Starting phenix.real_space_refine on Fri Jul 3 20:23:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yaq_39104/07_2026/8yaq_39104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yaq_39104/07_2026/8yaq_39104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yaq_39104/07_2026/8yaq_39104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yaq_39104/07_2026/8yaq_39104.map" model { file = "/net/cci-nas-00/data/ceres_data/8yaq_39104/07_2026/8yaq_39104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yaq_39104/07_2026/8yaq_39104.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 64 5.16 5 Cl 5 4.86 5 C 10142 2.51 5 N 2627 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15860 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7877 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 33, 'TRANS': 950} Chain: "B" Number of atoms: 7887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7887 Classifications: {'peptide': 985} Link IDs: {'PTRANS': 33, 'TRANS': 951} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'BGC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CL': 2} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' CL': 3} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N PHE A 295 " occ=0.90 ... (9 atoms not shown) pdb=" CZ PHE A 295 " occ=0.90 residue: pdb=" N PHE B 295 " occ=0.95 ... (9 atoms not shown) pdb=" CZ PHE B 295 " occ=0.95 residue: pdb=" C1 BGC D 2 " occ=0.68 ... (9 atoms not shown) pdb=" O6 BGC D 2 " occ=0.68 residue: pdb=" C1 BGC D 3 " occ=0.78 ... (9 atoms not shown) pdb=" O6 BGC D 3 " occ=0.78 residue: pdb=" C1 BGC D 4 " occ=0.64 ... (9 atoms not shown) pdb=" O6 BGC D 4 " occ=0.64 residue: pdb=" C1 BGC D 5 " occ=0.58 ... (9 atoms not shown) pdb=" O6 BGC D 5 " occ=0.58 residue: pdb=" C1 BGC C 2 " occ=0.36 ... (9 atoms not shown) pdb=" O6 BGC C 2 " occ=0.36 residue: pdb=" C1 BGC C 3 " occ=0.44 ... (9 atoms not shown) pdb=" O6 BGC C 3 " occ=0.44 Time building chain proxies: 3.83, per 1000 atoms: 0.24 Number of scatterers: 15860 At special positions: 0 Unit cell: (92.13, 112.88, 146.91, 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) Cl 5 17.00 S 64 16.00 O 3022 8.00 N 2627 7.00 C 10142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BGC C 1 " - " BGC C 2 " " BGC C 2 " - " BGC C 3 " " BGC D 1 " - " BGC D 2 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 813.5 milliseconds 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3690 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 24 sheets defined 35.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.588A pdb=" N VAL A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 72 removed outlier: 3.775A pdb=" N GLN A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 291 through 297 removed outlier: 4.171A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.585A pdb=" N MET A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 453 removed outlier: 4.180A pdb=" N VAL A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.221A pdb=" N ALA A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 531 Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.899A pdb=" N TRP A 559 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.880A pdb=" N VAL A 576 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.585A pdb=" N SER A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 Processing helix chain 'A' and resid 665 through 685 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 749 through 759 removed outlier: 3.902A pdb=" N PHE A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 777 Processing helix chain 'A' and resid 816 through 831 Processing helix chain 'A' and resid 835 through 852 removed outlier: 3.685A pdb=" N LEU A 852 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 removed outlier: 5.902A pdb=" N TYR A 856 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 859 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 890 through 904 Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 101 through 112 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 297 through 304 removed outlier: 3.687A pdb=" N THR B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.653A pdb=" N MET B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 453 removed outlier: 4.374A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 472 through 485 Processing helix chain 'B' and resid 501 through 504 Processing helix chain 'B' and resid 505 through 515 removed outlier: 5.472A pdb=" N TYR B 511 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 531 Processing helix chain 'B' and resid 558 through 572 removed outlier: 4.133A pdb=" N GLN B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 593 through 606 removed outlier: 3.553A pdb=" N SER B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 650 Processing helix chain 'B' and resid 665 through 685 Processing helix chain 'B' and resid 687 through 709 Processing helix chain 'B' and resid 749 through 759 removed outlier: 3.984A pdb=" N PHE B 753 " --> pdb=" O PHE B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 777 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 799 through 803 Processing helix chain 'B' and resid 816 through 831 Processing helix chain 'B' and resid 835 through 852 removed outlier: 3.634A pdb=" N LEU B 852 " --> pdb=" O PHE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 860 removed outlier: 5.867A pdb=" N TYR B 856 " --> pdb=" O VAL B 853 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 859 " --> pdb=" O TYR B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 866 Processing helix chain 'B' and resid 889 through 903 removed outlier: 4.580A pdb=" N THR B 893 " --> pdb=" O SER B 889 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.440A pdb=" N GLN B 306 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 308 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B 320 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 310 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 318 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 338 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ARG B 334 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR B 324 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ASP B 332 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 222 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.440A pdb=" N GLN B 306 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 308 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B 320 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 310 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 318 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 338 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ARG B 334 " --> pdb=" O PRO B 322 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR B 324 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ASP B 332 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 345 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.787A pdb=" N PHE A 31 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP A 33 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA A 48 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 35 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY A 46 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLU A 83 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N LEU A 50 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.537A pdb=" N GLU A 222 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 3.537A pdb=" N GLU A 222 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASP A 332 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N TYR A 324 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG A 334 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 318 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 310 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A 320 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 308 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN A 306 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 147 Processing sheet with id=AA7, first strand: chain 'A' and resid 208 through 212 removed outlier: 6.485A pdb=" N LEU A 203 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR A 212 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE A 201 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 200 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 457 through 459 removed outlier: 6.581A pdb=" N SER A 935 " --> pdb=" O HIS A 977 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 979 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS A 937 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 981 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A 939 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N PHE A 983 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR A 941 " --> pdb=" O PHE A 983 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 953 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.449A pdb=" N ASN A 540 " --> pdb=" O PRO A 550 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN A 542 " --> pdb=" O LYS A 548 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 582 Processing sheet with id=AB2, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AB3, first strand: chain 'A' and resid 779 through 780 Processing sheet with id=AB4, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AB5, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AB6, first strand: chain 'B' and resid 32 through 36 removed outlier: 5.879A pdb=" N GLU B 83 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AB8, first strand: chain 'B' and resid 208 through 212 removed outlier: 6.505A pdb=" N LEU B 203 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR B 212 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE B 201 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 200 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 457 through 459 removed outlier: 6.598A pdb=" N SER B 935 " --> pdb=" O HIS B 977 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL B 979 " --> pdb=" O SER B 935 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS B 937 " --> pdb=" O VAL B 979 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 981 " --> pdb=" O LYS B 937 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER B 939 " --> pdb=" O LEU B 981 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N PHE B 983 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR B 941 " --> pdb=" O PHE B 983 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B 953 " --> pdb=" O LYS B 984 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU B 956 " --> pdb=" O ILE B 963 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 498 through 499 removed outlier: 6.437A pdb=" N ASN B 540 " --> pdb=" O PRO B 550 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 542 " --> pdb=" O LYS B 548 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 580 through 582 Processing sheet with id=AC3, first strand: chain 'B' and resid 663 through 664 Processing sheet with id=AC4, first strand: chain 'B' and resid 779 through 780 Processing sheet with id=AC5, first strand: chain 'B' and resid 814 through 815 Processing sheet with id=AC6, first strand: chain 'B' and resid 907 through 908 761 hydrogen bonds defined for protein. 2103 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: 3.60 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5123 1.34 - 1.46: 3883 1.46 - 1.58: 7095 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 16207 Sorted by residual: bond pdb=" CB GLN B 86 " pdb=" CG GLN B 86 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" CB GLN A 689 " pdb=" CG GLN A 689 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLN A 692 " pdb=" CG GLN A 692 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CB PRO B 75 " pdb=" CG PRO B 75 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.19e+00 bond pdb=" C ILE B 516 " pdb=" O ILE B 516 " ideal model delta sigma weight residual 1.236 1.225 0.012 1.19e-02 7.06e+03 9.62e-01 ... (remaining 16202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 21666 1.63 - 3.26: 220 3.26 - 4.89: 35 4.89 - 6.52: 9 6.52 - 8.15: 5 Bond angle restraints: 21935 Sorted by residual: angle pdb=" CA GLN A 689 " pdb=" CB GLN A 689 " pdb=" CG GLN A 689 " ideal model delta sigma weight residual 114.10 121.80 -7.70 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLN B 86 " pdb=" CB GLN B 86 " pdb=" CG GLN B 86 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N VAL A 853 " pdb=" CA VAL A 853 " pdb=" C VAL A 853 " ideal model delta sigma weight residual 113.53 110.25 3.28 9.80e-01 1.04e+00 1.12e+01 angle pdb=" CA GLN A 692 " pdb=" CB GLN A 692 " pdb=" CG GLN A 692 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB GLN A 689 " pdb=" CG GLN A 689 " pdb=" CD GLN A 689 " ideal model delta sigma weight residual 112.60 117.84 -5.24 1.70e+00 3.46e-01 9.49e+00 ... (remaining 21930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.75: 9478 24.75 - 49.50: 250 49.50 - 74.24: 26 74.24 - 98.99: 5 98.99 - 123.74: 2 Dihedral angle restraints: 9761 sinusoidal: 4006 harmonic: 5755 Sorted by residual: dihedral pdb=" CA VAL A 74 " pdb=" C VAL A 74 " pdb=" N PRO A 75 " pdb=" CA PRO A 75 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" C2 BGC D 5 " pdb=" C1 BGC D 5 " pdb=" O5 BGC D 5 " pdb=" C5 BGC D 5 " ideal model delta sinusoidal sigma weight residual -65.02 58.72 -123.74 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" CA ALA B 620 " pdb=" C ALA B 620 " pdb=" N ASP B 621 " pdb=" CA ASP B 621 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1489 0.029 - 0.058: 628 0.058 - 0.087: 162 0.087 - 0.116: 120 0.116 - 0.145: 26 Chirality restraints: 2425 Sorted by residual: chirality pdb=" CB VAL A 74 " pdb=" CA VAL A 74 " pdb=" CG1 VAL A 74 " pdb=" CG2 VAL A 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE B 339 " pdb=" N ILE B 339 " pdb=" C ILE B 339 " pdb=" CB ILE B 339 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL B 164 " pdb=" N VAL B 164 " pdb=" C VAL B 164 " pdb=" CB VAL B 164 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2422 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 74 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 75 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 565 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C TYR A 565 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR A 565 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 566 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 446 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE B 446 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE B 446 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 447 " 0.009 2.00e-02 2.50e+03 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4002 2.79 - 3.32: 14583 3.32 - 3.85: 26514 3.85 - 4.37: 33071 4.37 - 4.90: 56187 Nonbonded interactions: 134357 Sorted by model distance: nonbonded pdb=" OG1 THR B 780 " pdb=" O GLY B 783 " model vdw 2.267 3.040 nonbonded pdb=" N GLU A 415 " pdb=" OE1 GLU A 415 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP B 621 " pdb=" NH1 ARG B 717 " model vdw 2.289 3.120 nonbonded pdb=" O GLU A 124 " pdb=" OG SER A 468 " model vdw 2.293 3.040 nonbonded pdb=" O THR A 156 " pdb=" OG1 THR A 160 " model vdw 2.310 3.040 ... (remaining 134352 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' selection = (chain 'B' and (resid 2 through 985 or resid 1002 through 1003)) } 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=0.36 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: 4.190 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.610 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 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 : 0.003 0.054 16213 Z= 0.126 Angle : 0.465 8.148 21953 Z= 0.253 Chirality : 0.040 0.145 2425 Planarity : 0.003 0.048 2826 Dihedral : 11.192 123.737 6071 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 0.18 % Allowed : 6.22 % Favored : 93.60 % 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: 0.83 (0.19), residues: 1965 helix: 1.45 (0.21), residues: 630 sheet: 1.39 (0.28), residues: 338 loop : -0.31 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.012 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.010 0.001 TRP A 755 HIS 0.003 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16207) covalent geometry : angle 0.46341 / 0.25 (21935) hydrogen bonds : bond 0.14367 / 9.49 ( 707) hydrogen bonds : angle 6.23155 / 4.51 ( 2103) link_BETA1-4 : bond 0.00559 / 0.27 ( 6) link_BETA1-4 : angle 1.22447 / 0.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.647 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.8052 time to fit residues: 60.1909 Evaluate side-chains 66 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0050 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.060194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.042970 restraints weight = 32806.922| |-----------------------------------------------------------------------------| r_work (start): 0.2432 rms_B_bonded: 2.91 r_work: 0.2281 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2157 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2170 r_free = 0.2170 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2170 r_free = 0.2170 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16213 Z= 0.130 Angle : 0.470 7.149 21953 Z= 0.255 Chirality : 0.041 0.140 2425 Planarity : 0.003 0.046 2826 Dihedral : 6.177 115.005 2304 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.76 % Allowed : 5.87 % Favored : 93.36 % 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: 1.11 (0.19), residues: 1965 helix: 1.98 (0.21), residues: 628 sheet: 1.32 (0.29), residues: 338 loop : -0.26 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 909 TYR 0.012 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.011 0.001 TRP A 755 HIS 0.002 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16207) covalent geometry : angle 0.46767 / 0.25 (21935) hydrogen bonds : bond 0.04225 / 2.81 ( 707) hydrogen bonds : angle 4.73980 / 3.39 ( 2103) link_BETA1-4 : bond 0.00479 / 0.23 ( 6) link_BETA1-4 : angle 1.83761 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.657 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 77 average time/residue: 0.7544 time to fit residues: 63.9243 Evaluate side-chains 67 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 125 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 25 optimal weight: 0.0770 chunk 175 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.059443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.042148 restraints weight = 33395.214| |-----------------------------------------------------------------------------| r_work (start): 0.2412 rms_B_bonded: 2.93 r_work: 0.2261 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2135 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2148 r_free = 0.2148 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2148 r_free = 0.2148 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16213 Z= 0.154 Angle : 0.472 7.406 21953 Z= 0.254 Chirality : 0.041 0.137 2425 Planarity : 0.003 0.042 2826 Dihedral : 5.946 114.192 2301 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.70 % Allowed : 5.64 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 1965 helix: 2.06 (0.21), residues: 628 sheet: 1.38 (0.29), residues: 338 loop : -0.30 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 909 TYR 0.012 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.014 0.001 TRP A 755 HIS 0.003 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (16207) covalent geometry : angle 0.46893 / 0.25 (21935) hydrogen bonds : bond 0.04095 / 2.72 ( 707) hydrogen bonds : angle 4.54248 / 3.25 ( 2103) link_BETA1-4 : bond 0.00521 / 0.25 ( 6) link_BETA1-4 : angle 1.81857 / 1.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.670 Fit side-chains REVERT: A 689 GLN cc_start: 0.8745 (pp30) cc_final: 0.8490 (tm-30) REVERT: A 949 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8586 (mtm) REVERT: B 96 GLN cc_start: 0.8520 (mt0) cc_final: 0.8241 (mt0) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 0.8060 time to fit residues: 65.5015 Evaluate side-chains 69 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.059569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.042314 restraints weight = 32881.824| |-----------------------------------------------------------------------------| r_work (start): 0.2417 rms_B_bonded: 2.91 r_work: 0.2266 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2140 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2153 r_free = 0.2153 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2153 r_free = 0.2153 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16213 Z= 0.144 Angle : 0.463 7.683 21953 Z= 0.250 Chirality : 0.041 0.136 2425 Planarity : 0.003 0.052 2826 Dihedral : 5.874 113.076 2301 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.41 % Allowed : 6.40 % Favored : 93.19 % 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: 1.15 (0.19), residues: 1965 helix: 2.10 (0.21), residues: 627 sheet: 1.37 (0.29), residues: 338 loop : -0.31 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 909 TYR 0.012 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.014 0.001 TRP B 755 HIS 0.003 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16207) covalent geometry : angle 0.46042 / 0.25 (21935) hydrogen bonds : bond 0.03866 / 2.56 ( 707) hydrogen bonds : angle 4.45577 / 3.20 ( 2103) link_BETA1-4 : bond 0.00539 / 0.26 ( 6) link_BETA1-4 : angle 1.82042 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.618 Fit side-chains REVERT: B 798 ASP cc_start: 0.8932 (t70) cc_final: 0.8685 (t0) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.6899 time to fit residues: 53.7929 Evaluate side-chains 69 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 0.6980 chunk 102 optimal weight: 0.0070 chunk 41 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.060081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.042855 restraints weight = 32909.894| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 2.92 r_work: 0.2280 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2155 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2168 r_free = 0.2168 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2168 r_free = 0.2168 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16213 Z= 0.119 Angle : 0.453 7.794 21953 Z= 0.244 Chirality : 0.041 0.134 2425 Planarity : 0.003 0.047 2826 Dihedral : 5.793 112.271 2301 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.65 % Allowed : 6.69 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.19), residues: 1965 helix: 2.10 (0.21), residues: 630 sheet: 1.41 (0.29), residues: 334 loop : -0.27 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.011 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.014 0.001 TRP A 755 HIS 0.003 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16207) covalent geometry : angle 0.45009 / 0.24 (21935) hydrogen bonds : bond 0.03645 / 2.42 ( 707) hydrogen bonds : angle 4.39184 / 3.15 ( 2103) link_BETA1-4 : bond 0.00547 / 0.26 ( 6) link_BETA1-4 : angle 1.76134 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.645 Fit side-chains REVERT: A 692 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 798 ASP cc_start: 0.8917 (t70) cc_final: 0.8677 (t0) outliers start: 11 outliers final: 4 residues processed: 75 average time/residue: 0.7222 time to fit residues: 59.7351 Evaluate side-chains 68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 0.0060 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.058246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2344 r_free = 0.2344 target = 0.041206 restraints weight = 33243.266| |-----------------------------------------------------------------------------| r_work (start): 0.2390 rms_B_bonded: 2.88 r_work: 0.2237 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2111 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2122 r_free = 0.2122 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2122 r_free = 0.2122 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9161 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16213 Z= 0.210 Angle : 0.498 7.729 21953 Z= 0.268 Chirality : 0.043 0.146 2425 Planarity : 0.003 0.046 2826 Dihedral : 5.941 113.081 2301 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.47 % Allowed : 6.99 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1965 helix: 2.13 (0.21), residues: 620 sheet: 1.29 (0.28), residues: 341 loop : -0.33 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.014 0.001 TYR A 236 PHE 0.013 0.001 PHE B 476 TRP 0.015 0.001 TRP B 755 HIS 0.004 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (16207) covalent geometry : angle 0.49540 / 0.27 (21935) hydrogen bonds : bond 0.04242 / 2.81 ( 707) hydrogen bonds : angle 4.47251 / 3.20 ( 2103) link_BETA1-4 : bond 0.00572 / 0.27 ( 6) link_BETA1-4 : angle 1.90760 / 1.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.670 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.7720 time to fit residues: 60.3533 Evaluate side-chains 68 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 156 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 180 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.059322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.042437 restraints weight = 32827.373| |-----------------------------------------------------------------------------| r_work (start): 0.2418 rms_B_bonded: 2.85 r_work: 0.2268 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2140 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2154 r_free = 0.2154 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2154 r_free = 0.2154 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16213 Z= 0.136 Angle : 0.471 7.930 21953 Z= 0.254 Chirality : 0.041 0.172 2425 Planarity : 0.003 0.044 2826 Dihedral : 5.840 111.792 2301 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.94 % Allowed : 6.64 % Favored : 92.43 % 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: 1.15 (0.19), residues: 1965 helix: 2.10 (0.21), residues: 626 sheet: 1.42 (0.28), residues: 336 loop : -0.32 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.012 0.001 TYR A 236 PHE 0.012 0.001 PHE A 927 TRP 0.015 0.001 TRP B 755 HIS 0.003 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16207) covalent geometry : angle 0.46887 / 0.25 (21935) hydrogen bonds : bond 0.03759 / 2.49 ( 707) hydrogen bonds : angle 4.41259 / 3.16 ( 2103) link_BETA1-4 : bond 0.00557 / 0.27 ( 6) link_BETA1-4 : angle 1.79540 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.676 Fit side-chains REVERT: A 188 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.8109 (mmm) REVERT: A 864 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8987 (tt0) REVERT: B 116 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.9025 (mppt) outliers start: 16 outliers final: 5 residues processed: 78 average time/residue: 0.7450 time to fit residues: 64.3083 Evaluate side-chains 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 864 GLN Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 65 optimal weight: 0.0570 chunk 30 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.0050 chunk 155 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.061348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.044128 restraints weight = 32839.285| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 2.92 r_work: 0.2273 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2146 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2197 r_free = 0.2197 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2197 r_free = 0.2197 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16213 Z= 0.090 Angle : 0.449 8.135 21953 Z= 0.241 Chirality : 0.040 0.157 2425 Planarity : 0.003 0.041 2826 Dihedral : 5.662 110.154 2301 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.59 % Allowed : 7.05 % Favored : 92.37 % 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: 1.23 (0.19), residues: 1965 helix: 2.13 (0.21), residues: 631 sheet: 1.37 (0.29), residues: 331 loop : -0.21 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.009 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.014 0.001 TRP A 755 HIS 0.002 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (16207) covalent geometry : angle 0.44709 / 0.24 (21935) hydrogen bonds : bond 0.03264 / 2.16 ( 707) hydrogen bonds : angle 4.29171 / 3.08 ( 2103) link_BETA1-4 : bond 0.00545 / 0.25 ( 6) link_BETA1-4 : angle 1.67176 / 1.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.748 Fit side-chains REVERT: A 188 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: A 864 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8889 (tt0) REVERT: B 116 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.9014 (mppt) outliers start: 10 outliers final: 2 residues processed: 73 average time/residue: 0.7532 time to fit residues: 60.6454 Evaluate side-chains 70 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 864 GLN Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 529 TRP Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.060663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.043427 restraints weight = 32941.230| |-----------------------------------------------------------------------------| r_work (start): 0.2441 rms_B_bonded: 2.92 r_work: 0.2291 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2165 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2179 r_free = 0.2179 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2179 r_free = 0.2179 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16213 Z= 0.122 Angle : 0.467 8.075 21953 Z= 0.250 Chirality : 0.041 0.159 2425 Planarity : 0.003 0.041 2826 Dihedral : 5.604 110.456 2299 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.53 % Allowed : 7.11 % Favored : 92.37 % 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: 1.23 (0.19), residues: 1965 helix: 2.13 (0.21), residues: 631 sheet: 1.38 (0.29), residues: 330 loop : -0.22 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.010 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.015 0.001 TRP B 755 HIS 0.003 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (16207) covalent geometry : angle 0.46474 / 0.25 (21935) hydrogen bonds : bond 0.03491 / 2.31 ( 707) hydrogen bonds : angle 4.28705 / 3.08 ( 2103) link_BETA1-4 : bond 0.00542 / 0.25 ( 6) link_BETA1-4 : angle 1.71627 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.094 Fit side-chains REVERT: A 188 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8072 (mmm) REVERT: A 864 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8945 (tt0) REVERT: B 116 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.9013 (mppt) outliers start: 9 outliers final: 4 residues processed: 73 average time/residue: 0.7460 time to fit residues: 60.0907 Evaluate side-chains 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 864 GLN Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.058524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.041443 restraints weight = 33193.942| |-----------------------------------------------------------------------------| r_work (start): 0.2399 rms_B_bonded: 2.88 r_work: 0.2247 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2120 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2130 r_free = 0.2130 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2130 r_free = 0.2130 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16213 Z= 0.198 Angle : 0.508 8.054 21953 Z= 0.273 Chirality : 0.042 0.158 2425 Planarity : 0.003 0.041 2826 Dihedral : 5.784 111.499 2299 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 0.47 % Allowed : 7.34 % Favored : 92.19 % 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: 1.17 (0.19), residues: 1965 helix: 2.14 (0.21), residues: 621 sheet: 1.38 (0.29), residues: 332 loop : -0.29 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 909 TYR 0.014 0.001 TYR A 236 PHE 0.013 0.001 PHE B 476 TRP 0.015 0.001 TRP B 755 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (16207) covalent geometry : angle 0.50580 / 0.27 (21935) hydrogen bonds : bond 0.04120 / 2.73 ( 707) hydrogen bonds : angle 4.41494 / 3.16 ( 2103) link_BETA1-4 : bond 0.00558 / 0.27 ( 6) link_BETA1-4 : angle 1.86499 / 1.15 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3930 Ramachandran restraints generated. 1965 Oldfield, 0 Emsley, 1965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.710 Fit side-chains REVERT: B 116 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.9016 (mppt) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.8199 time to fit residues: 63.2276 Evaluate side-chains 69 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 175 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.060044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.042821 restraints weight = 32667.320| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 2.90 r_work: 0.2281 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2154 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2168 r_free = 0.2168 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2168 r_free = 0.2168 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16213 Z= 0.118 Angle : 0.477 8.641 21953 Z= 0.255 Chirality : 0.041 0.154 2425 Planarity : 0.003 0.041 2826 Dihedral : 5.655 109.993 2299 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 0.41 % Allowed : 7.34 % Favored : 92.25 % 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: 1.20 (0.19), residues: 1965 helix: 2.14 (0.21), residues: 624 sheet: 1.40 (0.29), residues: 331 loop : -0.26 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 909 TYR 0.011 0.001 TYR A 236 PHE 0.011 0.001 PHE A 927 TRP 0.016 0.001 TRP B 755 HIS 0.003 0.000 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16207) covalent geometry : angle 0.47472 / 0.25 (21935) hydrogen bonds : bond 0.03596 / 2.39 ( 707) hydrogen bonds : angle 4.34721 / 3.12 ( 2103) link_BETA1-4 : bond 0.00560 / 0.26 ( 6) link_BETA1-4 : angle 1.76316 / 1.12 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5865.92 seconds wall clock time: 100 minutes 59.51 seconds (6059.51 seconds total)