Starting phenix.real_space_refine on Wed Jun 11 09:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyk_26183/06_2025/7tyk_26183_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyk_26183/06_2025/7tyk_26183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyk_26183/06_2025/7tyk_26183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyk_26183/06_2025/7tyk_26183.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyk_26183/06_2025/7tyk_26183_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyk_26183/06_2025/7tyk_26183_neut.cif" } resolution = 3.5 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 8034 2.51 5 N 2260 2.21 5 O 2326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12698 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6349 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 44, 'TRANS': 764} Chain breaks: 4 Chain: "B" Number of atoms: 6349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6349 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 44, 'TRANS': 764} Chain breaks: 4 Time building chain proxies: 7.87, per 1000 atoms: 0.62 Number of scatterers: 12698 At special positions: 0 Unit cell: (141.48, 113.4, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2326 8.00 N 2260 7.00 C 8034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 838 " distance=2.03 Simple disulfide: pdb=" SG CYS A 764 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 232 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 423 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 838 " distance=2.03 Simple disulfide: pdb=" SG CYS B 764 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 2.0 seconds 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 32 sheets defined 11.4% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.770A pdb=" N GLN A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.598A pdb=" N PHE A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.592A pdb=" N ASN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.521A pdb=" N CYS A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.063A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 678 through 693 removed outlier: 4.024A pdb=" N ASN A 693 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 848 removed outlier: 3.858A pdb=" N PHE A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 removed outlier: 3.769A pdb=" N GLN B 18 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 removed outlier: 3.599A pdb=" N PHE B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.593A pdb=" N ASN B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 removed outlier: 3.520A pdb=" N CYS B 220 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 311 through 316 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.063A pdb=" N ILE B 427 " --> pdb=" O CYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 678 through 693 removed outlier: 4.024A pdb=" N ASN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 848 removed outlier: 3.858A pdb=" N PHE B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 8.120A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 10 removed outlier: 8.120A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 57 " --> pdb=" O HIS A 28 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN A 30 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU A 59 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 32 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 61 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 57 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 92 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 59 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG A 114 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 90 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLU A 116 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE A 92 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 243 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.511A pdb=" N HIS A 292 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309 removed outlier: 7.137A pdb=" N CYS A 302 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER A 327 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 304 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ILE A 329 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N THR A 306 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 7.137A pdb=" N CYS A 302 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N SER A 327 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 304 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ILE A 329 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N THR A 306 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 356 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU A 391 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A 358 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A 415 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR A 389 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA A 417 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU A 391 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 459 through 460 removed outlier: 6.100A pdb=" N ARG A 459 " --> pdb=" O GLN A 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 463 through 468 removed outlier: 6.632A pdb=" N ARG A 476 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 466 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 474 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR A 468 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 518 through 522 Processing sheet with id=AB3, first strand: chain 'A' and resid 583 through 591 removed outlier: 5.926A pdb=" N ASP A 584 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 600 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 590 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 737 through 741 removed outlier: 3.670A pdb=" N TYR A 611 " --> pdb=" O CYS A 764 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 756 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 797 through 800 Processing sheet with id=AB6, first strand: chain 'A' and resid 835 through 840 removed outlier: 7.219A pdb=" N THR A 867 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 835 through 840 Processing sheet with id=AB8, first strand: chain 'B' and resid 5 through 10 removed outlier: 8.121A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 5 through 10 removed outlier: 8.121A pdb=" N GLN B 30 " --> pdb=" O PRO B 5 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 7 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LEU B 32 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE B 9 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 34 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 57 " --> pdb=" O HIS B 28 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLN B 30 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 59 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 32 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG B 61 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 57 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE B 92 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 59 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG B 114 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 90 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU B 116 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE B 92 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 167 through 169 Processing sheet with id=AC2, first strand: chain 'B' and resid 226 through 228 Processing sheet with id=AC3, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AC4, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.511A pdb=" N HIS B 292 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 301 through 309 removed outlier: 7.136A pdb=" N CYS B 302 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 327 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 304 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ILE B 329 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR B 306 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 301 through 309 removed outlier: 7.136A pdb=" N CYS B 302 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N SER B 327 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 304 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ILE B 329 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR B 306 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU B 356 " --> pdb=" O TYR B 389 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU B 391 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 358 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 415 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR B 389 " --> pdb=" O TYR B 415 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA B 417 " --> pdb=" O TYR B 389 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 391 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 459 through 460 removed outlier: 6.100A pdb=" N ARG B 459 " --> pdb=" O GLN B 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 463 through 468 removed outlier: 6.631A pdb=" N ARG B 476 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN B 466 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 474 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR B 468 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 518 through 522 Processing sheet with id=AD1, first strand: chain 'B' and resid 583 through 591 removed outlier: 5.925A pdb=" N ASP B 584 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 600 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B 590 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 737 through 741 removed outlier: 3.671A pdb=" N TYR B 611 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 756 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 797 through 800 Processing sheet with id=AD4, first strand: chain 'B' and resid 835 through 840 removed outlier: 7.219A pdb=" N THR B 867 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 835 through 840 282 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.24: 1729 1.24 - 1.55: 11175 1.55 - 1.86: 94 1.86 - 2.17: 0 2.17 - 2.48: 2 Bond restraints: 13000 Sorted by residual: bond pdb=" CB PRO A 136 " pdb=" CG PRO A 136 " ideal model delta sigma weight residual 1.492 2.479 -0.987 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CB PRO B 136 " pdb=" CG PRO B 136 " ideal model delta sigma weight residual 1.492 2.479 -0.987 5.00e-02 4.00e+02 3.90e+02 bond pdb=" CG PRO B 136 " pdb=" CD PRO B 136 " ideal model delta sigma weight residual 1.503 0.930 0.573 3.40e-02 8.65e+02 2.84e+02 bond pdb=" CG PRO A 136 " pdb=" CD PRO A 136 " ideal model delta sigma weight residual 1.503 0.930 0.573 3.40e-02 8.65e+02 2.84e+02 bond pdb=" CG PRO B 482 " pdb=" CD PRO B 482 " ideal model delta sigma weight residual 1.503 1.143 0.360 3.40e-02 8.65e+02 1.12e+02 ... (remaining 12995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 17664 21.22 - 42.44: 6 42.44 - 63.65: 0 63.65 - 84.87: 0 84.87 - 106.09: 2 Bond angle restraints: 17672 Sorted by residual: angle pdb=" CB PRO B 136 " pdb=" CG PRO B 136 " pdb=" CD PRO B 136 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CB PRO A 136 " pdb=" CG PRO A 136 " pdb=" CD PRO A 136 " ideal model delta sigma weight residual 106.10 0.03 106.07 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO A 482 " pdb=" CD PRO A 482 " pdb=" CG PRO A 482 " ideal model delta sigma weight residual 103.20 77.23 25.97 1.50e+00 4.44e-01 3.00e+02 angle pdb=" N PRO B 482 " pdb=" CD PRO B 482 " pdb=" CG PRO B 482 " ideal model delta sigma weight residual 103.20 77.26 25.94 1.50e+00 4.44e-01 2.99e+02 angle pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " pdb=" CG PRO B 482 " ideal model delta sigma weight residual 104.50 74.57 29.93 1.90e+00 2.77e-01 2.48e+02 ... (remaining 17667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 7363 29.64 - 59.28: 419 59.28 - 88.92: 56 88.92 - 118.56: 1 118.56 - 148.20: 1 Dihedral angle restraints: 7840 sinusoidal: 3170 harmonic: 4670 Sorted by residual: dihedral pdb=" N PRO B 136 " pdb=" CG PRO B 136 " pdb=" CD PRO B 136 " pdb=" CB PRO B 136 " ideal model delta sinusoidal sigma weight residual 30.00 178.20 -148.20 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 184 " pdb=" CB CYS A 184 " ideal model delta sinusoidal sigma weight residual -86.00 -161.75 75.75 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS B 165 " pdb=" SG CYS B 165 " pdb=" SG CYS B 184 " pdb=" CB CYS B 184 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 7837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1289 0.032 - 0.064: 443 0.064 - 0.096: 120 0.096 - 0.128: 106 0.128 - 0.160: 10 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" C PRO A 136 " pdb=" CB PRO A 136 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CA PRO B 136 " pdb=" N PRO B 136 " pdb=" C PRO B 136 " pdb=" CB PRO B 136 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE B 91 " pdb=" N ILE B 91 " pdb=" C ILE B 91 " pdb=" CB ILE B 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1965 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 482 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C PRO A 482 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO A 482 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 483 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 482 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PRO B 482 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO B 482 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 483 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 135 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C ALA B 135 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA B 135 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO B 136 " 0.014 2.00e-02 2.50e+03 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 729 2.73 - 3.27: 12103 3.27 - 3.82: 19660 3.82 - 4.36: 23600 4.36 - 4.90: 41473 Nonbonded interactions: 97565 Sorted by model distance: nonbonded pdb=" O HIS B 766 " pdb=" OG1 THR B 770 " model vdw 2.189 3.040 nonbonded pdb=" O HIS A 766 " pdb=" OG1 THR A 770 " model vdw 2.190 3.040 nonbonded pdb=" O LEU A 461 " pdb=" OG SER A 567 " model vdw 2.264 3.040 nonbonded pdb=" O SER A 265 " pdb=" NH2 ARG A 284 " model vdw 2.264 3.120 nonbonded pdb=" O SER B 265 " pdb=" NH2 ARG B 284 " model vdw 2.264 3.120 ... (remaining 97560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.040 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.760 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.015 0.987 13032 Z= 0.376 Angle : 1.389 106.088 17736 Z= 0.582 Chirality : 0.042 0.160 1968 Planarity : 0.003 0.034 2296 Dihedral : 17.403 148.196 4736 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.51 % Favored : 91.11 % Rotamer: Outliers : 0.65 % Allowed : 23.37 % Favored : 75.98 % Cbeta Deviations : 0.13 % 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: -1.65 (0.21), residues: 1598 helix: 1.31 (0.50), residues: 132 sheet: -0.35 (0.25), residues: 432 loop : -1.86 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 179 HIS 0.006 0.001 HIS B 762 PHE 0.012 0.001 PHE B 548 TYR 0.008 0.001 TYR A 56 ARG 0.003 0.000 ARG A 284 Details of bonding type rmsd hydrogen bonds : bond 0.13828 ( 270) hydrogen bonds : angle 5.16037 ( 714) SS BOND : bond 0.00173 ( 32) SS BOND : angle 0.82381 ( 64) covalent geometry : bond 0.01508 (13000) covalent geometry : angle 1.39102 (17672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.2493 time to fit residues: 43.1209 Evaluate side-chains 114 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 371 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 0.0000 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 331 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 ASN B 139 ASN B 331 ASN B 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.178614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144406 restraints weight = 16643.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.144671 restraints weight = 15888.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.145834 restraints weight = 16449.157| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 13032 Z= 0.106 Angle : 0.558 12.268 17736 Z= 0.286 Chirality : 0.042 0.133 1968 Planarity : 0.004 0.086 2296 Dihedral : 4.284 23.870 1782 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.26 % Favored : 91.36 % Rotamer: Outliers : 2.90 % Allowed : 21.99 % Favored : 75.11 % 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: -1.68 (0.21), residues: 1598 helix: 1.27 (0.51), residues: 132 sheet: -0.42 (0.25), residues: 426 loop : -1.84 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 179 HIS 0.005 0.001 HIS B 762 PHE 0.013 0.001 PHE A 548 TYR 0.010 0.001 TYR B 494 ARG 0.003 0.000 ARG A 224 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 270) hydrogen bonds : angle 4.52870 ( 714) SS BOND : bond 0.00172 ( 32) SS BOND : angle 0.77758 ( 64) covalent geometry : bond 0.00247 (13000) covalent geometry : angle 0.55733 (17672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.395 Fit side-chains REVERT: A 484 GLU cc_start: 0.7164 (tt0) cc_final: 0.6928 (tt0) REVERT: A 520 LEU cc_start: 0.8691 (tt) cc_final: 0.8441 (tp) REVERT: B 484 GLU cc_start: 0.7155 (tt0) cc_final: 0.6915 (tt0) REVERT: B 520 LEU cc_start: 0.8679 (tt) cc_final: 0.8422 (tp) outliers start: 40 outliers final: 15 residues processed: 170 average time/residue: 0.2460 time to fit residues: 61.6534 Evaluate side-chains 128 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 89 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 689 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS B 466 ASN B 689 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139945 restraints weight = 16790.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.137987 restraints weight = 15323.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139774 restraints weight = 16029.506| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13032 Z= 0.153 Angle : 0.569 6.543 17736 Z= 0.293 Chirality : 0.044 0.142 1968 Planarity : 0.004 0.037 2296 Dihedral : 4.448 22.536 1772 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.57 % Favored : 90.05 % Rotamer: Outliers : 3.92 % Allowed : 22.28 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.74 (0.21), residues: 1598 helix: 1.09 (0.52), residues: 134 sheet: -0.49 (0.26), residues: 426 loop : -1.86 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.006 0.001 HIS B 762 PHE 0.015 0.001 PHE A 548 TYR 0.014 0.001 TYR B 389 ARG 0.003 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 270) hydrogen bonds : angle 4.57180 ( 714) SS BOND : bond 0.00264 ( 32) SS BOND : angle 0.93082 ( 64) covalent geometry : bond 0.00369 (13000) covalent geometry : angle 0.56766 (17672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6452 (t70) REVERT: A 520 LEU cc_start: 0.9010 (tt) cc_final: 0.8733 (tp) REVERT: A 766 HIS cc_start: 0.6476 (OUTLIER) cc_final: 0.5069 (m90) REVERT: B 344 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6463 (t70) REVERT: B 520 LEU cc_start: 0.9010 (tt) cc_final: 0.8733 (tp) outliers start: 54 outliers final: 23 residues processed: 161 average time/residue: 0.3004 time to fit residues: 72.3435 Evaluate side-chains 128 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 62 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 46 optimal weight: 0.0270 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS A 466 ASN A 628 ASN B 344 HIS B 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139093 restraints weight = 16488.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138630 restraints weight = 12934.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140600 restraints weight = 12304.384| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13032 Z= 0.117 Angle : 0.549 8.852 17736 Z= 0.281 Chirality : 0.043 0.139 1968 Planarity : 0.004 0.033 2296 Dihedral : 4.396 22.568 1772 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.26 % Favored : 91.36 % Rotamer: Outliers : 4.50 % Allowed : 22.13 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.69 (0.21), residues: 1598 helix: 1.10 (0.51), residues: 134 sheet: -0.46 (0.26), residues: 426 loop : -1.82 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 179 HIS 0.008 0.001 HIS A 344 PHE 0.015 0.001 PHE B 170 TYR 0.010 0.001 TYR A 389 ARG 0.002 0.000 ARG A 224 Details of bonding type rmsd hydrogen bonds : bond 0.02753 ( 270) hydrogen bonds : angle 4.54851 ( 714) SS BOND : bond 0.00188 ( 32) SS BOND : angle 0.87466 ( 64) covalent geometry : bond 0.00276 (13000) covalent geometry : angle 0.54729 (17672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 1.427 Fit side-chains REVERT: A 34 MET cc_start: 0.8073 (mmt) cc_final: 0.7861 (mtt) REVERT: A 49 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7519 (mtm180) REVERT: A 154 CYS cc_start: 0.4441 (m) cc_final: 0.4200 (m) REVERT: A 289 ILE cc_start: 0.7620 (mm) cc_final: 0.7221 (mm) REVERT: A 344 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6082 (t70) REVERT: A 520 LEU cc_start: 0.8977 (tt) cc_final: 0.8697 (tp) REVERT: A 766 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.5175 (m90) REVERT: B 34 MET cc_start: 0.8079 (mmt) cc_final: 0.7874 (mtt) REVERT: B 49 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7518 (mtm180) REVERT: B 289 ILE cc_start: 0.7629 (mm) cc_final: 0.7283 (mm) REVERT: B 344 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.6081 (t70) REVERT: B 520 LEU cc_start: 0.8976 (tt) cc_final: 0.8701 (tp) outliers start: 62 outliers final: 37 residues processed: 174 average time/residue: 0.2790 time to fit residues: 70.6794 Evaluate side-chains 143 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 51 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 13 optimal weight: 0.0020 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.175461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141843 restraints weight = 16773.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140709 restraints weight = 15169.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142211 restraints weight = 15101.813| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13032 Z= 0.111 Angle : 0.537 7.066 17736 Z= 0.276 Chirality : 0.043 0.137 1968 Planarity : 0.004 0.033 2296 Dihedral : 4.350 22.434 1772 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.57 % Favored : 91.05 % Rotamer: Outliers : 4.79 % Allowed : 22.28 % Favored : 72.93 % 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: -1.71 (0.21), residues: 1598 helix: 1.05 (0.51), residues: 134 sheet: -0.42 (0.26), residues: 428 loop : -1.85 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.007 0.001 HIS A 344 PHE 0.014 0.001 PHE A 170 TYR 0.010 0.001 TYR B 630 ARG 0.002 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 270) hydrogen bonds : angle 4.48750 ( 714) SS BOND : bond 0.00142 ( 32) SS BOND : angle 0.87557 ( 64) covalent geometry : bond 0.00263 (13000) covalent geometry : angle 0.53552 (17672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 110 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7518 (mtm180) REVERT: A 289 ILE cc_start: 0.7637 (mm) cc_final: 0.7238 (mm) REVERT: A 344 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6471 (t70) REVERT: A 520 LEU cc_start: 0.8986 (tt) cc_final: 0.8697 (tp) REVERT: A 684 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6497 (mt0) REVERT: A 766 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.5087 (m90) REVERT: B 289 ILE cc_start: 0.7649 (mm) cc_final: 0.7244 (mm) REVERT: B 344 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6461 (t70) REVERT: B 520 LEU cc_start: 0.8972 (tt) cc_final: 0.8685 (tp) REVERT: B 684 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6500 (mt0) outliers start: 66 outliers final: 36 residues processed: 171 average time/residue: 0.2907 time to fit residues: 72.9349 Evaluate side-chains 140 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 344 HIS Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 344 HIS Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 4 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.171429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137578 restraints weight = 16750.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135808 restraints weight = 14315.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137695 restraints weight = 14279.150| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13032 Z= 0.142 Angle : 0.559 6.319 17736 Z= 0.287 Chirality : 0.043 0.135 1968 Planarity : 0.004 0.033 2296 Dihedral : 4.501 22.992 1772 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.57 % Favored : 90.18 % Rotamer: Outliers : 5.01 % Allowed : 21.84 % Favored : 73.15 % 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: -1.78 (0.21), residues: 1598 helix: 0.99 (0.51), residues: 134 sheet: -0.50 (0.26), residues: 426 loop : -1.90 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 179 HIS 0.005 0.001 HIS A 762 PHE 0.014 0.001 PHE B 548 TYR 0.012 0.001 TYR B 389 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02784 ( 270) hydrogen bonds : angle 4.50706 ( 714) SS BOND : bond 0.00232 ( 32) SS BOND : angle 0.92065 ( 64) covalent geometry : bond 0.00341 (13000) covalent geometry : angle 0.55677 (17672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 103 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 LEU cc_start: 0.9051 (tt) cc_final: 0.8835 (tp) REVERT: A 641 ASN cc_start: 0.8157 (t0) cc_final: 0.7671 (t0) REVERT: A 684 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6506 (mt0) REVERT: A 766 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.5075 (m90) REVERT: B 641 ASN cc_start: 0.8145 (t0) cc_final: 0.7664 (t0) REVERT: B 684 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6546 (mt0) outliers start: 69 outliers final: 43 residues processed: 169 average time/residue: 0.2828 time to fit residues: 70.5264 Evaluate side-chains 141 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 155 optimal weight: 0.0470 chunk 98 optimal weight: 0.0570 chunk 86 optimal weight: 0.6980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144485 restraints weight = 16807.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144191 restraints weight = 15520.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145682 restraints weight = 14649.442| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13032 Z= 0.084 Angle : 0.517 5.621 17736 Z= 0.266 Chirality : 0.042 0.136 1968 Planarity : 0.003 0.034 2296 Dihedral : 4.160 22.329 1772 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.01 % Favored : 91.74 % Rotamer: Outliers : 3.41 % Allowed : 23.08 % Favored : 73.51 % 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: -1.66 (0.21), residues: 1598 helix: 1.01 (0.50), residues: 134 sheet: -0.33 (0.26), residues: 428 loop : -1.84 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 179 HIS 0.003 0.001 HIS B 762 PHE 0.020 0.001 PHE A 170 TYR 0.009 0.001 TYR B 56 ARG 0.003 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.02323 ( 270) hydrogen bonds : angle 4.32383 ( 714) SS BOND : bond 0.00163 ( 32) SS BOND : angle 0.78740 ( 64) covalent geometry : bond 0.00182 (13000) covalent geometry : angle 0.51605 (17672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 520 LEU cc_start: 0.8789 (tt) cc_final: 0.8506 (tp) REVERT: A 641 ASN cc_start: 0.7980 (t0) cc_final: 0.7715 (t0) REVERT: A 684 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6347 (mp10) REVERT: A 766 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.5089 (m90) REVERT: B 520 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 641 ASN cc_start: 0.7974 (t0) cc_final: 0.7716 (t0) REVERT: B 684 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6347 (mp10) outliers start: 47 outliers final: 26 residues processed: 151 average time/residue: 0.2380 time to fit residues: 52.5361 Evaluate side-chains 124 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN B 123 HIS B 192 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.170440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136353 restraints weight = 16693.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136291 restraints weight = 13185.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137923 restraints weight = 14268.884| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13032 Z= 0.154 Angle : 0.570 5.296 17736 Z= 0.293 Chirality : 0.044 0.140 1968 Planarity : 0.004 0.033 2296 Dihedral : 4.547 23.130 1772 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.01 % Favored : 89.74 % Rotamer: Outliers : 3.70 % Allowed : 23.22 % Favored : 73.08 % 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: -1.77 (0.21), residues: 1598 helix: 1.03 (0.50), residues: 134 sheet: -0.46 (0.26), residues: 428 loop : -1.90 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 179 HIS 0.006 0.001 HIS A 762 PHE 0.015 0.002 PHE B 548 TYR 0.014 0.001 TYR A 389 ARG 0.002 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.02816 ( 270) hydrogen bonds : angle 4.46714 ( 714) SS BOND : bond 0.00192 ( 32) SS BOND : angle 0.98734 ( 64) covalent geometry : bond 0.00374 (13000) covalent geometry : angle 0.56786 (17672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 91 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 ILE cc_start: 0.8585 (mm) cc_final: 0.8246 (mm) REVERT: A 641 ASN cc_start: 0.8271 (t0) cc_final: 0.7745 (t0) REVERT: A 684 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6511 (mt0) REVERT: A 766 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.4964 (m90) REVERT: B 552 ILE cc_start: 0.8578 (mm) cc_final: 0.8240 (mm) REVERT: B 641 ASN cc_start: 0.8266 (t0) cc_final: 0.7742 (t0) REVERT: B 684 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6512 (mt0) REVERT: B 766 HIS cc_start: 0.6414 (OUTLIER) cc_final: 0.4930 (m90) outliers start: 51 outliers final: 34 residues processed: 140 average time/residue: 0.3374 time to fit residues: 69.5323 Evaluate side-chains 131 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 629 ASP Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN B 123 HIS B 192 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.172909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139261 restraints weight = 16549.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138483 restraints weight = 14825.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140641 restraints weight = 12845.166| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13032 Z= 0.105 Angle : 0.537 5.378 17736 Z= 0.277 Chirality : 0.043 0.136 1968 Planarity : 0.004 0.033 2296 Dihedral : 4.402 23.022 1772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.89 % Favored : 90.86 % Rotamer: Outliers : 2.98 % Allowed : 24.02 % Favored : 73.00 % 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: -1.75 (0.21), residues: 1598 helix: 1.02 (0.50), residues: 134 sheet: -0.43 (0.26), residues: 428 loop : -1.90 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 179 HIS 0.004 0.001 HIS A 762 PHE 0.012 0.001 PHE B 548 TYR 0.009 0.001 TYR B 56 ARG 0.002 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.02510 ( 270) hydrogen bonds : angle 4.44327 ( 714) SS BOND : bond 0.00159 ( 32) SS BOND : angle 0.81897 ( 64) covalent geometry : bond 0.00245 (13000) covalent geometry : angle 0.53566 (17672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 ILE cc_start: 0.8442 (mm) cc_final: 0.8139 (mm) REVERT: A 630 TYR cc_start: 0.7245 (m-10) cc_final: 0.5749 (t80) REVERT: A 641 ASN cc_start: 0.8132 (t0) cc_final: 0.7745 (t0) REVERT: A 684 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6479 (mt0) REVERT: A 766 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.4985 (m90) REVERT: B 552 ILE cc_start: 0.8456 (mm) cc_final: 0.8154 (mm) REVERT: B 630 TYR cc_start: 0.7293 (m-10) cc_final: 0.5648 (t80) REVERT: B 641 ASN cc_start: 0.8152 (t0) cc_final: 0.7770 (t0) REVERT: B 684 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6486 (mt0) REVERT: B 766 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.4902 (m90) outliers start: 41 outliers final: 34 residues processed: 136 average time/residue: 0.2689 time to fit residues: 54.0644 Evaluate side-chains 130 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 371 LYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 141 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN B 123 HIS ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142059 restraints weight = 16742.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140757 restraints weight = 16179.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142427 restraints weight = 17378.193| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13032 Z= 0.092 Angle : 0.527 5.203 17736 Z= 0.272 Chirality : 0.042 0.135 1968 Planarity : 0.003 0.033 2296 Dihedral : 4.286 22.709 1772 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.14 % Favored : 90.61 % Rotamer: Outliers : 2.83 % Allowed : 24.17 % Favored : 73.00 % 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: -1.71 (0.21), residues: 1598 helix: 1.08 (0.50), residues: 134 sheet: -0.41 (0.26), residues: 426 loop : -1.86 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 179 HIS 0.004 0.001 HIS B 762 PHE 0.016 0.001 PHE B 290 TYR 0.012 0.001 TYR A 630 ARG 0.002 0.000 ARG A 224 Details of bonding type rmsd hydrogen bonds : bond 0.02407 ( 270) hydrogen bonds : angle 4.35317 ( 714) SS BOND : bond 0.00162 ( 32) SS BOND : angle 0.78121 ( 64) covalent geometry : bond 0.00212 (13000) covalent geometry : angle 0.52546 (17672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 ILE cc_start: 0.8493 (mm) cc_final: 0.8193 (mm) REVERT: A 630 TYR cc_start: 0.7406 (m-10) cc_final: 0.5728 (t80) REVERT: A 641 ASN cc_start: 0.8116 (t0) cc_final: 0.7728 (t0) REVERT: A 684 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6402 (mt0) REVERT: A 766 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.4842 (m90) REVERT: B 425 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 552 ILE cc_start: 0.8490 (mm) cc_final: 0.8184 (mm) REVERT: B 630 TYR cc_start: 0.7389 (m-10) cc_final: 0.5718 (t80) REVERT: B 641 ASN cc_start: 0.8119 (t0) cc_final: 0.7734 (t0) REVERT: B 684 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6408 (mt0) REVERT: B 766 HIS cc_start: 0.6252 (OUTLIER) cc_final: 0.4849 (m90) outliers start: 39 outliers final: 30 residues processed: 137 average time/residue: 0.3702 time to fit residues: 77.9960 Evaluate side-chains 131 residues out of total 1378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 684 GLN Chi-restraints excluded: chain A residue 690 PHE Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 437 ARG Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 684 GLN Chi-restraints excluded: chain B residue 690 PHE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 819 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 5 optimal weight: 0.0670 chunk 94 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 153 optimal weight: 0.0050 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.177932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.143710 restraints weight = 16697.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142684 restraints weight = 15564.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144562 restraints weight = 15285.134| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13032 Z= 0.087 Angle : 0.521 6.096 17736 Z= 0.268 Chirality : 0.042 0.134 1968 Planarity : 0.003 0.033 2296 Dihedral : 4.162 22.431 1772 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.39 % Favored : 91.36 % Rotamer: Outliers : 3.19 % Allowed : 23.88 % Favored : 72.93 % 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: -1.64 (0.21), residues: 1598 helix: 1.12 (0.50), residues: 134 sheet: -0.36 (0.26), residues: 426 loop : -1.82 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 179 HIS 0.003 0.001 HIS A 192 PHE 0.010 0.001 PHE B 548 TYR 0.008 0.001 TYR B 56 ARG 0.001 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.02292 ( 270) hydrogen bonds : angle 4.26327 ( 714) SS BOND : bond 0.00164 ( 32) SS BOND : angle 0.75887 ( 64) covalent geometry : bond 0.00190 (13000) covalent geometry : angle 0.52014 (17672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4367.50 seconds wall clock time: 79 minutes 29.69 seconds (4769.69 seconds total)