Starting phenix.real_space_refine on Thu Mar 5 11:34:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wad_32382/03_2026/7wad_32382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wad_32382/03_2026/7wad_32382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wad_32382/03_2026/7wad_32382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wad_32382/03_2026/7wad_32382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wad_32382/03_2026/7wad_32382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wad_32382/03_2026/7wad_32382.map" } resolution = 2.96 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= 0.007 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 14000 2.51 5 N 3884 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5504 Classifications: {'peptide': 723} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 694} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.44, per 1000 atoms: 0.24 Number of scatterers: 22268 At special positions: 0 Unit cell: (146.08, 139.92, 104.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 24 15.00 Mg 4 11.99 O 4276 8.00 N 3884 7.00 C 14000 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: 1.82 Conformation dependent library (CDL) restraints added in 773.3 milliseconds 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 44.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.868A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 3.844A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.723A pdb=" N ALA A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.784A pdb=" N GLN A 198 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 219 through 230 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.662A pdb=" N LEU A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.678A pdb=" N ALA A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.500A pdb=" N LEU A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 4.113A pdb=" N GLY A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.959A pdb=" N ILE A 408 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 424 Processing helix chain 'A' and resid 456 through 460 removed outlier: 4.342A pdb=" N MET A 459 " --> pdb=" O GLY A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 498 through 513 removed outlier: 3.676A pdb=" N GLN A 512 " --> pdb=" O HIS A 508 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.595A pdb=" N HIS A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 545 " --> pdb=" O GLN A 541 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 594 through 608 removed outlier: 4.064A pdb=" N VAL A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.957A pdb=" N ALA A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.901A pdb=" N ILE A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 695 " --> pdb=" O PRO A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.870A pdb=" N VAL B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 3.884A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.734A pdb=" N ALA B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.784A pdb=" N GLN B 198 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.676A pdb=" N LEU B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.663A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 345 removed outlier: 4.629A pdb=" N GLU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 374 removed outlier: 4.123A pdb=" N GLY B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.016A pdb=" N ILE B 408 " --> pdb=" O THR B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 424 Processing helix chain 'B' and resid 456 through 460 removed outlier: 4.310A pdb=" N MET B 459 " --> pdb=" O GLY B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 498 through 513 removed outlier: 3.674A pdb=" N GLN B 512 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.582A pdb=" N HIS B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU B 545 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 594 through 608 removed outlier: 4.058A pdb=" N VAL B 604 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 627 through 629 No H-bonds generated for 'chain 'B' and resid 627 through 629' Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.944A pdb=" N ALA B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 690 through 706 removed outlier: 3.893A pdb=" N ILE B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 695 " --> pdb=" O PRO B 691 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 76 through 92 removed outlier: 3.856A pdb=" N VAL C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.833A pdb=" N VAL C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 164 through 177 removed outlier: 3.715A pdb=" N ALA C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.784A pdb=" N GLN C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 219 through 230 Processing helix chain 'C' and resid 242 through 254 removed outlier: 3.602A pdb=" N LEU C 246 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASP C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.690A pdb=" N ALA C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 345 removed outlier: 3.501A pdb=" N LEU C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 341 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 4.104A pdb=" N GLY C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.959A pdb=" N ILE C 408 " --> pdb=" O THR C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 409 through 424 Processing helix chain 'C' and resid 456 through 460 removed outlier: 4.378A pdb=" N MET C 459 " --> pdb=" O GLY C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 498 through 513 removed outlier: 3.677A pdb=" N GLN C 512 " --> pdb=" O HIS C 508 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 513 " --> pdb=" O ILE C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 549 removed outlier: 3.567A pdb=" N HIS C 544 " --> pdb=" O PRO C 540 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 546 " --> pdb=" O SER C 542 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 568 Processing helix chain 'C' and resid 594 through 608 removed outlier: 4.065A pdb=" N VAL C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 606 " --> pdb=" O LYS C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.950A pdb=" N ALA C 653 " --> pdb=" O ARG C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 686 Processing helix chain 'C' and resid 690 through 706 removed outlier: 3.914A pdb=" N ILE C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 695 " --> pdb=" O PRO C 691 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 704 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 720 Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.973A pdb=" N GLY D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 65 through 73 Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.871A pdb=" N VAL D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 140 removed outlier: 3.814A pdb=" N VAL D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.741A pdb=" N ALA D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.785A pdb=" N GLN D 198 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 219 through 230 Processing helix chain 'D' and resid 242 through 254 removed outlier: 3.633A pdb=" N LEU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 251 " --> pdb=" O GLN D 247 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.650A pdb=" N ALA D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.506A pdb=" N LEU D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 374 removed outlier: 4.116A pdb=" N GLY D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 408 removed outlier: 4.012A pdb=" N ILE D 408 " --> pdb=" O THR D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 405 through 408' Processing helix chain 'D' and resid 409 through 424 Processing helix chain 'D' and resid 456 through 460 removed outlier: 4.348A pdb=" N MET D 459 " --> pdb=" O GLY D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 498 through 513 removed outlier: 3.674A pdb=" N GLN D 512 " --> pdb=" O HIS D 508 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 548 removed outlier: 3.571A pdb=" N HIS D 544 " --> pdb=" O PRO D 540 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU D 545 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D 546 " --> pdb=" O SER D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 568 Processing helix chain 'D' and resid 594 through 608 removed outlier: 4.061A pdb=" N VAL D 604 " --> pdb=" O LYS D 600 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 626 Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 644 through 653 removed outlier: 3.963A pdb=" N ALA D 653 " --> pdb=" O ARG D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 686 Processing helix chain 'D' and resid 690 through 706 removed outlier: 3.918A pdb=" N ILE D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 695 " --> pdb=" O PRO D 691 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 720 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 6.056A pdb=" N ILE A 3 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP A 28 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 5 " --> pdb=" O ARG A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 403 removed outlier: 5.071A pdb=" N VAL A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 313 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 319 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP A 307 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 434 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 450 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 433 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILE A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA6, first strand: chain 'A' and resid 530 through 534 removed outlier: 5.830A pdb=" N LEU A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE A 527 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 491 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 490 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 578 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 492 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU A 575 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 618 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN A 634 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 613 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA A 636 " --> pdb=" O GLY A 613 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA A 615 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 638 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 617 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ALA A 658 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR A 637 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N TYR A 660 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 665 " --> pdb=" O ILE A 676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.031A pdb=" N ILE B 3 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP B 28 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 5 " --> pdb=" O ARG B 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 237 through 240 Processing sheet with id=AB1, first strand: chain 'B' and resid 400 through 403 removed outlier: 5.058A pdb=" N VAL B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 313 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 319 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP B 307 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 434 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 450 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 433 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE B 448 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AB3, first strand: chain 'B' and resid 530 through 534 removed outlier: 5.818A pdb=" N LEU B 531 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE B 527 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU B 491 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 490 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE B 578 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 492 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU B 575 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 618 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN B 634 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY B 613 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA B 636 " --> pdb=" O GLY B 613 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA B 615 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE B 638 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 617 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ALA B 658 " --> pdb=" O VAL B 635 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR B 637 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N TYR B 660 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 665 " --> pdb=" O ILE B 676 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 9 removed outlier: 6.013A pdb=" N ILE C 3 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS C 5 " --> pdb=" O ARG C 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=AB7, first strand: chain 'C' and resid 400 through 403 removed outlier: 5.109A pdb=" N VAL C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 313 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 319 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP C 307 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 434 " --> pdb=" O LYS C 306 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU C 450 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 433 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE C 448 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AB9, first strand: chain 'C' and resid 530 through 534 removed outlier: 5.822A pdb=" N LEU C 531 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 527 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 491 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 490 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE C 578 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER C 492 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLU C 575 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C 618 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN C 634 " --> pdb=" O PRO C 611 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY C 613 " --> pdb=" O GLN C 634 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA C 636 " --> pdb=" O GLY C 613 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA C 615 " --> pdb=" O ALA C 636 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE C 638 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 617 " --> pdb=" O PHE C 638 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ALA C 658 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR C 637 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N TYR C 660 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 665 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 2 through 9 removed outlier: 6.060A pdb=" N ILE D 3 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP D 28 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS D 5 " --> pdb=" O ARG D 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'D' and resid 237 through 240 Processing sheet with id=AC4, first strand: chain 'D' and resid 400 through 403 removed outlier: 5.064A pdb=" N VAL D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 313 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 319 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP D 307 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 434 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 450 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 433 " --> pdb=" O ILE D 448 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE D 448 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AC6, first strand: chain 'D' and resid 530 through 534 removed outlier: 5.838A pdb=" N LEU D 531 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 527 " --> pdb=" O LEU D 531 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU D 491 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE D 490 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE D 578 " --> pdb=" O ILE D 490 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER D 492 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU D 575 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN D 618 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN D 634 " --> pdb=" O PRO D 611 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY D 613 " --> pdb=" O GLN D 634 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA D 636 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA D 615 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE D 638 " --> pdb=" O ALA D 615 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 617 " --> pdb=" O PHE D 638 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ALA D 658 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR D 637 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N TYR D 660 " --> pdb=" O TYR D 637 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE D 665 " --> pdb=" O ILE D 676 " (cutoff:3.500A) 998 hydrogen bonds defined for protein. 2802 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: 4.36 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 7591 1.37 - 1.51: 7151 1.51 - 1.66: 7770 1.66 - 1.80: 109 1.80 - 1.95: 19 Bond restraints: 22640 Sorted by residual: bond pdb=" CA GLY A 518 " pdb=" C GLY A 518 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.24e+00 bond pdb=" CA GLY C 518 " pdb=" C GLY C 518 " ideal model delta sigma weight residual 1.520 1.509 0.011 7.30e-03 1.88e+04 2.11e+00 bond pdb=" CA GLY D 518 " pdb=" C GLY D 518 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 2.03e+00 bond pdb=" CA GLY B 518 " pdb=" C GLY B 518 " ideal model delta sigma weight residual 1.520 1.510 0.010 7.30e-03 1.88e+04 1.89e+00 bond pdb=" C PRO A 455 " pdb=" N GLY A 456 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.86e+00 ... (remaining 22635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 29990 1.51 - 3.03: 658 3.03 - 4.54: 96 4.54 - 6.06: 12 6.06 - 7.57: 4 Bond angle restraints: 30760 Sorted by residual: angle pdb=" N GLY B 655 " pdb=" CA GLY B 655 " pdb=" C GLY B 655 " ideal model delta sigma weight residual 110.20 114.98 -4.78 1.32e+00 5.74e-01 1.31e+01 angle pdb=" N GLY C 655 " pdb=" CA GLY C 655 " pdb=" C GLY C 655 " ideal model delta sigma weight residual 110.20 114.96 -4.76 1.32e+00 5.74e-01 1.30e+01 angle pdb=" N GLY D 655 " pdb=" CA GLY D 655 " pdb=" C GLY D 655 " ideal model delta sigma weight residual 110.20 114.96 -4.76 1.32e+00 5.74e-01 1.30e+01 angle pdb=" N GLY A 655 " pdb=" CA GLY A 655 " pdb=" C GLY A 655 " ideal model delta sigma weight residual 110.20 114.93 -4.73 1.32e+00 5.74e-01 1.28e+01 angle pdb=" N THR C 204 " pdb=" CA THR C 204 " pdb=" C THR C 204 " ideal model delta sigma weight residual 114.56 110.78 3.78 1.27e+00 6.20e-01 8.84e+00 ... (remaining 30755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 13135 27.56 - 55.13: 426 55.13 - 82.69: 66 82.69 - 110.25: 13 110.25 - 137.82: 4 Dihedral angle restraints: 13644 sinusoidal: 5460 harmonic: 8184 Sorted by residual: dihedral pdb=" O1A AGS B1003 " pdb=" O3A AGS B1003 " pdb=" PA AGS B1003 " pdb=" PB AGS B1003 " ideal model delta sinusoidal sigma weight residual 292.27 154.45 137.82 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS A1003 " pdb=" O3A AGS A1003 " pdb=" PA AGS A1003 " pdb=" PB AGS A1003 " ideal model delta sinusoidal sigma weight residual 292.27 157.95 134.32 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O1A AGS C1003 " pdb=" O3A AGS C1003 " pdb=" PA AGS C1003 " pdb=" PB AGS C1003 " ideal model delta sinusoidal sigma weight residual 292.27 158.03 134.24 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 13641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2235 0.035 - 0.070: 958 0.070 - 0.105: 272 0.105 - 0.140: 146 0.140 - 0.175: 5 Chirality restraints: 3616 Sorted by residual: chirality pdb=" CB ILE D 40 " pdb=" CA ILE D 40 " pdb=" CG1 ILE D 40 " pdb=" CG2 ILE D 40 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA ILE B 260 " pdb=" N ILE B 260 " pdb=" C ILE B 260 " pdb=" CB ILE B 260 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 3613 not shown) Planarity restraints: 3920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 60 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 61 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 61 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 61 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 60 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO D 61 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 60 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 61 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.026 5.00e-02 4.00e+02 ... (remaining 3917 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 145 2.57 - 3.16: 17640 3.16 - 3.74: 32945 3.74 - 4.32: 45425 4.32 - 4.90: 78040 Nonbonded interactions: 174195 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O2B AGS A1003 " model vdw 1.992 2.170 nonbonded pdb="MG MG B1001 " pdb=" O2B AGS B1003 " model vdw 1.993 2.170 nonbonded pdb="MG MG C1001 " pdb=" O2B AGS C1003 " model vdw 1.994 2.170 nonbonded pdb="MG MG D1001 " pdb=" O2B AGS D1003 " model vdw 1.995 2.170 nonbonded pdb="MG MG A1001 " pdb=" O3G AGS A1003 " model vdw 2.081 2.170 ... (remaining 174190 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.570 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.024 22640 Z= 0.150 Angle : 0.577 7.570 30760 Z= 0.338 Chirality : 0.045 0.175 3616 Planarity : 0.004 0.045 3920 Dihedral : 13.991 137.817 8436 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 2884 helix: 1.38 (0.16), residues: 1048 sheet: 0.20 (0.23), residues: 512 loop : -1.27 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 458 TYR 0.009 0.001 TYR A 33 PHE 0.024 0.001 PHE D 43 TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00311 (22640) covalent geometry : angle 0.57682 (30760) hydrogen bonds : bond 0.16243 ( 998) hydrogen bonds : angle 5.88653 ( 2802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8337 (tp30) cc_final: 0.8109 (tp30) REVERT: A 33 TYR cc_start: 0.8039 (p90) cc_final: 0.7819 (p90) REVERT: A 150 ASP cc_start: 0.6921 (m-30) cc_final: 0.6619 (m-30) REVERT: A 160 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8358 (tm-30) REVERT: A 173 GLU cc_start: 0.8298 (tp30) cc_final: 0.8021 (mm-30) REVERT: A 300 GLU cc_start: 0.7793 (mp0) cc_final: 0.7299 (mp0) REVERT: B 30 GLU cc_start: 0.8623 (tp30) cc_final: 0.8343 (tp30) REVERT: B 33 TYR cc_start: 0.8096 (p90) cc_final: 0.7799 (p90) REVERT: B 150 ASP cc_start: 0.6737 (m-30) cc_final: 0.6368 (m-30) REVERT: B 160 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8470 (tm-30) REVERT: B 173 GLU cc_start: 0.8327 (tp30) cc_final: 0.8033 (mm-30) REVERT: B 300 GLU cc_start: 0.7475 (mp0) cc_final: 0.7189 (mp0) REVERT: C 33 TYR cc_start: 0.8187 (p90) cc_final: 0.7927 (p90) REVERT: C 89 GLN cc_start: 0.8007 (tt0) cc_final: 0.7623 (tt0) REVERT: C 150 ASP cc_start: 0.6929 (m-30) cc_final: 0.6635 (m-30) REVERT: C 173 GLU cc_start: 0.8308 (tp30) cc_final: 0.8030 (mm-30) REVERT: C 236 ARG cc_start: 0.6387 (ptm160) cc_final: 0.5870 (ptm160) REVERT: C 300 GLU cc_start: 0.7823 (mp0) cc_final: 0.7346 (mp0) REVERT: D 30 GLU cc_start: 0.8508 (tp30) cc_final: 0.8287 (tp30) REVERT: D 150 ASP cc_start: 0.6822 (m-30) cc_final: 0.6482 (m-30) REVERT: D 173 GLU cc_start: 0.8309 (tp30) cc_final: 0.8031 (mm-30) REVERT: D 236 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6539 (ptm160) REVERT: D 300 GLU cc_start: 0.7465 (mp0) cc_final: 0.7196 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.7857 time to fit residues: 196.5894 Evaluate side-chains 180 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 HIS ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.089976 restraints weight = 36917.146| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.59 r_work: 0.2773 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22640 Z= 0.221 Angle : 0.575 7.535 30760 Z= 0.308 Chirality : 0.048 0.171 3616 Planarity : 0.004 0.043 3920 Dihedral : 8.985 119.988 3284 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.98 % Allowed : 6.69 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 2884 helix: 1.24 (0.16), residues: 1112 sheet: 0.17 (0.23), residues: 520 loop : -1.31 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 102 TYR 0.008 0.001 TYR D 116 PHE 0.017 0.002 PHE B 43 TRP 0.008 0.001 TRP D 15 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00532 (22640) covalent geometry : angle 0.57470 (30760) hydrogen bonds : bond 0.05029 ( 998) hydrogen bonds : angle 4.86882 ( 2802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8781 (tp30) cc_final: 0.8398 (tp30) REVERT: A 33 TYR cc_start: 0.8221 (p90) cc_final: 0.7984 (p90) REVERT: A 150 ASP cc_start: 0.7005 (m-30) cc_final: 0.6699 (m-30) REVERT: A 160 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8467 (tp-100) REVERT: A 168 GLU cc_start: 0.8736 (pt0) cc_final: 0.8273 (tp30) REVERT: A 300 GLU cc_start: 0.7855 (mp0) cc_final: 0.7449 (mp0) REVERT: B 30 GLU cc_start: 0.8901 (tp30) cc_final: 0.8504 (tp30) REVERT: B 33 TYR cc_start: 0.8267 (p90) cc_final: 0.7991 (p90) REVERT: B 150 ASP cc_start: 0.6885 (m-30) cc_final: 0.6552 (m-30) REVERT: B 168 GLU cc_start: 0.8739 (pt0) cc_final: 0.8245 (tp30) REVERT: B 300 GLU cc_start: 0.7515 (mp0) cc_final: 0.7314 (mp0) REVERT: B 607 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8698 (mt-10) REVERT: C 33 TYR cc_start: 0.8313 (p90) cc_final: 0.8091 (p90) REVERT: C 150 ASP cc_start: 0.7020 (m-30) cc_final: 0.6718 (m-30) REVERT: C 168 GLU cc_start: 0.8750 (pt0) cc_final: 0.8277 (tp30) REVERT: C 236 ARG cc_start: 0.7170 (ptm160) cc_final: 0.6624 (ptm160) REVERT: C 300 GLU cc_start: 0.7833 (mp0) cc_final: 0.7440 (mp0) REVERT: D 30 GLU cc_start: 0.8863 (tp30) cc_final: 0.8508 (tp30) REVERT: D 150 ASP cc_start: 0.6916 (m-30) cc_final: 0.6600 (m-30) REVERT: D 168 GLU cc_start: 0.8731 (pt0) cc_final: 0.8264 (tp30) REVERT: D 236 ARG cc_start: 0.7395 (ttp-170) cc_final: 0.6863 (ptt180) REVERT: D 300 GLU cc_start: 0.7506 (mp0) cc_final: 0.7282 (mp0) outliers start: 23 outliers final: 10 residues processed: 189 average time/residue: 0.7535 time to fit residues: 159.9653 Evaluate side-chains 177 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 68 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 216 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 226 optimal weight: 30.0000 chunk 142 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091954 restraints weight = 36480.114| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.44 r_work: 0.2888 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22640 Z= 0.203 Angle : 0.546 7.583 30760 Z= 0.292 Chirality : 0.047 0.149 3616 Planarity : 0.004 0.048 3920 Dihedral : 8.730 115.125 3284 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.28 % Allowed : 9.84 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 2884 helix: 1.35 (0.16), residues: 1112 sheet: 0.27 (0.23), residues: 516 loop : -1.34 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 102 TYR 0.009 0.001 TYR C 519 PHE 0.011 0.001 PHE D 43 TRP 0.007 0.001 TRP B 15 HIS 0.003 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00485 (22640) covalent geometry : angle 0.54600 (30760) hydrogen bonds : bond 0.04521 ( 998) hydrogen bonds : angle 4.67388 ( 2802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8693 (tp30) cc_final: 0.8363 (tp30) REVERT: A 33 TYR cc_start: 0.8254 (p90) cc_final: 0.8044 (p90) REVERT: A 150 ASP cc_start: 0.7101 (m-30) cc_final: 0.6816 (m-30) REVERT: A 160 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8486 (tp-100) REVERT: A 168 GLU cc_start: 0.8764 (pt0) cc_final: 0.8327 (tp30) REVERT: A 236 ARG cc_start: 0.7166 (ptm160) cc_final: 0.6796 (ptm160) REVERT: A 300 GLU cc_start: 0.7951 (mp0) cc_final: 0.7549 (mp0) REVERT: B 26 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8175 (mtm180) REVERT: B 30 GLU cc_start: 0.8867 (tp30) cc_final: 0.8506 (tp30) REVERT: B 33 TYR cc_start: 0.8240 (p90) cc_final: 0.7976 (p90) REVERT: B 150 ASP cc_start: 0.6995 (m-30) cc_final: 0.6639 (m-30) REVERT: B 168 GLU cc_start: 0.8727 (pt0) cc_final: 0.8319 (tp30) REVERT: B 300 GLU cc_start: 0.7639 (mp0) cc_final: 0.7427 (mp0) REVERT: B 607 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8681 (mt-10) REVERT: C 33 TYR cc_start: 0.8317 (p90) cc_final: 0.8091 (p90) REVERT: C 150 ASP cc_start: 0.7081 (m-30) cc_final: 0.6798 (m-30) REVERT: C 168 GLU cc_start: 0.8774 (pt0) cc_final: 0.8335 (tp30) REVERT: C 236 ARG cc_start: 0.7283 (ptm160) cc_final: 0.6944 (ptm160) REVERT: C 300 GLU cc_start: 0.7985 (mp0) cc_final: 0.7603 (mp0) REVERT: D 30 GLU cc_start: 0.8723 (tp30) cc_final: 0.8411 (tp30) REVERT: D 168 GLU cc_start: 0.8764 (pt0) cc_final: 0.8332 (tp30) REVERT: D 236 ARG cc_start: 0.7389 (ttp-170) cc_final: 0.6796 (ptm160) REVERT: D 300 GLU cc_start: 0.7618 (mp0) cc_final: 0.7405 (mp0) REVERT: D 607 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8795 (mt-10) outliers start: 30 outliers final: 8 residues processed: 183 average time/residue: 0.7416 time to fit residues: 151.8047 Evaluate side-chains 171 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 213 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092304 restraints weight = 36345.795| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.48 r_work: 0.2901 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.004 0.041 22640 Z= 0.173 Angle : 0.520 7.950 30760 Z= 0.277 Chirality : 0.046 0.147 3616 Planarity : 0.004 0.043 3920 Dihedral : 8.529 113.448 3284 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.62 % Allowed : 11.37 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 2884 helix: 1.47 (0.16), residues: 1108 sheet: 0.29 (0.23), residues: 512 loop : -1.31 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.008 0.001 TYR C 519 PHE 0.011 0.001 PHE D 43 TRP 0.007 0.001 TRP B 15 HIS 0.002 0.001 HIS D 57 Details of bonding type rmsd covalent geometry : bond 0.00411 (22640) covalent geometry : angle 0.51990 (30760) hydrogen bonds : bond 0.04064 ( 998) hydrogen bonds : angle 4.54440 ( 2802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8680 (tp30) cc_final: 0.8345 (tp30) REVERT: A 33 TYR cc_start: 0.8289 (p90) cc_final: 0.8077 (p90) REVERT: A 150 ASP cc_start: 0.7209 (m-30) cc_final: 0.6914 (m-30) REVERT: A 160 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8460 (tp-100) REVERT: A 168 GLU cc_start: 0.8737 (pt0) cc_final: 0.8323 (tp30) REVERT: A 236 ARG cc_start: 0.7195 (ptm160) cc_final: 0.6973 (ptm160) REVERT: A 300 GLU cc_start: 0.7869 (mp0) cc_final: 0.7508 (mp0) REVERT: B 26 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8185 (mtm180) REVERT: B 30 GLU cc_start: 0.8854 (tp30) cc_final: 0.8498 (tp30) REVERT: B 33 TYR cc_start: 0.8218 (p90) cc_final: 0.7956 (p90) REVERT: B 102 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7604 (ttp-110) REVERT: B 150 ASP cc_start: 0.6997 (m-30) cc_final: 0.6652 (m-30) REVERT: B 168 GLU cc_start: 0.8707 (pt0) cc_final: 0.8332 (tp30) REVERT: B 300 GLU cc_start: 0.7626 (mp0) cc_final: 0.7420 (mp0) REVERT: C 33 TYR cc_start: 0.8296 (p90) cc_final: 0.8092 (p90) REVERT: C 150 ASP cc_start: 0.7108 (m-30) cc_final: 0.6825 (m-30) REVERT: C 168 GLU cc_start: 0.8733 (pt0) cc_final: 0.8356 (tp30) REVERT: C 236 ARG cc_start: 0.7258 (ptm160) cc_final: 0.6914 (ptm160) REVERT: C 300 GLU cc_start: 0.7918 (mp0) cc_final: 0.7479 (mp0) REVERT: D 26 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8451 (mtm180) REVERT: D 30 GLU cc_start: 0.8725 (tp30) cc_final: 0.8421 (tp30) REVERT: D 168 GLU cc_start: 0.8723 (pt0) cc_final: 0.8317 (tp30) REVERT: D 236 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.6749 (ptm160) outliers start: 38 outliers final: 15 residues processed: 187 average time/residue: 0.7125 time to fit residues: 149.7483 Evaluate side-chains 177 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 0.6980 chunk 219 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.152763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.092066 restraints weight = 36103.635| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.45 r_work: 0.2895 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 22640 Z= 0.181 Angle : 0.517 7.769 30760 Z= 0.276 Chirality : 0.046 0.145 3616 Planarity : 0.004 0.044 3920 Dihedral : 8.355 113.382 3284 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.62 % Allowed : 12.69 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 2884 helix: 1.54 (0.16), residues: 1108 sheet: 0.30 (0.23), residues: 512 loop : -1.33 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 102 TYR 0.009 0.001 TYR B 116 PHE 0.014 0.001 PHE B 43 TRP 0.007 0.001 TRP C 15 HIS 0.002 0.001 HIS A 409 Details of bonding type rmsd covalent geometry : bond 0.00433 (22640) covalent geometry : angle 0.51681 (30760) hydrogen bonds : bond 0.04100 ( 998) hydrogen bonds : angle 4.50735 ( 2802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8691 (tp30) cc_final: 0.8349 (tp30) REVERT: A 33 TYR cc_start: 0.8261 (p90) cc_final: 0.8042 (p90) REVERT: A 160 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8458 (tp-100) REVERT: A 168 GLU cc_start: 0.8747 (pt0) cc_final: 0.8368 (tp30) REVERT: A 236 ARG cc_start: 0.7237 (ptm160) cc_final: 0.6995 (ptm160) REVERT: A 300 GLU cc_start: 0.7880 (mp0) cc_final: 0.7426 (mp0) REVERT: B 26 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8203 (mtm180) REVERT: B 30 GLU cc_start: 0.8867 (tp30) cc_final: 0.8512 (tp30) REVERT: B 33 TYR cc_start: 0.8232 (p90) cc_final: 0.7962 (p90) REVERT: B 102 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7665 (ttp-110) REVERT: B 103 GLU cc_start: 0.7189 (tp30) cc_final: 0.6948 (tp30) REVERT: B 150 ASP cc_start: 0.6968 (m-30) cc_final: 0.6653 (m-30) REVERT: B 151 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7213 (mm) REVERT: B 168 GLU cc_start: 0.8702 (pt0) cc_final: 0.8370 (tp30) REVERT: B 300 GLU cc_start: 0.7610 (mp0) cc_final: 0.7377 (mp0) REVERT: C 168 GLU cc_start: 0.8737 (pt0) cc_final: 0.8423 (tp30) REVERT: C 236 ARG cc_start: 0.7241 (ptm160) cc_final: 0.6861 (ptm160) REVERT: C 300 GLU cc_start: 0.7932 (mp0) cc_final: 0.7457 (mp0) REVERT: D 26 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8399 (mtm180) REVERT: D 30 GLU cc_start: 0.8747 (tp30) cc_final: 0.8410 (tp30) REVERT: D 168 GLU cc_start: 0.8730 (pt0) cc_final: 0.8373 (tp30) REVERT: D 300 GLU cc_start: 0.7563 (mp0) cc_final: 0.7299 (mp0) outliers start: 38 outliers final: 19 residues processed: 188 average time/residue: 0.7214 time to fit residues: 152.1186 Evaluate side-chains 179 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 75 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 39 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094411 restraints weight = 36141.689| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.47 r_work: 0.2942 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22640 Z= 0.107 Angle : 0.480 8.519 30760 Z= 0.255 Chirality : 0.044 0.146 3616 Planarity : 0.003 0.045 3920 Dihedral : 8.035 110.544 3284 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.06 % Allowed : 14.01 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2884 helix: 1.75 (0.16), residues: 1104 sheet: 0.28 (0.23), residues: 520 loop : -1.30 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 102 TYR 0.008 0.001 TYR C 519 PHE 0.011 0.001 PHE A 43 TRP 0.006 0.001 TRP B 15 HIS 0.002 0.000 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00238 (22640) covalent geometry : angle 0.47964 (30760) hydrogen bonds : bond 0.03204 ( 998) hydrogen bonds : angle 4.32768 ( 2802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8642 (tp30) cc_final: 0.8307 (tp30) REVERT: A 33 TYR cc_start: 0.8226 (p90) cc_final: 0.7996 (p90) REVERT: A 160 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8452 (tp-100) REVERT: A 168 GLU cc_start: 0.8682 (pt0) cc_final: 0.8356 (tp30) REVERT: A 236 ARG cc_start: 0.7195 (ptm160) cc_final: 0.6927 (ptm160) REVERT: A 300 GLU cc_start: 0.7900 (mp0) cc_final: 0.7429 (mp0) REVERT: A 634 GLN cc_start: 0.9075 (mp10) cc_final: 0.8714 (mp10) REVERT: B 30 GLU cc_start: 0.8844 (tp30) cc_final: 0.8501 (tp30) REVERT: B 33 TYR cc_start: 0.8234 (p90) cc_final: 0.7963 (p90) REVERT: B 103 GLU cc_start: 0.7081 (tp30) cc_final: 0.6869 (tp30) REVERT: B 134 GLN cc_start: 0.7945 (tt0) cc_final: 0.7570 (tp-100) REVERT: B 150 ASP cc_start: 0.6982 (m-30) cc_final: 0.6666 (m-30) REVERT: B 151 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7329 (mm) REVERT: B 160 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8370 (tp-100) REVERT: B 168 GLU cc_start: 0.8655 (pt0) cc_final: 0.8302 (tp30) REVERT: B 236 ARG cc_start: 0.7394 (mtm180) cc_final: 0.6436 (ptm160) REVERT: B 607 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8758 (mt-10) REVERT: B 634 GLN cc_start: 0.9075 (mp10) cc_final: 0.8729 (mp10) REVERT: C 168 GLU cc_start: 0.8706 (pt0) cc_final: 0.8362 (tp30) REVERT: C 236 ARG cc_start: 0.7158 (ptm160) cc_final: 0.6756 (ptm160) REVERT: C 300 GLU cc_start: 0.7970 (mp0) cc_final: 0.7386 (mp0) REVERT: C 634 GLN cc_start: 0.9060 (mp10) cc_final: 0.8699 (mp10) REVERT: D 26 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8412 (mtm180) REVERT: D 30 GLU cc_start: 0.8674 (tp30) cc_final: 0.8355 (tp30) REVERT: D 94 MET cc_start: 0.7677 (mtm) cc_final: 0.7393 (mtt) REVERT: D 168 GLU cc_start: 0.8681 (pt0) cc_final: 0.8364 (tp30) REVERT: D 236 ARG cc_start: 0.7345 (ttp-170) cc_final: 0.6770 (ptm160) REVERT: D 300 GLU cc_start: 0.7402 (mp0) cc_final: 0.7066 (mp0) REVERT: D 634 GLN cc_start: 0.9039 (mp10) cc_final: 0.8673 (mp10) outliers start: 25 outliers final: 13 residues processed: 187 average time/residue: 0.7268 time to fit residues: 152.7348 Evaluate side-chains 180 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 66 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 235 optimal weight: 7.9990 chunk 182 optimal weight: 0.0470 chunk 277 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 overall best weight: 5.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 208 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN C 208 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.152418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.091929 restraints weight = 36111.286| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.43 r_work: 0.2887 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22640 Z= 0.212 Angle : 0.526 8.425 30760 Z= 0.280 Chirality : 0.046 0.145 3616 Planarity : 0.004 0.043 3920 Dihedral : 8.063 113.597 3284 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 14.74 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2884 helix: 1.68 (0.16), residues: 1108 sheet: 0.33 (0.23), residues: 512 loop : -1.33 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 102 TYR 0.010 0.001 TYR D 116 PHE 0.012 0.001 PHE B 43 TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00510 (22640) covalent geometry : angle 0.52559 (30760) hydrogen bonds : bond 0.04246 ( 998) hydrogen bonds : angle 4.44455 ( 2802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8692 (tp30) cc_final: 0.8337 (tp30) REVERT: A 33 TYR cc_start: 0.8258 (p90) cc_final: 0.8028 (p90) REVERT: A 168 GLU cc_start: 0.8759 (pt0) cc_final: 0.8456 (tp30) REVERT: A 236 ARG cc_start: 0.7221 (ptm160) cc_final: 0.6947 (ptm160) REVERT: A 300 GLU cc_start: 0.7940 (mp0) cc_final: 0.7402 (mp0) REVERT: A 634 GLN cc_start: 0.9108 (mp10) cc_final: 0.8719 (mp10) REVERT: B 26 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8187 (mtm180) REVERT: B 30 GLU cc_start: 0.8875 (tp30) cc_final: 0.8512 (tp30) REVERT: B 33 TYR cc_start: 0.8267 (p90) cc_final: 0.8001 (p90) REVERT: B 102 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7243 (ttp-110) REVERT: B 150 ASP cc_start: 0.6998 (m-30) cc_final: 0.6681 (m-30) REVERT: B 151 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7317 (mm) REVERT: B 160 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8350 (tp-100) REVERT: B 168 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: B 236 ARG cc_start: 0.7400 (mtm180) cc_final: 0.6520 (ptm160) REVERT: B 300 GLU cc_start: 0.7541 (mp0) cc_final: 0.7271 (mp0) REVERT: B 607 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8774 (mt-10) REVERT: C 168 GLU cc_start: 0.8756 (pt0) cc_final: 0.8445 (tp30) REVERT: C 236 ARG cc_start: 0.7182 (ptm160) cc_final: 0.6857 (ptm160) REVERT: C 300 GLU cc_start: 0.7996 (mp0) cc_final: 0.7501 (mp0) REVERT: C 634 GLN cc_start: 0.9104 (mp10) cc_final: 0.8724 (mp10) REVERT: D 26 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (mtm180) REVERT: D 30 GLU cc_start: 0.8757 (tp30) cc_final: 0.8407 (tp30) REVERT: D 168 GLU cc_start: 0.8751 (pt0) cc_final: 0.8446 (tp30) REVERT: D 300 GLU cc_start: 0.7437 (mp0) cc_final: 0.7098 (mp0) outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 0.7705 time to fit residues: 151.9909 Evaluate side-chains 175 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 100 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 254 optimal weight: 0.0050 chunk 97 optimal weight: 20.0000 chunk 283 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092396 restraints weight = 35972.648| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.40 r_work: 0.2891 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22640 Z= 0.187 Angle : 0.522 8.750 30760 Z= 0.278 Chirality : 0.046 0.144 3616 Planarity : 0.004 0.048 3920 Dihedral : 7.970 113.742 3284 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.06 % Allowed : 15.08 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 2884 helix: 1.65 (0.16), residues: 1108 sheet: 0.32 (0.23), residues: 512 loop : -1.35 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 102 TYR 0.009 0.001 TYR B 116 PHE 0.014 0.001 PHE B 43 TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00446 (22640) covalent geometry : angle 0.52177 (30760) hydrogen bonds : bond 0.04038 ( 998) hydrogen bonds : angle 4.41024 ( 2802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8750 (tp30) cc_final: 0.8372 (tp30) REVERT: A 33 TYR cc_start: 0.8260 (p90) cc_final: 0.8025 (p90) REVERT: A 168 GLU cc_start: 0.8762 (pt0) cc_final: 0.8446 (tp30) REVERT: A 236 ARG cc_start: 0.7135 (ptm160) cc_final: 0.6853 (ptm160) REVERT: A 300 GLU cc_start: 0.7952 (mp0) cc_final: 0.7413 (mp0) REVERT: A 634 GLN cc_start: 0.9098 (mp10) cc_final: 0.8701 (mp10) REVERT: B 1 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.7847 (mmt) REVERT: B 26 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8185 (mtm180) REVERT: B 30 GLU cc_start: 0.8878 (tp30) cc_final: 0.8527 (tp30) REVERT: B 33 TYR cc_start: 0.8260 (p90) cc_final: 0.7987 (p90) REVERT: B 102 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7230 (ttp-110) REVERT: B 151 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7365 (mm) REVERT: B 160 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8369 (tp-100) REVERT: B 168 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (tp30) REVERT: B 236 ARG cc_start: 0.7390 (mtm180) cc_final: 0.6490 (ptm160) REVERT: B 300 GLU cc_start: 0.7437 (mp0) cc_final: 0.7119 (mp0) REVERT: B 607 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8783 (mt-10) REVERT: B 634 GLN cc_start: 0.9097 (mp10) cc_final: 0.8720 (mp10) REVERT: C 168 GLU cc_start: 0.8759 (pt0) cc_final: 0.8440 (tp30) REVERT: C 236 ARG cc_start: 0.7122 (ptm160) cc_final: 0.6805 (ptm160) REVERT: C 300 GLU cc_start: 0.7993 (mp0) cc_final: 0.7483 (mp0) REVERT: C 634 GLN cc_start: 0.9099 (mp10) cc_final: 0.8709 (mp10) REVERT: D 26 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8326 (mtm180) REVERT: D 30 GLU cc_start: 0.8733 (tp30) cc_final: 0.8396 (tp30) REVERT: D 168 GLU cc_start: 0.8752 (pt0) cc_final: 0.8444 (tp30) REVERT: D 300 GLU cc_start: 0.7405 (mp0) cc_final: 0.7058 (mp0) REVERT: D 634 GLN cc_start: 0.9079 (mp10) cc_final: 0.8682 (mp10) outliers start: 25 outliers final: 16 residues processed: 173 average time/residue: 0.7769 time to fit residues: 150.9337 Evaluate side-chains 176 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 58 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 258 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093165 restraints weight = 36034.258| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.43 r_work: 0.2879 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22640 Z= 0.147 Angle : 0.497 8.952 30760 Z= 0.264 Chirality : 0.045 0.145 3616 Planarity : 0.003 0.052 3920 Dihedral : 7.767 112.575 3284 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.94 % Allowed : 15.37 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2884 helix: 1.73 (0.16), residues: 1108 sheet: 0.36 (0.23), residues: 512 loop : -1.31 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 102 TYR 0.008 0.001 TYR B 519 PHE 0.013 0.001 PHE A 43 TRP 0.007 0.001 TRP D 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00347 (22640) covalent geometry : angle 0.49690 (30760) hydrogen bonds : bond 0.03640 ( 998) hydrogen bonds : angle 4.33638 ( 2802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8771 (tp30) cc_final: 0.8392 (tp30) REVERT: A 33 TYR cc_start: 0.8254 (p90) cc_final: 0.8024 (p90) REVERT: A 168 GLU cc_start: 0.8756 (pt0) cc_final: 0.8417 (tp30) REVERT: A 236 ARG cc_start: 0.7007 (ptm160) cc_final: 0.6715 (ptm160) REVERT: A 300 GLU cc_start: 0.7913 (mp0) cc_final: 0.7380 (mp0) REVERT: A 634 GLN cc_start: 0.9083 (mp10) cc_final: 0.8684 (mp10) REVERT: B 26 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8083 (mtm180) REVERT: B 30 GLU cc_start: 0.8905 (tp30) cc_final: 0.8538 (tp30) REVERT: B 33 TYR cc_start: 0.8288 (p90) cc_final: 0.8040 (p90) REVERT: B 102 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7118 (ttp-110) REVERT: B 160 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8375 (tp-100) REVERT: B 168 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8352 (tp30) REVERT: B 236 ARG cc_start: 0.7358 (mtm180) cc_final: 0.6487 (ptm160) REVERT: B 300 GLU cc_start: 0.7361 (mp0) cc_final: 0.7064 (mp0) REVERT: B 607 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8744 (mt-10) REVERT: B 634 GLN cc_start: 0.9105 (mp10) cc_final: 0.8713 (mp10) REVERT: C 168 GLU cc_start: 0.8761 (pt0) cc_final: 0.8413 (tp30) REVERT: C 236 ARG cc_start: 0.7051 (ptm160) cc_final: 0.6738 (ptm160) REVERT: C 300 GLU cc_start: 0.7959 (mp0) cc_final: 0.7364 (mp0) REVERT: C 634 GLN cc_start: 0.9096 (mp10) cc_final: 0.8698 (mp10) REVERT: D 30 GLU cc_start: 0.8754 (tp30) cc_final: 0.8423 (tp30) REVERT: D 168 GLU cc_start: 0.8756 (pt0) cc_final: 0.8416 (tp30) REVERT: D 236 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6571 (ptm160) REVERT: D 286 ASP cc_start: 0.9022 (m-30) cc_final: 0.8819 (m-30) REVERT: D 300 GLU cc_start: 0.7347 (mp0) cc_final: 0.7064 (mp0) REVERT: D 634 GLN cc_start: 0.9062 (mp10) cc_final: 0.8655 (mp10) outliers start: 22 outliers final: 15 residues processed: 173 average time/residue: 0.7916 time to fit residues: 153.3206 Evaluate side-chains 175 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 253 optimal weight: 40.0000 chunk 220 optimal weight: 7.9990 chunk 38 optimal weight: 40.0000 chunk 140 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 196 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.092186 restraints weight = 36140.650| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.42 r_work: 0.2886 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22640 Z= 0.198 Angle : 0.535 8.901 30760 Z= 0.284 Chirality : 0.046 0.174 3616 Planarity : 0.004 0.055 3920 Dihedral : 7.741 113.855 3284 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.89 % Allowed : 15.84 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2884 helix: 1.67 (0.16), residues: 1108 sheet: 0.34 (0.23), residues: 512 loop : -1.33 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 102 TYR 0.009 0.001 TYR B 116 PHE 0.015 0.001 PHE B 43 TRP 0.008 0.001 TRP D 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00477 (22640) covalent geometry : angle 0.53533 (30760) hydrogen bonds : bond 0.04128 ( 998) hydrogen bonds : angle 4.39925 ( 2802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5768 Ramachandran restraints generated. 2884 Oldfield, 0 Emsley, 2884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8769 (tp30) cc_final: 0.8387 (tp30) REVERT: A 33 TYR cc_start: 0.8268 (p90) cc_final: 0.8038 (p90) REVERT: A 168 GLU cc_start: 0.8780 (pt0) cc_final: 0.8457 (tp30) REVERT: A 236 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6751 (ptm160) REVERT: A 300 GLU cc_start: 0.7958 (mp0) cc_final: 0.7438 (mp0) REVERT: A 634 GLN cc_start: 0.9116 (mp10) cc_final: 0.8716 (mp10) REVERT: B 26 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8148 (mtm180) REVERT: B 30 GLU cc_start: 0.8892 (tp30) cc_final: 0.8576 (tp30) REVERT: B 33 TYR cc_start: 0.8292 (p90) cc_final: 0.8035 (p90) REVERT: B 102 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7171 (ttp-110) REVERT: B 160 GLN cc_start: 0.8615 (tp40) cc_final: 0.8389 (tp-100) REVERT: B 168 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: B 236 ARG cc_start: 0.7393 (mtm180) cc_final: 0.6500 (ptm160) REVERT: B 300 GLU cc_start: 0.7421 (mp0) cc_final: 0.7107 (mp0) REVERT: B 607 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8765 (mt-10) REVERT: C 168 GLU cc_start: 0.8783 (pt0) cc_final: 0.8453 (tp30) REVERT: C 236 ARG cc_start: 0.7100 (ptm160) cc_final: 0.6785 (ptm160) REVERT: C 300 GLU cc_start: 0.8025 (mp0) cc_final: 0.7463 (mp0) REVERT: C 634 GLN cc_start: 0.9109 (mp10) cc_final: 0.8712 (mp10) REVERT: D 30 GLU cc_start: 0.8744 (tp30) cc_final: 0.8420 (tp30) REVERT: D 168 GLU cc_start: 0.8777 (pt0) cc_final: 0.8457 (tp30) REVERT: D 286 ASP cc_start: 0.9022 (m-30) cc_final: 0.8816 (m-30) REVERT: D 300 GLU cc_start: 0.7415 (mp0) cc_final: 0.7129 (mp0) REVERT: D 634 GLN cc_start: 0.9097 (mp10) cc_final: 0.8691 (mp10) outliers start: 21 outliers final: 15 residues processed: 174 average time/residue: 0.7915 time to fit residues: 154.7970 Evaluate side-chains 173 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 251 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 246 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093814 restraints weight = 35918.522| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.42 r_work: 0.2919 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22640 Z= 0.128 Angle : 0.491 9.023 30760 Z= 0.260 Chirality : 0.045 0.185 3616 Planarity : 0.003 0.042 3920 Dihedral : 7.515 111.660 3284 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.77 % Allowed : 16.35 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2884 helix: 1.76 (0.16), residues: 1112 sheet: 0.30 (0.23), residues: 520 loop : -1.32 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 102 TYR 0.008 0.001 TYR B 519 PHE 0.014 0.001 PHE B 43 TRP 0.007 0.001 TRP D 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00300 (22640) covalent geometry : angle 0.49053 (30760) hydrogen bonds : bond 0.03413 ( 998) hydrogen bonds : angle 4.27682 ( 2802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7376.35 seconds wall clock time: 126 minutes 21.25 seconds (7581.25 seconds total)