Starting phenix.real_space_refine on Sun Aug 24 02:18:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnu_34918/08_2025/8hnu_34918.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnu_34918/08_2025/8hnu_34918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnu_34918/08_2025/8hnu_34918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnu_34918/08_2025/8hnu_34918.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnu_34918/08_2025/8hnu_34918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnu_34918/08_2025/8hnu_34918.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 4 4.86 5 C 10156 2.51 5 N 2640 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16178 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7939 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} Conformer: "B" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} bond proxies already assigned to first conformer: 8000 Conformer: "C" Number of residues, atoms: 980, 7843 Classifications: {'peptide': 980} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 946} Chain breaks: 5 bond proxies already assigned to first conformer: 8000 Chain: "B" Number of atoms: 7919 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} Conformer: "B" Number of residues, atoms: 985, 7880 Classifications: {'peptide': 985} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 951} bond proxies already assigned to first conformer: 8010 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Residues with excluded nonbonded symmetry interactions: 30 residue: pdb=" N ASP A 39 " occ=0.97 ... (6 atoms not shown) pdb=" OD2 ASP A 39 " occ=0.97 residue: pdb=" N ASER A 114 " occ=0.65 ... (10 atoms not shown) pdb=" OG BSER A 114 " occ=0.35 residue: pdb=" N GLU A 125 " occ=0.79 ... (7 atoms not shown) pdb=" OE2 GLU A 125 " occ=0.79 residue: pdb=" N ATHR A 157 " occ=0.66 ... (12 atoms not shown) pdb=" CG2BTHR A 157 " occ=0.34 residue: pdb=" N AARG A 171 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG A 171 " occ=0.48 residue: pdb=" N APHE A 296 " occ=0.36 ... (31 atoms not shown) pdb=" CZ CPHE A 296 " occ=0.39 residue: pdb=" N ATHR A 338 " occ=0.91 ... (12 atoms not shown) pdb=" CG2BTHR A 338 " occ=0.09 residue: pdb=" N GLU A 446 " occ=0.83 ... (7 atoms not shown) pdb=" OE2 GLU A 446 " occ=0.83 residue: pdb=" N ASP A 625 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 625 " occ=0.62 residue: pdb=" N ASER A 626 " occ=0.40 ... (10 atoms not shown) pdb=" OG BSER A 626 " occ=0.60 residue: pdb=" N GLU A 766 " occ=0.67 ... (7 atoms not shown) pdb=" OE2 GLU A 766 " occ=0.67 residue: pdb=" N ASP A 799 " occ=0.66 ... (6 atoms not shown) pdb=" OD2 ASP A 799 " occ=0.66 ... (remaining 18 not shown) Time building chain proxies: 8.67, per 1000 atoms: 0.54 Number of scatterers: 16178 At special positions: 0 Unit cell: (115.37, 131.14, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 42 16.00 O 3336 8.00 N 2640 7.00 C 10156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3710 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 25 sheets defined 37.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.547A pdb=" N ASN A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.637A pdb=" N MET A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 455 removed outlier: 4.391A pdb=" N VAL A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 486 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 506 through 516 removed outlier: 5.669A pdb=" N TYR A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 559 through 573 removed outlier: 4.378A pdb=" N GLN A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.019A pdb=" N VAL A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 688 through 710 Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.822A pdb=" N PHE A 754 " --> pdb=" O PHE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.777A pdb=" N LYS A 795 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 832 Processing helix chain 'A' and resid 836 through 853 removed outlier: 3.616A pdb=" N LEU A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 removed outlier: 6.053A pdb=" N TYR A 857 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 890 through 904 removed outlier: 4.646A pdb=" N THR A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 115 through 119 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.574A pdb=" N THR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.537A pdb=" N ILE B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N APHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 419 through 434 removed outlier: 3.633A pdb=" N MET B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 455 removed outlier: 4.411A pdb=" N VAL B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 473 through 486 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 506 through 516 removed outlier: 5.671A pdb=" N TYR B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 559 through 573 removed outlier: 4.389A pdb=" N GLN B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.007A pdb=" N VAL B 577 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 635 through 651 Processing helix chain 'B' and resid 666 through 686 Processing helix chain 'B' and resid 688 through 710 Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.805A pdb=" N PHE B 754 " --> pdb=" O PHE B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 792 through 796 removed outlier: 3.791A pdb=" N LYS B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 832 Processing helix chain 'B' and resid 836 through 853 removed outlier: 3.620A pdb=" N LEU B 853 " --> pdb=" O PHE B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 861 removed outlier: 6.045A pdb=" N TYR B 857 " --> pdb=" O VAL B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 890 through 904 removed outlier: 4.644A pdb=" N THR B 894 " --> pdb=" O SER B 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.380A pdb=" N GLN B 307 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 309 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 321 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 311 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 319 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 339 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG B 335 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR B 325 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N ASP B 333 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.380A pdb=" N GLN B 307 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 309 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE B 321 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 311 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 319 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 339 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG B 335 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR B 325 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N ASP B 333 " --> pdb=" O TYR B 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.299A pdb=" N VAL A 45 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N PHE A 82 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY A 47 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N GLU A 84 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.801A pdb=" N ARG A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.801A pdb=" N ARG A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N ASP A 333 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 325 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A 335 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 339 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 319 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 311 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 321 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 309 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN A 307 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 145 through 148 Processing sheet with id=AA7, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.421A pdb=" N LEU A 204 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR A 213 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A 202 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN A 201 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 460 removed outlier: 6.646A pdb=" N SER A 936 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 980 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS A 938 " --> pdb=" O VAL A 980 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 982 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER A 940 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE A 984 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 942 " --> pdb=" O PHE A 984 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 499 through 500 removed outlier: 6.421A pdb=" N ASN A 541 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 543 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 712 removed outlier: 3.568A pdb=" N PHE A 715 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 780 through 781 Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 816 Processing sheet with id=AB6, first strand: chain 'A' and resid 906 through 909 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 37 removed outlier: 3.808A pdb=" N PHE B 32 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 34 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA B 49 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 36 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLY B 47 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 45 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N PHE B 82 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B 47 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N GLU B 84 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ALA B 49 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AB9, first strand: chain 'B' and resid 209 through 213 removed outlier: 6.423A pdb=" N LEU B 204 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR B 213 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE B 202 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 458 through 461 removed outlier: 3.603A pdb=" N ASN B 927 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER B 936 " --> pdb=" O HIS B 978 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL B 980 " --> pdb=" O SER B 936 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 938 " --> pdb=" O VAL B 980 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU B 982 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 940 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N PHE B 984 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 942 " --> pdb=" O PHE B 984 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU B 957 " --> pdb=" O ILE B 964 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 499 through 500 removed outlier: 6.415A pdb=" N ASN B 541 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 543 " --> pdb=" O LYS B 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'B' and resid 664 through 665 Processing sheet with id=AC5, first strand: chain 'B' and resid 780 through 781 Processing sheet with id=AC6, first strand: chain 'B' and resid 815 through 816 Processing sheet with id=AC7, first strand: chain 'B' and resid 906 through 909 785 hydrogen bonds defined for protein. 2157 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: 4.18 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5156 1.34 - 1.46: 3235 1.46 - 1.58: 7748 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 16223 Sorted by residual: bond pdb=" CA ASN A 588 " pdb=" CB ASN A 588 " ideal model delta sigma weight residual 1.533 1.550 -0.017 1.37e-02 5.33e+03 1.49e+00 bond pdb=" CB GLN A 87 " pdb=" CG GLN A 87 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.42e+00 bond pdb=" CB ASN A 588 " pdb=" CG ASN A 588 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.05e+00 bond pdb=" CB LYS B 648 " pdb=" CG LYS B 648 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.87e-01 ... (remaining 16218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 21652 1.45 - 2.91: 258 2.91 - 4.36: 47 4.36 - 5.82: 10 5.82 - 7.27: 4 Bond angle restraints: 21971 Sorted by residual: angle pdb=" C LYS A 712 " pdb=" N GLU A 713 " pdb=" CA GLU A 713 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 angle pdb=" C LYS B 712 " pdb=" N GLU B 713 " pdb=" CA GLU B 713 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" CB GLN A 87 " pdb=" CG GLN A 87 " pdb=" CD GLN A 87 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.70e+00 3.46e-01 8.82e+00 angle pdb=" CA ASN A 588 " pdb=" CB ASN A 588 " pdb=" CG ASN A 588 " ideal model delta sigma weight residual 112.60 115.49 -2.89 1.00e+00 1.00e+00 8.32e+00 angle pdb=" C THR B 407 " pdb=" N GLY B 408 " pdb=" CA GLY B 408 " ideal model delta sigma weight residual 120.91 116.99 3.92 1.38e+00 5.25e-01 8.06e+00 ... (remaining 21966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8561 17.93 - 35.86: 809 35.86 - 53.79: 223 53.79 - 71.72: 55 71.72 - 89.65: 22 Dihedral angle restraints: 9670 sinusoidal: 3870 harmonic: 5800 Sorted by residual: dihedral pdb=" CA LYS A 712 " pdb=" C LYS A 712 " pdb=" N GLU A 713 " pdb=" CA GLU A 713 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASP A 218 " pdb=" CB ASP A 218 " pdb=" CG ASP A 218 " pdb=" OD1 ASP A 218 " ideal model delta sinusoidal sigma weight residual -30.00 -88.24 58.24 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASN A 303 " pdb=" CB ASN A 303 " pdb=" CG ASN A 303 " pdb=" OD1 ASN A 303 " ideal model delta sinusoidal sigma weight residual -90.00 -162.14 72.14 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 9667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1340 0.027 - 0.055: 689 0.055 - 0.082: 210 0.082 - 0.109: 116 0.109 - 0.137: 45 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CA VAL A 166 " pdb=" N VAL A 166 " pdb=" C VAL A 166 " pdb=" CB VAL A 166 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE B 340 " pdb=" N ILE B 340 " pdb=" C ILE B 340 " pdb=" CB ILE B 340 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CB ILE B 775 " pdb=" CA ILE B 775 " pdb=" CG1 ILE B 775 " pdb=" CG2 ILE B 775 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 2397 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 588 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C ASN A 588 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 588 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 589 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 196 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 197 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 322 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 323 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.019 5.00e-02 4.00e+02 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 639 2.72 - 3.26: 15664 3.26 - 3.81: 28174 3.81 - 4.35: 37822 4.35 - 4.90: 60805 Nonbonded interactions: 143104 Sorted by model distance: nonbonded pdb=" N GLN A 690 " pdb=" OE1 GLN A 690 " model vdw 2.170 3.120 nonbonded pdb=" N GLN B 690 " pdb=" OE1 GLN B 690 " model vdw 2.171 3.120 nonbonded pdb=" O ASN A 588 " pdb=" ND2 ASN A 588 " model vdw 2.173 3.120 nonbonded pdb=" O MET B 537 " pdb=" O HOH B1101 " model vdw 2.243 3.040 nonbonded pdb=" O LEU A 260 " pdb=" O HOH A1101 " model vdw 2.258 3.040 ... (remaining 143099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 113 or resid 115 through 156 or resid 158 throug \ h 170 or resid 172 through 295 or resid 297 through 337 or resid 339 through 343 \ or resid 345 through 625 or resid 627 through 785 or resid 787 through 1002)) selection = (chain 'B' and (resid 2 through 113 or resid 115 through 156 or resid 158 throug \ h 170 or resid 172 through 295 or resid 297 through 337 or resid 339 through 343 \ or resid 345 through 625 or resid 627 through 785 or resid 787 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.07 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.930 Find NCS groups from input model: 0.290 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:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16223 Z= 0.125 Angle : 0.449 7.270 21971 Z= 0.250 Chirality : 0.041 0.137 2400 Planarity : 0.003 0.034 2853 Dihedral : 16.204 89.651 5960 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 1.52 % Allowed : 13.08 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 2002 helix: 1.69 (0.21), residues: 622 sheet: 0.95 (0.29), residues: 340 loop : 0.09 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 810 TYR 0.012 0.001 TYR A 237 PHE 0.011 0.001 PHE B 928 TRP 0.010 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00285 (16223) covalent geometry : angle 0.44904 (21971) hydrogen bonds : bond 0.13102 ( 728) hydrogen bonds : angle 5.79353 ( 2157) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.707 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 22 residues processed: 112 average time/residue: 0.7587 time to fit residues: 93.5588 Evaluate side-chains 110 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 799 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 851 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 459 GLN B 461 ASN B 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.069808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.047434 restraints weight = 139193.272| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 4.19 r_work: 0.2302 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2292 r_free = 0.2292 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2292 r_free = 0.2292 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16223 Z= 0.128 Angle : 0.471 8.042 21971 Z= 0.265 Chirality : 0.042 0.140 2400 Planarity : 0.003 0.035 2853 Dihedral : 5.307 66.332 2207 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.05 % Allowed : 13.02 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 2002 helix: 1.63 (0.21), residues: 638 sheet: 0.88 (0.29), residues: 340 loop : 0.05 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.011 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.011 0.001 TRP B 756 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00287 (16223) covalent geometry : angle 0.47100 (21971) hydrogen bonds : bond 0.04432 ( 728) hydrogen bonds : angle 4.84606 ( 2157) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: B 264 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8825 (tt) outliers start: 16 outliers final: 5 residues processed: 104 average time/residue: 0.8208 time to fit residues: 93.6792 Evaluate side-chains 98 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 605 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 482 GLN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.069079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.046555 restraints weight = 139559.817| |-----------------------------------------------------------------------------| r_work (start): 0.2473 rms_B_bonded: 4.17 r_work: 0.2280 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2271 r_free = 0.2271 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2271 r_free = 0.2271 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16223 Z= 0.147 Angle : 0.483 7.912 21971 Z= 0.271 Chirality : 0.042 0.141 2400 Planarity : 0.003 0.033 2853 Dihedral : 4.342 42.500 2172 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.93 % Allowed : 12.84 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 2002 helix: 1.60 (0.21), residues: 634 sheet: 0.83 (0.29), residues: 340 loop : -0.02 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 473 TYR 0.011 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.013 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00339 (16223) covalent geometry : angle 0.48262 (21971) hydrogen bonds : bond 0.04607 ( 728) hydrogen bonds : angle 4.78197 ( 2157) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 264 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8836 (tt) REVERT: B 346 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5804 (pp20) outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 0.8134 time to fit residues: 90.1753 Evaluate side-chains 98 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 72 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 193 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.068251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.045072 restraints weight = 141844.685| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 4.25 r_work: 0.2256 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2245 r_free = 0.2245 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2245 r_free = 0.2245 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16223 Z= 0.180 Angle : 0.502 7.752 21971 Z= 0.282 Chirality : 0.043 0.146 2400 Planarity : 0.003 0.035 2853 Dihedral : 4.347 41.513 2168 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.82 % Allowed : 13.31 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 2002 helix: 1.66 (0.21), residues: 618 sheet: 0.65 (0.29), residues: 344 loop : -0.01 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 232 TYR 0.013 0.001 TYR A 237 PHE 0.014 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.005 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00422 (16223) covalent geometry : angle 0.50236 (21971) hydrogen bonds : bond 0.04924 ( 728) hydrogen bonds : angle 4.83375 ( 2157) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 346 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5791 (pp20) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.8150 time to fit residues: 87.3858 Evaluate side-chains 98 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 713 GLU Chi-restraints excluded: chain B residue 799 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 126 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 109 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.047175 restraints weight = 144715.848| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 4.22 r_work: 0.2299 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16223 Z= 0.121 Angle : 0.467 7.626 21971 Z= 0.262 Chirality : 0.041 0.140 2400 Planarity : 0.003 0.035 2853 Dihedral : 4.031 19.968 2166 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.88 % Allowed : 13.54 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 2002 helix: 1.55 (0.21), residues: 638 sheet: 0.83 (0.29), residues: 338 loop : -0.03 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.011 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00272 (16223) covalent geometry : angle 0.46734 (21971) hydrogen bonds : bond 0.04193 ( 728) hydrogen bonds : angle 4.69841 ( 2157) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7171 (tm-30) REVERT: B 264 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8845 (tt) outliers start: 13 outliers final: 6 residues processed: 102 average time/residue: 0.7705 time to fit residues: 86.5968 Evaluate side-chains 97 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 461 ASN B 588 ASN B 962 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.070645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.047370 restraints weight = 144721.218| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.36 r_work: 0.2294 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2302 r_free = 0.2302 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2303 r_free = 0.2303 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16223 Z= 0.108 Angle : 0.454 7.556 21971 Z= 0.254 Chirality : 0.041 0.138 2400 Planarity : 0.003 0.034 2853 Dihedral : 3.895 19.412 2166 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 13.66 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2002 helix: 1.65 (0.21), residues: 638 sheet: 0.84 (0.29), residues: 340 loop : 0.00 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.010 0.001 TYR B 237 PHE 0.012 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.003 0.000 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00238 (16223) covalent geometry : angle 0.45382 (21971) hydrogen bonds : bond 0.03918 ( 728) hydrogen bonds : angle 4.59480 ( 2157) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8824 (tt) outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.7750 time to fit residues: 86.0658 Evaluate side-chains 97 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 111 optimal weight: 0.0040 chunk 169 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 178 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.070067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.047696 restraints weight = 135505.241| |-----------------------------------------------------------------------------| r_work (start): 0.2481 rms_B_bonded: 4.14 r_work: 0.2290 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2299 r_free = 0.2299 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2299 r_free = 0.2299 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16223 Z= 0.117 Angle : 0.462 7.755 21971 Z= 0.259 Chirality : 0.041 0.139 2400 Planarity : 0.003 0.034 2853 Dihedral : 3.938 19.432 2166 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.99 % Allowed : 13.54 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2002 helix: 1.64 (0.21), residues: 638 sheet: 0.84 (0.29), residues: 340 loop : 0.01 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.010 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.003 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00261 (16223) covalent geometry : angle 0.46216 (21971) hydrogen bonds : bond 0.04076 ( 728) hydrogen bonds : angle 4.60508 ( 2157) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7151 (tm-30) REVERT: B 264 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8846 (tt) REVERT: B 346 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5821 (pp20) outliers start: 15 outliers final: 7 residues processed: 102 average time/residue: 0.7898 time to fit residues: 88.3289 Evaluate side-chains 99 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 109 optimal weight: 0.0370 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.047239 restraints weight = 138735.665| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.17 r_work: 0.2299 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2289 r_free = 0.2289 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2289 r_free = 0.2289 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16223 Z= 0.127 Angle : 0.472 7.439 21971 Z= 0.265 Chirality : 0.041 0.139 2400 Planarity : 0.003 0.033 2853 Dihedral : 3.995 19.535 2166 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.82 % Allowed : 13.84 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2002 helix: 1.66 (0.21), residues: 634 sheet: 0.85 (0.29), residues: 338 loop : -0.03 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.010 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00287 (16223) covalent geometry : angle 0.47193 (21971) hydrogen bonds : bond 0.04228 ( 728) hydrogen bonds : angle 4.63651 ( 2157) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7149 (tm-30) REVERT: B 264 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8823 (tt) REVERT: B 346 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5837 (pp20) outliers start: 12 outliers final: 9 residues processed: 100 average time/residue: 0.7105 time to fit residues: 78.3703 Evaluate side-chains 101 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 167 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.047224 restraints weight = 145354.332| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.23 r_work: 0.2297 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2286 r_free = 0.2286 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 16223 Z= 0.160 Angle : 0.697 59.192 21971 Z= 0.416 Chirality : 0.042 0.349 2400 Planarity : 0.003 0.058 2853 Dihedral : 4.021 22.181 2166 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 0.88 % Allowed : 13.78 % Favored : 85.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2002 helix: 1.65 (0.21), residues: 634 sheet: 0.85 (0.29), residues: 338 loop : -0.03 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.010 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00339 (16223) covalent geometry : angle 0.69744 (21971) hydrogen bonds : bond 0.04238 ( 728) hydrogen bonds : angle 4.63571 ( 2157) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 588 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8808 (t0) REVERT: B 264 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8827 (tt) REVERT: B 346 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5828 (pp20) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.7461 time to fit residues: 81.7315 Evaluate side-chains 100 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 0.0770 chunk 67 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 461 ASN B 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.047441 restraints weight = 114618.035| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 3.92 r_work: 0.2310 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2301 r_free = 0.2301 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 16223 Z= 0.193 Angle : 0.684 47.905 21971 Z= 0.475 Chirality : 0.042 0.140 2400 Planarity : 0.003 0.063 2853 Dihedral : 4.021 22.191 2166 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 13.89 % Favored : 85.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2002 helix: 1.65 (0.21), residues: 634 sheet: 0.85 (0.29), residues: 338 loop : -0.03 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.010 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00402 (16223) covalent geometry : angle 0.68426 (21971) hydrogen bonds : bond 0.04238 ( 728) hydrogen bonds : angle 4.63571 ( 2157) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7130 (tm-30) REVERT: B 264 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8821 (tt) REVERT: B 346 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5831 (pp20) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.7579 time to fit residues: 82.2752 Evaluate side-chains 98 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 713 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 170 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 588 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.069931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.046502 restraints weight = 138161.213| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 4.30 r_work: 0.2293 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2284 r_free = 0.2284 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2284 r_free = 0.2284 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.304 16223 Z= 0.206 Angle : 0.690 59.178 21971 Z= 0.405 Chirality : 0.042 0.139 2400 Planarity : 0.003 0.065 2853 Dihedral : 4.001 19.475 2166 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 1.05 % Allowed : 13.60 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2002 helix: 1.65 (0.21), residues: 634 sheet: 0.85 (0.29), residues: 338 loop : -0.03 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 432 TYR 0.010 0.001 TYR A 237 PHE 0.013 0.001 PHE B 928 TRP 0.014 0.001 TRP A 756 HIS 0.004 0.001 HIS B 451 Details of bonding type rmsd covalent geometry : bond 0.00420 (16223) covalent geometry : angle 0.69004 (21971) hydrogen bonds : bond 0.04231 ( 728) hydrogen bonds : angle 4.63582 ( 2157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6478.73 seconds wall clock time: 111 minutes 26.77 seconds (6686.77 seconds total)