Starting phenix.real_space_refine on Sat Jun 14 10:52:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yaq_39104/06_2025/8yaq_39104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yaq_39104/06_2025/8yaq_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_39104/06_2025/8yaq_39104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yaq_39104/06_2025/8yaq_39104.map" model { file = "/net/cci-nas-00/data/ceres_data/8yaq_39104/06_2025/8yaq_39104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yaq_39104/06_2025/8yaq_39104.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 9.78, per 1000 atoms: 0.62 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: 4.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.24 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: 6.52 Time building geometry restraints manager: 4.77 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: 2.380 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.010 Find NCS groups from input model: 0.650 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (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 TRP 0.010 0.001 TRP A 755 HIS 0.003 0.000 HIS B 450 PHE 0.011 0.001 PHE A 927 TYR 0.012 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00559 ( 6) link_BETA1-4 : angle 1.22447 ( 18) hydrogen bonds : bond 0.14367 ( 707) hydrogen bonds : angle 6.23155 ( 2103) covalent geometry : bond 0.00286 (16207) covalent geometry : angle 0.46341 (21935) *********************** 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 : 2.033 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 1.7233 time to fit residues: 129.2780 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 : 1.711 ------------------------------------------------------------------------------- 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 165 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.2716 r_free = 0.2716 target = 0.057330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.040071 restraints weight = 33359.066| |-----------------------------------------------------------------------------| r_work (start): 0.2358 rms_B_bonded: 2.90 r_work: 0.2206 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2080 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2089 r_free = 0.2089 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2089 r_free = 0.2089 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16213 Z= 0.316 Angle : 0.564 7.130 21953 Z= 0.304 Chirality : 0.046 0.148 2425 Planarity : 0.004 0.048 2826 Dihedral : 6.457 115.785 2304 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 0.47 % Allowed : 5.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1965 helix: 1.78 (0.21), residues: 634 sheet: 1.25 (0.29), residues: 341 loop : -0.41 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 755 HIS 0.005 0.001 HIS B 450 PHE 0.014 0.001 PHE B 476 TYR 0.016 0.001 TYR A 236 ARG 0.005 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00530 ( 6) link_BETA1-4 : angle 2.12032 ( 18) hydrogen bonds : bond 0.05144 ( 707) hydrogen bonds : angle 4.82331 ( 2103) covalent geometry : bond 0.00746 (16207) covalent geometry : angle 0.56133 (21935) *********************** 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 73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.664 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 71 average time/residue: 1.6964 time to fit residues: 132.2881 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 : 1.752 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.2764 r_free = 0.2764 target = 0.059618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.042369 restraints weight = 32806.950| |-----------------------------------------------------------------------------| r_work (start): 0.2417 rms_B_bonded: 2.91 r_work: 0.2267 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2140 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2151 r_free = 0.2151 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 = 0.2151 r_free = 0.2151 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0740 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= 0.119 Angle : 0.464 7.455 21953 Z= 0.251 Chirality : 0.041 0.137 2425 Planarity : 0.003 0.047 2826 Dihedral : 6.047 113.977 2301 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 0.88 % Allowed : 5.58 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1965 helix: 2.01 (0.21), residues: 628 sheet: 1.39 (0.29), residues: 336 loop : -0.35 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 755 HIS 0.002 0.000 HIS B 450 PHE 0.012 0.001 PHE A 927 TYR 0.010 0.001 TYR A 236 ARG 0.005 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 1.79192 ( 18) hydrogen bonds : bond 0.03966 ( 707) hydrogen bonds : angle 4.58127 ( 2103) covalent geometry : bond 0.00267 (16207) covalent geometry : angle 0.46176 (21935) *********************** 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 80 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.929 Fit side-chains REVERT: A 689 GLN cc_start: 0.8704 (pp30) cc_final: 0.8420 (tm-30) outliers start: 15 outliers final: 4 residues processed: 77 average time/residue: 1.6106 time to fit residues: 136.5302 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 : 1.955 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.2768 r_free = 0.2768 target = 0.059782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.042539 restraints weight = 32714.925| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 2.91 r_work: 0.2273 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2146 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2160 r_free = 0.2160 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 = 0.2160 r_free = 0.2160 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16213 Z= 0.122 Angle : 0.461 7.668 21953 Z= 0.249 Chirality : 0.041 0.174 2425 Planarity : 0.003 0.051 2826 Dihedral : 5.868 112.784 2301 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 0.59 % Allowed : 6.11 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 1965 helix: 2.07 (0.21), residues: 629 sheet: 1.38 (0.29), residues: 338 loop : -0.31 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 755 HIS 0.002 0.000 HIS B 450 PHE 0.011 0.001 PHE A 927 TYR 0.011 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.80231 ( 18) hydrogen bonds : bond 0.03745 ( 707) hydrogen bonds : angle 4.44462 ( 2103) covalent geometry : bond 0.00278 (16207) covalent geometry : angle 0.45856 (21935) *********************** 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 75 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.877 Fit side-chains REVERT: A 692 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 798 ASP cc_start: 0.8950 (t70) cc_final: 0.8693 (t0) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 1.7131 time to fit residues: 138.7252 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 : 1.911 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.2755 r_free = 0.2755 target = 0.059319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.042058 restraints weight = 33078.955| |-----------------------------------------------------------------------------| r_work (start): 0.2406 rms_B_bonded: 2.91 r_work: 0.2254 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2129 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2142 r_free = 0.2142 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 = 0.2142 r_free = 0.2142 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16213 Z= 0.156 Angle : 0.473 7.727 21953 Z= 0.255 Chirality : 0.041 0.158 2425 Planarity : 0.003 0.048 2826 Dihedral : 5.877 112.813 2301 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 0.47 % Allowed : 6.52 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1965 helix: 2.11 (0.21), residues: 626 sheet: 1.38 (0.29), residues: 338 loop : -0.33 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 755 HIS 0.003 0.001 HIS B 450 PHE 0.011 0.001 PHE A 927 TYR 0.012 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00543 ( 6) link_BETA1-4 : angle 1.82158 ( 18) hydrogen bonds : bond 0.03932 ( 707) hydrogen bonds : angle 4.43022 ( 2103) covalent geometry : bond 0.00365 (16207) covalent geometry : angle 0.47035 (21935) *********************** 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 73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.752 Fit side-chains REVERT: A 864 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.9008 (tt0) REVERT: B 798 ASP cc_start: 0.8939 (t70) cc_final: 0.8720 (t0) outliers start: 8 outliers final: 5 residues processed: 72 average time/residue: 1.7865 time to fit residues: 143.1841 Evaluate side-chains 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 2.453 ------------------------------------------------------------------------------- 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 864 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.058332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2336 r_free = 0.2336 target = 0.041058 restraints weight = 33217.174| |-----------------------------------------------------------------------------| r_work (start): 0.2381 rms_B_bonded: 2.90 r_work: 0.2229 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2102 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2114 r_free = 0.2114 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2114 r_free = 0.2114 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.0950 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= 0.213 Angle : 0.503 7.722 21953 Z= 0.272 Chirality : 0.043 0.154 2425 Planarity : 0.003 0.047 2826 Dihedral : 5.983 113.213 2301 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 0.82 % Allowed : 6.58 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1965 helix: 2.12 (0.21), residues: 617 sheet: 1.29 (0.28), residues: 341 loop : -0.36 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 755 HIS 0.004 0.001 HIS B 450 PHE 0.013 0.001 PHE B 476 TYR 0.014 0.001 TYR A 236 ARG 0.006 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 1.92883 ( 18) hydrogen bonds : bond 0.04309 ( 707) hydrogen bonds : angle 4.49032 ( 2103) covalent geometry : bond 0.00503 (16207) covalent geometry : angle 0.50059 (21935) *********************** 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 79 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 2.094 Fit side-chains REVERT: A 154 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8857 (mmmt) REVERT: A 864 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.9023 (tt0) REVERT: B 116 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (mppt) outliers start: 14 outliers final: 5 residues processed: 78 average time/residue: 2.1835 time to fit residues: 189.3317 Evaluate side-chains 73 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LYS 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 B residue 73 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.2752 r_free = 0.2752 target = 0.059043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.041800 restraints weight = 33016.768| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 2.91 r_work: 0.2255 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2128 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2139 r_free = 0.2139 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 = 0.2139 r_free = 0.2139 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16213 Z= 0.141 Angle : 0.476 8.201 21953 Z= 0.257 Chirality : 0.041 0.152 2425 Planarity : 0.003 0.046 2826 Dihedral : 5.892 112.260 2301 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 0.59 % Allowed : 6.64 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1965 helix: 2.08 (0.21), residues: 625 sheet: 1.38 (0.29), residues: 337 loop : -0.33 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 755 HIS 0.003 0.000 HIS B 450 PHE 0.012 0.001 PHE A 927 TYR 0.012 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00548 ( 6) link_BETA1-4 : angle 1.82681 ( 18) hydrogen bonds : bond 0.03907 ( 707) hydrogen bonds : angle 4.43792 ( 2103) covalent geometry : bond 0.00326 (16207) covalent geometry : angle 0.47294 (21935) *********************** 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 76 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 3.330 Fit side-chains REVERT: A 864 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9008 (tt0) REVERT: B 116 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9009 (mppt) outliers start: 10 outliers final: 4 residues processed: 75 average time/residue: 2.1854 time to fit residues: 184.1878 Evaluate side-chains 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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 864 GLN 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 149 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.2725 r_free = 0.2725 target = 0.057726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.040466 restraints weight = 33116.011| |-----------------------------------------------------------------------------| r_work (start): 0.2369 rms_B_bonded: 2.89 r_work: 0.2217 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2090 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2104 r_free = 0.2104 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2104 r_free = 0.2104 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16213 Z= 0.239 Angle : 0.519 7.780 21953 Z= 0.279 Chirality : 0.043 0.151 2425 Planarity : 0.003 0.046 2826 Dihedral : 6.015 112.977 2301 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 0.65 % Allowed : 6.75 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1965 helix: 2.07 (0.21), residues: 617 sheet: 1.25 (0.28), residues: 341 loop : -0.38 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 755 HIS 0.004 0.001 HIS A 450 PHE 0.014 0.001 PHE B 476 TYR 0.014 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00583 ( 6) link_BETA1-4 : angle 1.96847 ( 18) hydrogen bonds : bond 0.04436 ( 707) hydrogen bonds : angle 4.51364 ( 2103) covalent geometry : bond 0.00564 (16207) covalent geometry : angle 0.51599 (21935) *********************** 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 77 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.743 Fit side-chains REVERT: A 864 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9022 (tt0) REVERT: B 116 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9010 (mppt) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 1.5799 time to fit residues: 132.4918 Evaluate side-chains 74 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 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 394 VAL 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 125 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 25 optimal weight: 0.0010 chunk 44 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.2764 r_free = 0.2764 target = 0.059673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.042830 restraints weight = 32750.340| |-----------------------------------------------------------------------------| r_work (start): 0.2428 rms_B_bonded: 2.86 r_work: 0.2278 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2151 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2164 r_free = 0.2164 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 = 0.2164 r_free = 0.2164 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16213 Z= 0.105 Angle : 0.468 8.582 21953 Z= 0.252 Chirality : 0.040 0.146 2425 Planarity : 0.003 0.044 2826 Dihedral : 5.801 111.044 2301 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.53 % Allowed : 6.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1965 helix: 2.11 (0.21), residues: 627 sheet: 1.35 (0.29), residues: 335 loop : -0.29 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 755 HIS 0.003 0.000 HIS B 450 PHE 0.011 0.001 PHE A 927 TYR 0.010 0.001 TYR B 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00573 ( 6) link_BETA1-4 : angle 1.78159 ( 18) hydrogen bonds : bond 0.03581 ( 707) hydrogen bonds : angle 4.38362 ( 2103) covalent geometry : bond 0.00235 (16207) covalent geometry : angle 0.46556 (21935) *********************** 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 75 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.701 Fit side-chains REVERT: A 864 GLN cc_start: 0.9342 (OUTLIER) cc_final: 0.8985 (tt0) REVERT: B 116 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9010 (mppt) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 1.5878 time to fit residues: 131.4990 Evaluate side-chains 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 864 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 189 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.2771 r_free = 0.2771 target = 0.059866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.042856 restraints weight = 33063.940| |-----------------------------------------------------------------------------| r_work (start): 0.2433 rms_B_bonded: 2.90 r_work: 0.2282 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2156 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2156 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1002 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= 0.113 Angle : 0.471 8.525 21953 Z= 0.252 Chirality : 0.041 0.147 2425 Planarity : 0.003 0.043 2826 Dihedral : 5.732 110.801 2301 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Rotamer: Outliers : 0.35 % Allowed : 7.16 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1965 helix: 2.15 (0.21), residues: 625 sheet: 1.37 (0.29), residues: 334 loop : -0.26 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 755 HIS 0.003 0.000 HIS B 450 PHE 0.011 0.001 PHE A 927 TYR 0.010 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00557 ( 6) link_BETA1-4 : angle 1.74458 ( 18) hydrogen bonds : bond 0.03552 ( 707) hydrogen bonds : angle 4.32217 ( 2103) covalent geometry : bond 0.00259 (16207) covalent geometry : angle 0.46806 (21935) ********************** 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 71 residues out of total 1703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.744 Fit side-chains REVERT: B 96 GLN cc_start: 0.8654 (mt0) cc_final: 0.8439 (mt0) REVERT: B 116 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9010 (mppt) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 1.6771 time to fit residues: 131.3982 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 : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 394 VAL 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 165 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.2774 r_free = 0.2774 target = 0.059996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.042768 restraints weight = 32839.200| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 2.92 r_work: 0.2281 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2154 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2167 r_free = 0.2167 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 = 0.2167 r_free = 0.2167 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16213 Z= 0.120 Angle : 0.474 8.444 21953 Z= 0.253 Chirality : 0.041 0.147 2425 Planarity : 0.003 0.041 2826 Dihedral : 5.645 110.681 2299 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 0.35 % Allowed : 7.05 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1965 helix: 2.16 (0.21), residues: 625 sheet: 1.38 (0.28), residues: 334 loop : -0.26 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 755 HIS 0.003 0.000 HIS B 450 PHE 0.011 0.001 PHE A 927 TYR 0.010 0.001 TYR A 236 ARG 0.007 0.000 ARG B 909 Details of bonding type rmsd link_BETA1-4 : bond 0.00548 ( 6) link_BETA1-4 : angle 1.74224 ( 18) hydrogen bonds : bond 0.03569 ( 707) hydrogen bonds : angle 4.31027 ( 2103) covalent geometry : bond 0.00276 (16207) covalent geometry : angle 0.47131 (21935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12913.45 seconds wall clock time: 229 minutes 25.62 seconds (13765.62 seconds total)