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 2884 helix: 2.25 (0.16), residues: 1116 sheet: 0.39 (0.22), residues: 512 loop : -0.93 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 278 HIS 0.002 0.001 HIS D 327 PHE 0.007 0.001 PHE B 638 TYR 0.018 0.001 TYR C 252 ARG 0.007 0.000 ARG D 70 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1020) hydrogen bonds : angle 3.81184 ( 2868) covalent geometry : bond 0.00332 (22376) covalent geometry : angle 0.47433 (30344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14014.59 seconds wall clock time: 244 minutes 0.48 seconds (14640.48 seconds total)