Starting phenix.real_space_refine on Sun Feb 8 04:01:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9syt_55353/02_2026/9syt_55353_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9syt_55353/02_2026/9syt_55353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9syt_55353/02_2026/9syt_55353_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9syt_55353/02_2026/9syt_55353_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9syt_55353/02_2026/9syt_55353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9syt_55353/02_2026/9syt_55353.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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: 5 Type Number sf(0) Gaussians S 103 5.16 5 C 12326 2.51 5 N 3248 2.21 5 O 3427 1.98 5 H 19582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38686 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 12955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 12955 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 36, 'TRANS': 806} Chain breaks: 1 Chain: "B" Number of atoms: 12817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 12817 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 36, 'TRANS': 797} Chain breaks: 2 Chain: "C" Number of atoms: 11087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11087 Classifications: {'peptide': 722} Link IDs: {'PTRANS': 30, 'TRANS': 691} Chain breaks: 1 Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 574 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 574 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 574 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.19 Number of scatterers: 38686 At special positions: 0 Unit cell: (165.1, 122.2, 145.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 O 3427 8.00 N 3248 7.00 C 12326 6.00 H 19582 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 434 " - pdb=" SG CYS E 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS D 39 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 8 sheets defined 73.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 27 through 46 removed outlier: 3.587A pdb=" N VAL A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.661A pdb=" N GLY A 72 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.607A pdb=" N ASP A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 4.111A pdb=" N VAL A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.550A pdb=" N THR A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 219 removed outlier: 4.178A pdb=" N ALA A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 249 removed outlier: 3.607A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 287 Processing helix chain 'A' and resid 290 through 319 removed outlier: 3.656A pdb=" N TYR A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 332 through 360 Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.851A pdb=" N GLY A 378 " --> pdb=" O TRP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.575A pdb=" N VAL A 388 " --> pdb=" O TRP A 384 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.510A pdb=" N TYR A 415 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 433 removed outlier: 3.997A pdb=" N ALA A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 4.310A pdb=" N VAL A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.689A pdb=" N SER A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 512 through 542 removed outlier: 3.805A pdb=" N ASP A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 632 through 678 removed outlier: 3.994A pdb=" N GLN A 636 " --> pdb=" O GLN A 632 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 4.352A pdb=" N PHE A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 692' Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 723 through 741 removed outlier: 3.995A pdb=" N LYS A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 730 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 791 removed outlier: 4.133A pdb=" N GLU A 765 " --> pdb=" O HIS A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 819 Processing helix chain 'A' and resid 829 through 857 Processing helix chain 'A' and resid 860 through 871 Processing helix chain 'A' and resid 871 through 889 removed outlier: 3.727A pdb=" N VAL A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 886 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 893 Processing helix chain 'A' and resid 895 through 915 removed outlier: 3.589A pdb=" N GLY A 899 " --> pdb=" O LEU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 928 removed outlier: 4.661A pdb=" N THR A 921 " --> pdb=" O ARG A 917 " (cutoff:3.500A) Proline residue: A 922 - end of helix Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 65 through 79 Processing helix chain 'B' and resid 99 through 115 removed outlier: 4.016A pdb=" N LYS B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.903A pdb=" N GLN B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 184 through 219 removed outlier: 3.800A pdb=" N ALA B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 249 Processing helix chain 'B' and resid 255 through 287 Processing helix chain 'B' and resid 290 through 319 removed outlier: 5.518A pdb=" N HIS B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 323 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 331 through 360 removed outlier: 3.551A pdb=" N SER B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Proline residue: B 351 - end of helix Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.636A pdb=" N VAL B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 401 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 420 through 433 removed outlier: 3.551A pdb=" N GLY B 425 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.876A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 543 removed outlier: 3.610A pdb=" N GLN B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 677 Proline residue: B 634 - end of helix Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 723 through 728 removed outlier: 3.504A pdb=" N LYS B 728 " --> pdb=" O PRO B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 Processing helix chain 'B' and resid 756 through 791 removed outlier: 3.632A pdb=" N ASP B 762 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 765 " --> pdb=" O HIS B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 820 Processing helix chain 'B' and resid 829 through 857 removed outlier: 3.506A pdb=" N VAL B 837 " --> pdb=" O MET B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 4.114A pdb=" N LYS B 874 " --> pdb=" O GLY B 870 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 875 " --> pdb=" O GLY B 871 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 893 Processing helix chain 'B' and resid 895 through 916 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 930 through 934 Processing helix chain 'C' and resid 18 through 27 removed outlier: 3.650A pdb=" N MET C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 65 through 79 Processing helix chain 'C' and resid 97 through 115 removed outlier: 3.815A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.763A pdb=" N GLN C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 172 Processing helix chain 'C' and resid 184 through 219 removed outlier: 3.645A pdb=" N HIS C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 249 removed outlier: 3.674A pdb=" N VAL C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 287 Processing helix chain 'C' and resid 290 through 319 removed outlier: 5.375A pdb=" N HIS C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL C 305 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 323 Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 331 through 360 Proline residue: C 351 - end of helix removed outlier: 3.800A pdb=" N PHE C 360 " --> pdb=" O VAL C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 removed outlier: 4.167A pdb=" N GLY C 378 " --> pdb=" O TRP C 374 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.787A pdb=" N VAL C 388 " --> pdb=" O TRP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.547A pdb=" N GLY C 405 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 removed outlier: 3.696A pdb=" N ALA C 428 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 removed outlier: 3.988A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 723 through 741 removed outlier: 3.567A pdb=" N LYS C 728 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 730 " --> pdb=" O GLY C 726 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP C 731 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 791 removed outlier: 3.730A pdb=" N PHE C 760 " --> pdb=" O THR C 756 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU C 765 " --> pdb=" O HIS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 820 Processing helix chain 'C' and resid 829 through 858 removed outlier: 4.053A pdb=" N VAL C 837 " --> pdb=" O MET C 833 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 858 " --> pdb=" O LYS C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 889 removed outlier: 3.840A pdb=" N LYS C 874 " --> pdb=" O GLY C 870 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 875 " --> pdb=" O GLY C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 893 Processing helix chain 'C' and resid 895 through 915 Processing helix chain 'C' and resid 915 through 929 removed outlier: 4.858A pdb=" N THR C 921 " --> pdb=" O ARG C 917 " (cutoff:3.500A) Proline residue: C 922 - end of helix Processing helix chain 'C' and resid 930 through 934 Processing helix chain 'D' and resid 6 through 27 Processing helix chain 'E' and resid 6 through 27 Processing helix chain 'F' and resid 8 through 27 removed outlier: 4.398A pdb=" N LEU F 12 " --> pdb=" O PRO F 8 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 3.867A pdb=" N GLN A 146 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.845A pdb=" N LEU A 716 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 476 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE A 714 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 122 removed outlier: 6.529A pdb=" N SER B 148 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL B 122 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN B 146 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.957A pdb=" N SER C 121 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 146 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 87 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 123 removed outlier: 3.957A pdb=" N SER C 121 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN C 146 " --> pdb=" O GLN C 123 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 87 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 1414 hydrogen bonds defined for protein. 4155 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: 10.26 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19582 1.03 - 1.23: 7 1.23 - 1.43: 7879 1.43 - 1.62: 11409 1.62 - 1.82: 200 Bond restraints: 39077 Sorted by residual: bond pdb=" C3' LMT A1001 " pdb=" O3' LMT A1001 " ideal model delta sigma weight residual 1.404 1.360 0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C2B LMT A1001 " pdb=" O2B LMT A1001 " ideal model delta sigma weight residual 1.410 1.367 0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C3' LMT C1001 " pdb=" O3' LMT C1001 " ideal model delta sigma weight residual 1.404 1.361 0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C3' LMT B1001 " pdb=" O3' LMT B1001 " ideal model delta sigma weight residual 1.404 1.362 0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" C6' LMT B1001 " pdb=" O6' LMT B1001 " ideal model delta sigma weight residual 1.407 1.365 0.042 2.00e-02 2.50e+03 4.39e+00 ... (remaining 39072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 69926 2.09 - 4.17: 764 4.17 - 6.26: 103 6.26 - 8.35: 17 8.35 - 10.44: 10 Bond angle restraints: 70820 Sorted by residual: angle pdb=" CA PRO A 493 " pdb=" N PRO A 493 " pdb=" CD PRO A 493 " ideal model delta sigma weight residual 112.00 106.85 5.15 1.40e+00 5.10e-01 1.35e+01 angle pdb=" C2 LMT A1001 " pdb=" C3 LMT A1001 " pdb=" C4 LMT A1001 " ideal model delta sigma weight residual 117.09 106.65 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET A 643 " pdb=" CG MET A 643 " pdb=" SD MET A 643 " ideal model delta sigma weight residual 112.70 122.84 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET B 661 " pdb=" CG MET B 661 " pdb=" SD MET B 661 " ideal model delta sigma weight residual 112.70 122.10 -9.40 3.00e+00 1.11e-01 9.83e+00 angle pdb=" CB MET A 640 " pdb=" CG MET A 640 " pdb=" SD MET A 640 " ideal model delta sigma weight residual 112.70 122.05 -9.35 3.00e+00 1.11e-01 9.72e+00 ... (remaining 70815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.44: 17046 25.44 - 50.88: 1028 50.88 - 76.33: 294 76.33 - 101.77: 39 101.77 - 127.21: 23 Dihedral angle restraints: 18430 sinusoidal: 10124 harmonic: 8306 Sorted by residual: dihedral pdb=" CB CYS C 434 " pdb=" SG CYS C 434 " pdb=" SG CYS D 39 " pdb=" CB CYS D 39 " ideal model delta sinusoidal sigma weight residual -86.00 -172.69 86.69 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 434 " pdb=" SG CYS A 434 " pdb=" SG CYS E 39 " pdb=" CB CYS E 39 " ideal model delta sinusoidal sigma weight residual -86.00 -139.77 53.77 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS B 434 " pdb=" SG CYS B 434 " pdb=" SG CYS F 39 " pdb=" CB CYS F 39 " ideal model delta sinusoidal sigma weight residual -86.00 -35.68 -50.32 1 1.00e+01 1.00e-02 3.47e+01 ... (remaining 18427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2937 0.072 - 0.145: 212 0.145 - 0.217: 10 0.217 - 0.290: 3 0.290 - 0.362: 3 Chirality restraints: 3165 Sorted by residual: chirality pdb=" C5' LMT A1001 " pdb=" C4' LMT A1001 " pdb=" C6' LMT A1001 " pdb=" O5' LMT A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.15 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C5' LMT C1001 " pdb=" C4' LMT C1001 " pdb=" C6' LMT C1001 " pdb=" O5' LMT C1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.17 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C5' LMT B1001 " pdb=" C4' LMT B1001 " pdb=" C6' LMT B1001 " pdb=" O5' LMT B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.20 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3162 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 494 " 0.017 2.00e-02 2.50e+03 1.98e-02 1.18e+01 pdb=" CG PHE A 494 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 494 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 494 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 494 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 494 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 494 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 494 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 494 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 494 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 494 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 494 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 492 " -0.039 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO A 493 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 29 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO C 30 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 30 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 30 " -0.031 5.00e-02 4.00e+02 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3544 2.23 - 2.82: 85749 2.82 - 3.42: 104342 3.42 - 4.01: 136992 4.01 - 4.60: 212321 Nonbonded interactions: 542948 Sorted by model distance: nonbonded pdb=" O ALA A 21 " pdb=" HD1 HIS A 25 " model vdw 1.641 2.450 nonbonded pdb=" O LEU A 625 " pdb=" H MET A 629 " model vdw 1.709 2.450 nonbonded pdb=" O GLY B 405 " pdb="HE21 GLN B 819 " model vdw 1.717 2.450 nonbonded pdb=" O GLY C 405 " pdb="HE22 GLN C 819 " model vdw 1.721 2.450 nonbonded pdb=" O GLN B 503 " pdb=" HG1 THR B 506 " model vdw 1.724 2.450 ... (remaining 542943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 487 or resid 690 through 716 or (resid 717 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD2 or name HE1 or name HE2)) or resid 718 through 819 or (resid 820 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 \ or name HE1 or name HE2)) or resid 821 through 826 or (resid 827 and (name N or \ name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or na \ me CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or n \ ame HE1 or name HE2)) or resid 828 through 1001)) selection = (chain 'B' and (resid 16 through 354 or (resid 355 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 356 through 487 or resid 690 through 1001)) selection = (chain 'C' and (resid 16 through 716 or (resid 717 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 718 through 1001)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.120 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: 0.250 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 37.510 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 : 0.004 0.046 19498 Z= 0.175 Angle : 0.685 10.436 26488 Z= 0.331 Chirality : 0.041 0.362 3165 Planarity : 0.005 0.057 3307 Dihedral : 17.239 127.209 7108 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.05 % Allowed : 12.86 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2487 helix: 0.86 (0.12), residues: 1662 sheet: -1.78 (0.42), residues: 150 loop : 0.23 (0.27), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 26 TYR 0.027 0.001 TYR C 299 PHE 0.058 0.001 PHE A 494 TRP 0.007 0.001 TRP B 126 HIS 0.009 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00406 (19495) covalent geometry : angle 0.68469 (26482) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.46583 ( 6) hydrogen bonds : bond 0.21984 ( 1411) hydrogen bonds : angle 7.76825 ( 4155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8839 (t0) cc_final: 0.8595 (t0) REVERT: A 481 ARG cc_start: 0.8385 (ttm110) cc_final: 0.8172 (ttm110) REVERT: A 654 MET cc_start: 0.7473 (ptp) cc_final: 0.7258 (ptp) REVERT: A 845 TYR cc_start: 0.6915 (m-10) cc_final: 0.6576 (m-10) REVERT: C 76 MET cc_start: 0.8306 (ttp) cc_final: 0.8074 (ttt) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.3057 time to fit residues: 105.7266 Evaluate side-chains 209 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.171728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110870 restraints weight = 82548.221| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.17 r_work: 0.3283 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19498 Z= 0.152 Angle : 0.561 8.532 26488 Z= 0.299 Chirality : 0.039 0.176 3165 Planarity : 0.005 0.051 3307 Dihedral : 10.243 100.774 2869 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.80 % Allowed : 12.26 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.17), residues: 2487 helix: 1.73 (0.12), residues: 1682 sheet: -1.39 (0.41), residues: 154 loop : 0.18 (0.27), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 475 TYR 0.016 0.001 TYR A 281 PHE 0.030 0.001 PHE B 276 TRP 0.007 0.001 TRP C 126 HIS 0.004 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00303 (19495) covalent geometry : angle 0.56102 (26482) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.23840 ( 6) hydrogen bonds : bond 0.05230 ( 1411) hydrogen bonds : angle 5.02539 ( 4155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8072 (t0) cc_final: 0.7829 (t0) REVERT: A 139 ASP cc_start: 0.8827 (t0) cc_final: 0.8616 (t0) REVERT: B 498 MET cc_start: 0.7151 (tpp) cc_final: 0.6724 (tmm) REVERT: B 675 PHE cc_start: 0.6854 (m-80) cc_final: 0.6417 (m-80) REVERT: C 23 MET cc_start: 0.7382 (mpp) cc_final: 0.6932 (mpp) REVERT: C 76 MET cc_start: 0.8162 (ttp) cc_final: 0.7936 (ttt) outliers start: 16 outliers final: 10 residues processed: 221 average time/residue: 0.3102 time to fit residues: 108.9114 Evaluate side-chains 218 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 883 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.171377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107778 restraints weight = 82180.809| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.84 r_work: 0.3292 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19498 Z= 0.149 Angle : 0.523 9.936 26488 Z= 0.271 Chirality : 0.038 0.191 3165 Planarity : 0.004 0.048 3307 Dihedral : 6.785 60.651 2869 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.75 % Allowed : 12.61 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.17), residues: 2487 helix: 2.04 (0.12), residues: 1690 sheet: -1.28 (0.42), residues: 153 loop : 0.20 (0.28), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 481 TYR 0.010 0.001 TYR A 281 PHE 0.034 0.001 PHE B 276 TRP 0.007 0.001 TRP C 126 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd covalent geometry : bond 0.00318 (19495) covalent geometry : angle 0.52294 (26482) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.34343 ( 6) hydrogen bonds : bond 0.04606 ( 1411) hydrogen bonds : angle 4.67043 ( 4155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8108 (t0) cc_final: 0.7798 (t0) REVERT: A 728 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8220 (mmmt) REVERT: B 498 MET cc_start: 0.7064 (tpp) cc_final: 0.6630 (tmm) REVERT: C 23 MET cc_start: 0.7459 (mpp) cc_final: 0.7074 (mpp) REVERT: C 76 MET cc_start: 0.8340 (ttp) cc_final: 0.8112 (ttt) REVERT: C 214 MET cc_start: 0.8035 (mmt) cc_final: 0.7704 (mmm) outliers start: 15 outliers final: 11 residues processed: 223 average time/residue: 0.3115 time to fit residues: 110.7774 Evaluate side-chains 217 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 139 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 chunk 121 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 131 optimal weight: 0.0870 chunk 240 optimal weight: 4.9990 overall best weight: 0.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.172841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109616 restraints weight = 81764.305| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.84 r_work: 0.3317 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19498 Z= 0.109 Angle : 0.468 7.336 26488 Z= 0.247 Chirality : 0.037 0.218 3165 Planarity : 0.004 0.047 3307 Dihedral : 5.188 56.157 2869 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.00 % Allowed : 12.56 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.17), residues: 2487 helix: 2.28 (0.12), residues: 1690 sheet: -1.16 (0.41), residues: 154 loop : 0.26 (0.27), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 513 TYR 0.009 0.001 TYR A 281 PHE 0.035 0.001 PHE B 276 TRP 0.005 0.001 TRP C 126 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00217 (19495) covalent geometry : angle 0.46849 (26482) SS BOND : bond 0.00105 ( 3) SS BOND : angle 0.24621 ( 6) hydrogen bonds : bond 0.03934 ( 1411) hydrogen bonds : angle 4.42365 ( 4155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7964 (t0) cc_final: 0.7665 (t0) REVERT: A 281 TYR cc_start: 0.5873 (t80) cc_final: 0.5611 (t80) REVERT: A 438 MET cc_start: 0.9087 (mmp) cc_final: 0.8622 (mmp) REVERT: A 671 MET cc_start: 0.8413 (tmm) cc_final: 0.8092 (tpp) REVERT: A 728 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8309 (mmmt) REVERT: A 750 LYS cc_start: 0.8188 (mttp) cc_final: 0.7661 (mtmt) REVERT: B 498 MET cc_start: 0.7018 (tpp) cc_final: 0.6623 (tmm) REVERT: C 23 MET cc_start: 0.7549 (mpp) cc_final: 0.7152 (mpp) REVERT: C 84 ASP cc_start: 0.8553 (p0) cc_final: 0.8321 (p0) REVERT: C 214 MET cc_start: 0.8015 (mmt) cc_final: 0.7692 (mmm) outliers start: 20 outliers final: 10 residues processed: 234 average time/residue: 0.3030 time to fit residues: 111.8293 Evaluate side-chains 217 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 177 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.171545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107973 restraints weight = 81952.222| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.83 r_work: 0.3281 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19498 Z= 0.154 Angle : 0.486 7.263 26488 Z= 0.257 Chirality : 0.037 0.171 3165 Planarity : 0.004 0.046 3307 Dihedral : 4.994 53.948 2869 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.00 % Allowed : 12.86 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.17), residues: 2487 helix: 2.33 (0.12), residues: 1689 sheet: -1.22 (0.41), residues: 157 loop : 0.19 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.009 0.001 TYR B 415 PHE 0.038 0.001 PHE B 276 TRP 0.007 0.001 TRP C 126 HIS 0.004 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00338 (19495) covalent geometry : angle 0.48641 (26482) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.34591 ( 6) hydrogen bonds : bond 0.03923 ( 1411) hydrogen bonds : angle 4.38865 ( 4155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8055 (t0) cc_final: 0.7689 (t0) REVERT: A 281 TYR cc_start: 0.5863 (t80) cc_final: 0.5635 (t80) REVERT: A 671 MET cc_start: 0.8376 (tmm) cc_final: 0.8035 (tpp) REVERT: A 728 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8383 (mmmt) REVERT: A 750 LYS cc_start: 0.8243 (mttp) cc_final: 0.7730 (mtmt) REVERT: B 498 MET cc_start: 0.7007 (tpp) cc_final: 0.6643 (tmm) REVERT: C 84 ASP cc_start: 0.8546 (p0) cc_final: 0.8274 (p0) REVERT: C 179 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7917 (mttm) REVERT: C 214 MET cc_start: 0.8019 (mmt) cc_final: 0.7717 (mmm) outliers start: 20 outliers final: 13 residues processed: 232 average time/residue: 0.3101 time to fit residues: 113.1368 Evaluate side-chains 224 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 131 optimal weight: 0.4980 chunk 200 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 HIS ** 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 = 0.4238 r_free = 0.4238 target = 0.171603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108060 restraints weight = 82098.149| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.82 r_work: 0.3294 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19498 Z= 0.145 Angle : 0.484 6.946 26488 Z= 0.256 Chirality : 0.037 0.149 3165 Planarity : 0.004 0.047 3307 Dihedral : 4.928 47.824 2869 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.05 % Allowed : 12.96 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.17), residues: 2487 helix: 2.37 (0.12), residues: 1690 sheet: -1.18 (0.41), residues: 156 loop : 0.19 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 24 TYR 0.010 0.001 TYR B 415 PHE 0.044 0.001 PHE B 276 TRP 0.007 0.001 TRP C 126 HIS 0.004 0.001 HIS A 717 Details of bonding type rmsd covalent geometry : bond 0.00317 (19495) covalent geometry : angle 0.48396 (26482) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.34901 ( 6) hydrogen bonds : bond 0.03796 ( 1411) hydrogen bonds : angle 4.32530 ( 4155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8040 (t0) cc_final: 0.7667 (t0) REVERT: A 728 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8374 (mmmt) REVERT: A 750 LYS cc_start: 0.8205 (mttp) cc_final: 0.7671 (mtmt) REVERT: B 498 MET cc_start: 0.7043 (tpp) cc_final: 0.6647 (tmm) REVERT: B 664 MET cc_start: 0.7238 (mmm) cc_final: 0.6911 (mmm) REVERT: C 214 MET cc_start: 0.8017 (mmt) cc_final: 0.7728 (mmm) outliers start: 21 outliers final: 18 residues processed: 233 average time/residue: 0.3216 time to fit residues: 118.5910 Evaluate side-chains 227 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 39 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 124 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.170377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106615 restraints weight = 82046.640| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.81 r_work: 0.3276 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19498 Z= 0.190 Angle : 0.510 7.371 26488 Z= 0.271 Chirality : 0.038 0.195 3165 Planarity : 0.004 0.047 3307 Dihedral : 5.108 53.801 2869 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.25 % Allowed : 13.56 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.17), residues: 2487 helix: 2.34 (0.12), residues: 1689 sheet: -1.26 (0.41), residues: 156 loop : 0.06 (0.27), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.013 0.001 TYR B 415 PHE 0.048 0.001 PHE B 276 TRP 0.009 0.001 TRP C 126 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00427 (19495) covalent geometry : angle 0.51035 (26482) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.50417 ( 6) hydrogen bonds : bond 0.03847 ( 1411) hydrogen bonds : angle 4.35659 ( 4155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8145 (t0) cc_final: 0.7786 (t0) REVERT: A 750 LYS cc_start: 0.8244 (mttp) cc_final: 0.7726 (mtmt) REVERT: B 498 MET cc_start: 0.7055 (tpp) cc_final: 0.6653 (tmm) REVERT: B 664 MET cc_start: 0.7272 (mmm) cc_final: 0.6946 (mmm) REVERT: C 214 MET cc_start: 0.8026 (mmt) cc_final: 0.7747 (mmm) outliers start: 25 outliers final: 22 residues processed: 228 average time/residue: 0.3032 time to fit residues: 110.3441 Evaluate side-chains 232 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 39 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 174 optimal weight: 0.6980 chunk 224 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.170567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107183 restraints weight = 81696.014| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.80 r_work: 0.3283 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19498 Z= 0.160 Angle : 0.494 6.668 26488 Z= 0.262 Chirality : 0.038 0.149 3165 Planarity : 0.004 0.047 3307 Dihedral : 5.073 54.881 2869 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.30 % Allowed : 13.81 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.17), residues: 2487 helix: 2.38 (0.12), residues: 1689 sheet: -1.19 (0.41), residues: 155 loop : 0.07 (0.27), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.017 0.001 TYR A 281 PHE 0.053 0.001 PHE B 276 TRP 0.008 0.001 TRP C 126 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00354 (19495) covalent geometry : angle 0.49451 (26482) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.39431 ( 6) hydrogen bonds : bond 0.03752 ( 1411) hydrogen bonds : angle 4.30561 ( 4155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8106 (t0) cc_final: 0.7741 (t0) REVERT: A 152 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8108 (t0) REVERT: A 750 LYS cc_start: 0.8229 (mttp) cc_final: 0.7709 (mtmt) REVERT: B 498 MET cc_start: 0.7040 (tpp) cc_final: 0.6650 (tmm) REVERT: B 664 MET cc_start: 0.7254 (mmm) cc_final: 0.6940 (mmm) REVERT: C 214 MET cc_start: 0.8057 (mmt) cc_final: 0.7789 (mmm) outliers start: 26 outliers final: 23 residues processed: 233 average time/residue: 0.3040 time to fit residues: 112.4421 Evaluate side-chains 235 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 39 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 234 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 HIS ** 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 = 0.4231 r_free = 0.4231 target = 0.170942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107301 restraints weight = 82158.379| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.81 r_work: 0.3285 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19498 Z= 0.150 Angle : 0.492 7.414 26488 Z= 0.259 Chirality : 0.037 0.148 3165 Planarity : 0.004 0.047 3307 Dihedral : 4.930 53.864 2869 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.35 % Allowed : 13.86 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.17), residues: 2487 helix: 2.43 (0.12), residues: 1690 sheet: -1.21 (0.42), residues: 156 loop : 0.07 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 481 TYR 0.019 0.001 TYR A 281 PHE 0.058 0.001 PHE B 276 TRP 0.008 0.001 TRP C 126 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00330 (19495) covalent geometry : angle 0.49240 (26482) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.36431 ( 6) hydrogen bonds : bond 0.03671 ( 1411) hydrogen bonds : angle 4.25910 ( 4155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8065 (t0) cc_final: 0.7688 (t0) REVERT: A 152 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8088 (t0) REVERT: A 750 LYS cc_start: 0.8201 (mttp) cc_final: 0.7672 (mtmt) REVERT: B 498 MET cc_start: 0.7028 (tpp) cc_final: 0.6659 (tmm) REVERT: B 664 MET cc_start: 0.7266 (mmm) cc_final: 0.6966 (mmm) REVERT: C 214 MET cc_start: 0.8034 (mmt) cc_final: 0.7774 (mmm) outliers start: 27 outliers final: 25 residues processed: 237 average time/residue: 0.3135 time to fit residues: 118.1488 Evaluate side-chains 235 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 933 TRP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 39 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 HIS ** 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 = 0.4230 r_free = 0.4230 target = 0.170751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.107100 restraints weight = 82077.099| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.81 r_work: 0.3278 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19498 Z= 0.162 Angle : 0.496 7.787 26488 Z= 0.262 Chirality : 0.038 0.194 3165 Planarity : 0.004 0.047 3307 Dihedral : 4.937 56.417 2869 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.35 % Allowed : 14.21 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.17), residues: 2487 helix: 2.43 (0.12), residues: 1689 sheet: -1.21 (0.41), residues: 156 loop : 0.04 (0.27), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 511 TYR 0.017 0.001 TYR A 281 PHE 0.052 0.001 PHE B 276 TRP 0.008 0.001 TRP C 126 HIS 0.004 0.001 HIS A 717 Details of bonding type rmsd covalent geometry : bond 0.00360 (19495) covalent geometry : angle 0.49627 (26482) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.39723 ( 6) hydrogen bonds : bond 0.03660 ( 1411) hydrogen bonds : angle 4.25991 ( 4155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.8079 (t0) cc_final: 0.7705 (t0) REVERT: A 152 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8088 (t0) REVERT: A 511 ARG cc_start: 0.6101 (mtm110) cc_final: 0.5642 (mtm110) REVERT: A 750 LYS cc_start: 0.8210 (mttp) cc_final: 0.7683 (mtmt) REVERT: B 56 ARG cc_start: 0.7900 (ttm-80) cc_final: 0.7396 (ttm-80) REVERT: B 498 MET cc_start: 0.7038 (tpp) cc_final: 0.6666 (tmm) REVERT: B 664 MET cc_start: 0.7265 (mmm) cc_final: 0.6968 (mmm) REVERT: C 214 MET cc_start: 0.8024 (mmt) cc_final: 0.7768 (mmm) outliers start: 27 outliers final: 26 residues processed: 232 average time/residue: 0.3146 time to fit residues: 115.7651 Evaluate side-chains 237 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 834 SER Chi-restraints excluded: chain A residue 933 TRP Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 39 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 HIS ** 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 = 0.4220 r_free = 0.4220 target = 0.169897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106222 restraints weight = 81869.252| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.80 r_work: 0.3269 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19498 Z= 0.184 Angle : 0.511 7.748 26488 Z= 0.270 Chirality : 0.038 0.215 3165 Planarity : 0.004 0.047 3307 Dihedral : 5.054 58.309 2869 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.35 % Allowed : 14.26 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.17), residues: 2487 helix: 2.42 (0.12), residues: 1683 sheet: -1.29 (0.41), residues: 157 loop : -0.08 (0.27), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 481 TYR 0.018 0.001 TYR A 281 PHE 0.054 0.001 PHE B 276 TRP 0.009 0.001 TRP C 126 HIS 0.005 0.001 HIS B 651 Details of bonding type rmsd covalent geometry : bond 0.00413 (19495) covalent geometry : angle 0.51105 (26482) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.50750 ( 6) hydrogen bonds : bond 0.03707 ( 1411) hydrogen bonds : angle 4.27499 ( 4155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13210.03 seconds wall clock time: 223 minutes 51.46 seconds (13431.46 seconds total)