Starting phenix.real_space_refine on Thu Jun 19 02:41:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wad_32382/06_2025/7wad_32382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wad_32382/06_2025/7wad_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wad_32382/06_2025/7wad_32382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wad_32382/06_2025/7wad_32382.map" model { file = "/net/cci-nas-00/data/ceres_data/7wad_32382/06_2025/7wad_32382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wad_32382/06_2025/7wad_32382.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.47, per 1000 atoms: 0.60 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: 5.64 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.34 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: 9.14 Time building geometry restraints manager: 6.44 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: 0.12 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: 19.350 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: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 52.800 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (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 TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS C 79 PHE 0.024 0.001 PHE D 43 TYR 0.009 0.001 TYR A 33 ARG 0.002 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.16243 ( 998) hydrogen bonds : angle 5.88653 ( 2802) covalent geometry : bond 0.00311 (22640) covalent geometry : angle 0.57682 (30760) *********************** 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 : 2.426 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: 0.7928 (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: 1.8107 time to fit residues: 455.2611 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 : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 50.0000 chunk 218 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 40.0000 chunk 261 optimal weight: 6.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 ** 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 = 0.3976 r_free = 0.3976 target = 0.151645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090830 restraints weight = 36807.036| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.50 r_work: 0.2841 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 22640 Z= 0.303 Angle : 0.626 7.394 30760 Z= 0.334 Chirality : 0.050 0.159 3616 Planarity : 0.004 0.043 3920 Dihedral : 9.027 118.885 3284 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.19 % Allowed : 6.69 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2884 helix: 1.15 (0.16), residues: 1112 sheet: 0.13 (0.23), residues: 524 loop : -1.38 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.004 0.001 HIS A 57 PHE 0.014 0.002 PHE B 43 TYR 0.010 0.001 TYR D 116 ARG 0.008 0.001 ARG B 102 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 998) hydrogen bonds : angle 4.93971 ( 2802) covalent geometry : bond 0.00733 (22640) covalent geometry : angle 0.62647 (30760) *********************** 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 206 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8729 (tp30) cc_final: 0.8379 (tp30) REVERT: A 33 TYR cc_start: 0.8317 (p90) cc_final: 0.8091 (p90) REVERT: A 150 ASP cc_start: 0.7097 (m-30) cc_final: 0.6783 (m-30) REVERT: A 160 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8508 (tp-100) REVERT: A 168 GLU cc_start: 0.8735 (pt0) cc_final: 0.8411 (tp30) REVERT: A 236 ARG cc_start: 0.7256 (ptm160) cc_final: 0.6995 (ptm160) REVERT: A 300 GLU cc_start: 0.8045 (mp0) cc_final: 0.7627 (mp0) REVERT: B 1 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8008 (mmt) REVERT: B 30 GLU cc_start: 0.8868 (tp30) cc_final: 0.8513 (tp30) REVERT: B 33 TYR cc_start: 0.8279 (p90) cc_final: 0.7995 (p90) REVERT: B 150 ASP cc_start: 0.7000 (m-30) cc_final: 0.6661 (m-30) REVERT: B 160 GLN cc_start: 0.8751 (tp-100) cc_final: 0.8499 (tp-100) REVERT: B 168 GLU cc_start: 0.8709 (pt0) cc_final: 0.8372 (tp30) REVERT: B 300 GLU cc_start: 0.7711 (mp0) cc_final: 0.7458 (mp0) REVERT: B 607 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8760 (mt-10) REVERT: C 33 TYR cc_start: 0.8333 (p90) cc_final: 0.8102 (p90) REVERT: C 150 ASP cc_start: 0.7137 (m-30) cc_final: 0.6820 (m-30) REVERT: C 168 GLU cc_start: 0.8744 (pt0) cc_final: 0.8429 (tp30) REVERT: C 236 ARG cc_start: 0.7403 (ptm160) cc_final: 0.6879 (ptm160) REVERT: C 300 GLU cc_start: 0.8015 (mp0) cc_final: 0.7593 (mp0) REVERT: D 30 GLU cc_start: 0.8796 (tp30) cc_final: 0.8451 (tp30) REVERT: D 150 ASP cc_start: 0.6993 (m-30) cc_final: 0.6674 (m-30) REVERT: D 168 GLU cc_start: 0.8743 (pt0) cc_final: 0.8426 (tp30) REVERT: D 236 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.6928 (ptt180) REVERT: D 300 GLU cc_start: 0.7704 (mp0) cc_final: 0.7470 (mp0) outliers start: 28 outliers final: 13 residues processed: 193 average time/residue: 1.5254 time to fit residues: 333.5447 Evaluate side-chains 186 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 3.743 ------------------------------------------------------------------------------- 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 1 MET 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 C residue 109 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 109 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 157 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 199 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.152727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.092401 restraints weight = 36119.912| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.43 r_work: 0.2896 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22640 Z= 0.168 Angle : 0.532 7.776 30760 Z= 0.285 Chirality : 0.046 0.190 3616 Planarity : 0.004 0.044 3920 Dihedral : 8.750 115.515 3284 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.28 % Allowed : 9.88 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 2884 helix: 1.35 (0.16), residues: 1104 sheet: 0.25 (0.23), residues: 516 loop : -1.34 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.002 0.001 HIS C 650 PHE 0.012 0.001 PHE D 43 TYR 0.009 0.001 TYR B 519 ARG 0.008 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 998) hydrogen bonds : angle 4.69744 ( 2802) covalent geometry : bond 0.00397 (22640) covalent geometry : angle 0.53192 (30760) *********************** 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 200 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8670 (tp30) cc_final: 0.8344 (tp30) REVERT: A 33 TYR cc_start: 0.8237 (p90) cc_final: 0.8024 (p90) REVERT: A 150 ASP cc_start: 0.7104 (m-30) cc_final: 0.6811 (m-30) REVERT: A 160 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8481 (tp-100) REVERT: A 168 GLU cc_start: 0.8752 (pt0) cc_final: 0.8348 (tp30) REVERT: A 300 GLU cc_start: 0.7980 (mp0) cc_final: 0.7570 (mp0) REVERT: B 26 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8131 (mtm180) REVERT: B 30 GLU cc_start: 0.8844 (tp30) cc_final: 0.8495 (tp30) REVERT: B 33 TYR cc_start: 0.8221 (p90) cc_final: 0.7967 (p90) REVERT: B 102 ARG cc_start: 0.7908 (mtp-110) cc_final: 0.7652 (ttp-110) REVERT: B 150 ASP cc_start: 0.6984 (m-30) cc_final: 0.6629 (m-30) REVERT: B 160 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8484 (tp-100) REVERT: B 168 GLU cc_start: 0.8706 (pt0) cc_final: 0.8294 (tp30) REVERT: B 607 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8667 (mt-10) REVERT: C 33 TYR cc_start: 0.8294 (p90) cc_final: 0.8072 (p90) REVERT: C 150 ASP cc_start: 0.7084 (m-30) cc_final: 0.6795 (m-30) REVERT: C 168 GLU cc_start: 0.8754 (pt0) cc_final: 0.8361 (tp30) REVERT: C 236 ARG cc_start: 0.7299 (ptm160) cc_final: 0.6980 (ptm160) REVERT: C 300 GLU cc_start: 0.7947 (mp0) cc_final: 0.7565 (mp0) REVERT: C 607 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8775 (mt-10) REVERT: D 30 GLU cc_start: 0.8699 (tp30) cc_final: 0.8398 (tp30) REVERT: D 168 GLU cc_start: 0.8740 (pt0) cc_final: 0.8355 (tp30) REVERT: D 236 ARG cc_start: 0.7400 (ttp-170) cc_final: 0.6821 (ptt180) outliers start: 30 outliers final: 9 residues processed: 187 average time/residue: 1.5463 time to fit residues: 326.2430 Evaluate side-chains 173 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 B residue 459 MET Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL 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 61 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN C 208 GLN C 355 ASN D 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.150278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089784 restraints weight = 36653.278| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.42 r_work: 0.2824 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 22640 Z= 0.309 Angle : 0.614 7.455 30760 Z= 0.328 Chirality : 0.049 0.153 3616 Planarity : 0.004 0.045 3920 Dihedral : 8.692 115.853 3284 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.62 % Allowed : 12.14 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 2884 helix: 1.24 (0.16), residues: 1108 sheet: 0.08 (0.23), residues: 524 loop : -1.42 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.004 0.001 HIS C 713 PHE 0.013 0.002 PHE B 457 TYR 0.013 0.001 TYR D 33 ARG 0.010 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 998) hydrogen bonds : angle 4.81064 ( 2802) covalent geometry : bond 0.00746 (22640) covalent geometry : angle 0.61390 (30760) *********************** 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 195 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 2.491 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: 0.8809 (tp30) cc_final: 0.8420 (tp30) REVERT: A 150 ASP cc_start: 0.7241 (m-30) cc_final: 0.6930 (m-30) REVERT: A 160 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8465 (tp-100) REVERT: A 168 GLU cc_start: 0.8798 (pt0) cc_final: 0.8387 (tp30) REVERT: A 300 GLU cc_start: 0.7868 (mp0) cc_final: 0.7468 (mp0) REVERT: B 26 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8115 (mtm180) REVERT: B 30 GLU cc_start: 0.8934 (tp30) cc_final: 0.8542 (tp30) REVERT: B 33 TYR cc_start: 0.8282 (p90) cc_final: 0.8012 (p90) REVERT: B 102 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7736 (ttp-110) REVERT: B 150 ASP cc_start: 0.6998 (m-30) cc_final: 0.6652 (m-30) REVERT: B 160 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8456 (tp-100) REVERT: B 168 GLU cc_start: 0.8753 (pt0) cc_final: 0.8388 (tp30) REVERT: B 300 GLU cc_start: 0.7566 (mp0) cc_final: 0.7339 (mp0) REVERT: C 168 GLU cc_start: 0.8790 (pt0) cc_final: 0.8401 (tp30) REVERT: C 236 ARG cc_start: 0.7336 (ptm160) cc_final: 0.6798 (ptm160) REVERT: C 300 GLU cc_start: 0.7949 (mp0) cc_final: 0.7512 (mp0) REVERT: C 607 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8788 (mt-10) REVERT: D 26 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8316 (mtm180) REVERT: D 30 GLU cc_start: 0.8789 (tp30) cc_final: 0.8471 (tp30) REVERT: D 168 GLU cc_start: 0.8788 (pt0) cc_final: 0.8394 (tp30) REVERT: D 300 GLU cc_start: 0.7549 (mp0) cc_final: 0.7290 (mp0) outliers start: 38 outliers final: 25 residues processed: 186 average time/residue: 1.5971 time to fit residues: 335.7998 Evaluate side-chains 178 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 2.387 ------------------------------------------------------------------------------- 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 151 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 81 ILE 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 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 151 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 109 VAL Chi-restraints excluded: chain D residue 151 LEU 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 28 optimal weight: 7.9990 chunk 258 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.152317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.091755 restraints weight = 36338.041| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.45 r_work: 0.2889 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 22640 Z= 0.176 Angle : 0.523 8.232 30760 Z= 0.280 Chirality : 0.046 0.147 3616 Planarity : 0.004 0.044 3920 Dihedral : 8.397 114.426 3284 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.45 % Allowed : 13.71 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.15), residues: 2884 helix: 1.44 (0.16), residues: 1108 sheet: 0.17 (0.23), residues: 512 loop : -1.41 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 15 HIS 0.002 0.001 HIS A 409 PHE 0.011 0.001 PHE C 43 TYR 0.009 0.001 TYR B 519 ARG 0.010 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 998) hydrogen bonds : angle 4.59926 ( 2802) covalent geometry : bond 0.00417 (22640) covalent geometry : angle 0.52285 (30760) *********************** 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 190 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 2.540 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: 0.8695 (tp30) cc_final: 0.8387 (tp30) REVERT: A 160 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8462 (tp-100) REVERT: A 168 GLU cc_start: 0.8745 (pt0) cc_final: 0.8362 (tp30) REVERT: A 300 GLU cc_start: 0.7874 (mp0) cc_final: 0.7448 (mp0) REVERT: B 26 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8143 (mtm180) REVERT: B 30 GLU cc_start: 0.8886 (tp30) cc_final: 0.8532 (tp30) REVERT: B 33 TYR cc_start: 0.8223 (p90) cc_final: 0.7951 (p90) REVERT: B 102 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7728 (ttp-110) REVERT: B 150 ASP cc_start: 0.6994 (m-30) cc_final: 0.6661 (m-30) REVERT: B 151 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7307 (mm) REVERT: B 160 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8484 (tp-100) REVERT: B 168 GLU cc_start: 0.8699 (pt0) cc_final: 0.8353 (tp30) REVERT: B 300 GLU cc_start: 0.7415 (mp0) cc_final: 0.7117 (mp0) REVERT: B 607 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8703 (mt-10) REVERT: C 168 GLU cc_start: 0.8733 (pt0) cc_final: 0.8373 (tp30) REVERT: C 236 ARG cc_start: 0.7283 (ptm160) cc_final: 0.6896 (ptm160) REVERT: C 300 GLU cc_start: 0.7929 (mp0) cc_final: 0.7482 (mp0) REVERT: D 26 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8366 (mtm180) REVERT: D 30 GLU cc_start: 0.8743 (tp30) cc_final: 0.8439 (tp30) REVERT: D 168 GLU cc_start: 0.8730 (pt0) cc_final: 0.8360 (tp30) REVERT: D 300 GLU cc_start: 0.7399 (mp0) cc_final: 0.7172 (mp0) outliers start: 34 outliers final: 16 residues processed: 183 average time/residue: 1.5706 time to fit residues: 323.4149 Evaluate side-chains 174 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 2.668 ------------------------------------------------------------------------------- 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 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 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 94 optimal weight: 1.9990 chunk 179 optimal weight: 40.0000 chunk 37 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 270 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 183 optimal weight: 40.0000 chunk 238 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.152687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092140 restraints weight = 36173.815| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.43 r_work: 0.2862 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22640 Z= 0.166 Angle : 0.512 8.382 30760 Z= 0.273 Chirality : 0.046 0.145 3616 Planarity : 0.004 0.040 3920 Dihedral : 8.132 113.247 3284 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.36 % Allowed : 14.91 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.15), residues: 2884 helix: 1.58 (0.16), residues: 1108 sheet: 0.13 (0.23), residues: 520 loop : -1.38 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 15 HIS 0.003 0.001 HIS B 18 PHE 0.012 0.001 PHE B 43 TYR 0.008 0.001 TYR B 116 ARG 0.008 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 998) hydrogen bonds : angle 4.48741 ( 2802) covalent geometry : bond 0.00395 (22640) covalent geometry : angle 0.51239 (30760) *********************** 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 188 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8718 (tp30) cc_final: 0.8396 (tp30) REVERT: A 160 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8432 (tp-100) REVERT: A 168 GLU cc_start: 0.8763 (pt0) cc_final: 0.8360 (tp30) REVERT: A 300 GLU cc_start: 0.7896 (mp0) cc_final: 0.7408 (mp0) REVERT: A 634 GLN cc_start: 0.9124 (mp10) cc_final: 0.8717 (mp10) REVERT: B 26 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8089 (mtm180) REVERT: B 30 GLU cc_start: 0.8878 (tp30) cc_final: 0.8596 (tp30) REVERT: B 33 TYR cc_start: 0.8253 (p90) cc_final: 0.7980 (p90) REVERT: B 102 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7658 (ttp-110) REVERT: B 150 ASP cc_start: 0.6993 (m-30) cc_final: 0.6668 (m-30) REVERT: B 151 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7222 (mm) REVERT: B 160 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8464 (tp-100) REVERT: B 168 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: B 236 ARG cc_start: 0.7325 (mtm180) cc_final: 0.6418 (ptm160) REVERT: B 300 GLU cc_start: 0.7387 (mp0) cc_final: 0.7090 (mp0) REVERT: B 607 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8712 (mt-10) REVERT: C 168 GLU cc_start: 0.8761 (pt0) cc_final: 0.8415 (tp30) REVERT: C 236 ARG cc_start: 0.7179 (ptm160) cc_final: 0.6758 (ptm160) REVERT: C 300 GLU cc_start: 0.7940 (mp0) cc_final: 0.7478 (mp0) REVERT: C 634 GLN cc_start: 0.9122 (mp10) cc_final: 0.8715 (mp10) REVERT: D 26 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8270 (mtm180) REVERT: D 30 GLU cc_start: 0.8773 (tp30) cc_final: 0.8455 (tp30) REVERT: D 168 GLU cc_start: 0.8760 (pt0) cc_final: 0.8362 (tp30) REVERT: D 300 GLU cc_start: 0.7443 (mp0) cc_final: 0.7115 (mp0) REVERT: D 634 GLN cc_start: 0.9102 (mp10) cc_final: 0.8685 (mp10) outliers start: 32 outliers final: 17 residues processed: 181 average time/residue: 1.5008 time to fit residues: 307.7275 Evaluate side-chains 176 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 2.355 ------------------------------------------------------------------------------- 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 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 168 GLU 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 112 VAL Chi-restraints excluded: chain C residue 204 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 249 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 225 optimal weight: 0.0570 chunk 280 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 overall best weight: 3.9904 ------------------------------------------------------------------------------- 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 355 ASN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.092295 restraints weight = 36257.503| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.46 r_work: 0.2871 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22640 Z= 0.163 Angle : 0.508 8.695 30760 Z= 0.270 Chirality : 0.045 0.143 3616 Planarity : 0.004 0.043 3920 Dihedral : 7.930 113.339 3284 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.32 % Allowed : 15.63 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 2884 helix: 1.64 (0.16), residues: 1112 sheet: 0.25 (0.23), residues: 512 loop : -1.35 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 15 HIS 0.003 0.001 HIS B 18 PHE 0.012 0.001 PHE A 43 TYR 0.008 0.001 TYR B 116 ARG 0.015 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 998) hydrogen bonds : angle 4.43391 ( 2802) covalent geometry : bond 0.00388 (22640) covalent geometry : angle 0.50839 (30760) *********************** 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 189 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8707 (tp30) cc_final: 0.8384 (tp30) REVERT: A 160 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8417 (tp-100) REVERT: A 168 GLU cc_start: 0.8741 (pt0) cc_final: 0.8360 (tp30) REVERT: A 300 GLU cc_start: 0.7938 (mp0) cc_final: 0.7437 (mp0) REVERT: A 634 GLN cc_start: 0.9102 (mp10) cc_final: 0.8701 (mp10) REVERT: B 26 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8122 (mtm180) REVERT: B 30 GLU cc_start: 0.8899 (tp30) cc_final: 0.8586 (tp30) REVERT: B 33 TYR cc_start: 0.8275 (p90) cc_final: 0.8013 (p90) REVERT: B 151 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7360 (mm) REVERT: B 160 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8480 (tp-100) REVERT: B 168 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: B 236 ARG cc_start: 0.7319 (mtm180) cc_final: 0.6437 (ptm160) REVERT: B 300 GLU cc_start: 0.7398 (mp0) cc_final: 0.7058 (mp0) REVERT: B 607 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8727 (mt-10) REVERT: B 634 GLN cc_start: 0.9117 (mp10) cc_final: 0.8723 (mp10) REVERT: C 168 GLU cc_start: 0.8761 (pt0) cc_final: 0.8424 (tp30) REVERT: C 236 ARG cc_start: 0.7142 (ptm160) cc_final: 0.6844 (ptm160) REVERT: C 300 GLU cc_start: 0.7965 (mp0) cc_final: 0.7394 (mp0) REVERT: C 634 GLN cc_start: 0.9100 (mp10) cc_final: 0.8706 (mp10) REVERT: D 26 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (mtm180) REVERT: D 30 GLU cc_start: 0.8776 (tp30) cc_final: 0.8457 (tp30) REVERT: D 168 GLU cc_start: 0.8738 (pt0) cc_final: 0.8367 (tp30) REVERT: D 300 GLU cc_start: 0.7472 (mp0) cc_final: 0.7200 (mp0) REVERT: D 634 GLN cc_start: 0.9095 (mp10) cc_final: 0.8691 (mp10) outliers start: 31 outliers final: 18 residues processed: 179 average time/residue: 1.5790 time to fit residues: 318.7251 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 : 2.365 ------------------------------------------------------------------------------- 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 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 168 GLU 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 112 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 272 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 39 optimal weight: 0.0030 chunk 139 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- 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 ** 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 = 0.3977 r_free = 0.3977 target = 0.152835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092283 restraints weight = 36262.246| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.43 r_work: 0.2860 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22640 Z= 0.170 Angle : 0.512 8.851 30760 Z= 0.272 Chirality : 0.046 0.145 3616 Planarity : 0.003 0.037 3920 Dihedral : 7.812 113.275 3284 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.41 % Allowed : 16.18 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2884 helix: 1.69 (0.16), residues: 1108 sheet: 0.26 (0.23), residues: 512 loop : -1.36 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.003 0.001 HIS B 18 PHE 0.015 0.001 PHE B 43 TYR 0.009 0.001 TYR B 116 ARG 0.007 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 998) hydrogen bonds : angle 4.41276 ( 2802) covalent geometry : bond 0.00406 (22640) covalent geometry : angle 0.51207 (30760) *********************** 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 189 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8727 (tp30) cc_final: 0.8394 (tp30) REVERT: A 160 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8397 (tp-100) REVERT: A 168 GLU cc_start: 0.8776 (pt0) cc_final: 0.8372 (tp30) REVERT: A 300 GLU cc_start: 0.7920 (mp0) cc_final: 0.7427 (mp0) REVERT: A 634 GLN cc_start: 0.9109 (mp10) cc_final: 0.8695 (mp10) REVERT: B 26 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8093 (mtm180) REVERT: B 30 GLU cc_start: 0.8905 (tp30) cc_final: 0.8596 (tp30) REVERT: B 33 TYR cc_start: 0.8271 (p90) cc_final: 0.8005 (p90) REVERT: B 102 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6978 (ttp-110) REVERT: B 160 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8433 (tp-100) REVERT: B 168 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: B 236 ARG cc_start: 0.7336 (mtm180) cc_final: 0.6496 (ptm160) REVERT: B 300 GLU cc_start: 0.7368 (mp0) cc_final: 0.7019 (mp0) REVERT: B 607 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8741 (mt-10) REVERT: B 634 GLN cc_start: 0.9116 (mp10) cc_final: 0.8713 (mp10) REVERT: C 168 GLU cc_start: 0.8783 (pt0) cc_final: 0.8433 (tp30) REVERT: C 236 ARG cc_start: 0.7126 (ptm160) cc_final: 0.6689 (ptm160) REVERT: C 300 GLU cc_start: 0.7958 (mp0) cc_final: 0.7397 (mp0) REVERT: C 634 GLN cc_start: 0.9107 (mp10) cc_final: 0.8696 (mp10) REVERT: D 26 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8212 (mtm180) REVERT: D 30 GLU cc_start: 0.8770 (tp30) cc_final: 0.8446 (tp30) REVERT: D 168 GLU cc_start: 0.8765 (pt0) cc_final: 0.8380 (tp30) REVERT: D 300 GLU cc_start: 0.7426 (mp0) cc_final: 0.7140 (mp0) REVERT: D 634 GLN cc_start: 0.9097 (mp10) cc_final: 0.8677 (mp10) outliers start: 33 outliers final: 22 residues processed: 178 average time/residue: 1.7892 time to fit residues: 360.4559 Evaluate side-chains 184 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.651 ------------------------------------------------------------------------------- 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 167 THR 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 167 THR 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 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 167 THR 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 167 THR 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 130 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 286 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 ** 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 = 0.3979 r_free = 0.3979 target = 0.152983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092306 restraints weight = 36202.436| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.45 r_work: 0.2885 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22640 Z= 0.168 Angle : 0.510 8.931 30760 Z= 0.270 Chirality : 0.045 0.144 3616 Planarity : 0.004 0.048 3920 Dihedral : 7.680 113.236 3284 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.15 % Allowed : 16.74 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2884 helix: 1.71 (0.16), residues: 1108 sheet: 0.28 (0.23), residues: 512 loop : -1.34 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 15 HIS 0.003 0.001 HIS B 18 PHE 0.013 0.001 PHE A 43 TYR 0.008 0.001 TYR B 116 ARG 0.015 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 998) hydrogen bonds : angle 4.39576 ( 2802) covalent geometry : bond 0.00401 (22640) covalent geometry : angle 0.51010 (30760) *********************** 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 188 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 2.450 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: 0.8377 (tp30) REVERT: A 160 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8446 (tp-100) REVERT: A 168 GLU cc_start: 0.8750 (pt0) cc_final: 0.8380 (tp30) REVERT: A 236 ARG cc_start: 0.7469 (ptm160) cc_final: 0.7139 (ptt180) REVERT: A 300 GLU cc_start: 0.7926 (mp0) cc_final: 0.7421 (mp0) REVERT: A 634 GLN cc_start: 0.9109 (mp10) cc_final: 0.8705 (mp10) REVERT: B 26 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8147 (mtm180) REVERT: B 30 GLU cc_start: 0.8875 (tp30) cc_final: 0.8573 (tp30) REVERT: B 33 TYR cc_start: 0.8290 (p90) cc_final: 0.8032 (p90) REVERT: B 102 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7063 (ttp-110) REVERT: B 160 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8459 (tp-100) REVERT: B 168 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: B 236 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6445 (ptm160) REVERT: B 300 GLU cc_start: 0.7368 (mp0) cc_final: 0.7005 (mp0) REVERT: B 607 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8763 (mt-10) REVERT: B 634 GLN cc_start: 0.9117 (mp10) cc_final: 0.8724 (mp10) REVERT: C 168 GLU cc_start: 0.8756 (pt0) cc_final: 0.8439 (tp30) REVERT: C 236 ARG cc_start: 0.7069 (ptm160) cc_final: 0.6747 (ptm160) REVERT: C 286 ASP cc_start: 0.8987 (m-30) cc_final: 0.8783 (m-30) REVERT: C 300 GLU cc_start: 0.7955 (mp0) cc_final: 0.7386 (mp0) REVERT: C 634 GLN cc_start: 0.9113 (mp10) cc_final: 0.8712 (mp10) REVERT: D 26 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8312 (mtm180) REVERT: D 30 GLU cc_start: 0.8750 (tp30) cc_final: 0.8429 (tp30) REVERT: D 168 GLU cc_start: 0.8734 (pt0) cc_final: 0.8420 (tp30) REVERT: D 300 GLU cc_start: 0.7422 (mp0) cc_final: 0.7126 (mp0) REVERT: D 634 GLN cc_start: 0.9098 (mp10) cc_final: 0.8688 (mp10) outliers start: 27 outliers final: 23 residues processed: 181 average time/residue: 1.9349 time to fit residues: 399.3804 Evaluate side-chains 185 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER 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 167 THR 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 167 THR 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 81 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 167 THR 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 167 THR 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 42 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093870 restraints weight = 36069.068| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.44 r_work: 0.2922 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22640 Z= 0.118 Angle : 0.491 9.008 30760 Z= 0.259 Chirality : 0.045 0.145 3616 Planarity : 0.003 0.040 3920 Dihedral : 7.462 111.192 3284 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.11 % Allowed : 17.12 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2884 helix: 1.82 (0.16), residues: 1108 sheet: 0.24 (0.23), residues: 520 loop : -1.33 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 15 HIS 0.004 0.001 HIS B 18 PHE 0.014 0.001 PHE B 43 TYR 0.008 0.001 TYR C 519 ARG 0.009 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 998) hydrogen bonds : angle 4.28768 ( 2802) covalent geometry : bond 0.00272 (22640) covalent geometry : angle 0.49057 (30760) ********************** 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 191 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8690 (tp30) cc_final: 0.8359 (tp30) REVERT: A 160 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8417 (tp-100) REVERT: A 168 GLU cc_start: 0.8719 (pt0) cc_final: 0.8389 (tp30) REVERT: A 236 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7194 (ptt180) REVERT: A 300 GLU cc_start: 0.7937 (mp0) cc_final: 0.7431 (mp0) REVERT: A 634 GLN cc_start: 0.9099 (mp10) cc_final: 0.8710 (mp10) REVERT: B 26 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8117 (mtm180) REVERT: B 30 GLU cc_start: 0.8868 (tp30) cc_final: 0.8539 (tp30) REVERT: B 33 TYR cc_start: 0.8300 (p90) cc_final: 0.8020 (p90) REVERT: B 102 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7036 (ttp-110) REVERT: B 160 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8444 (tp-100) REVERT: B 168 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: B 236 ARG cc_start: 0.7355 (mtm180) cc_final: 0.6486 (ptm160) REVERT: B 300 GLU cc_start: 0.7399 (mp0) cc_final: 0.7028 (mp0) REVERT: B 607 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8725 (mt-10) REVERT: B 634 GLN cc_start: 0.9107 (mp10) cc_final: 0.8727 (mp10) REVERT: C 168 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8420 (tp30) REVERT: C 236 ARG cc_start: 0.7103 (ptm160) cc_final: 0.6666 (ptm160) REVERT: C 286 ASP cc_start: 0.8984 (m-30) cc_final: 0.8779 (m-30) REVERT: C 300 GLU cc_start: 0.7991 (mp0) cc_final: 0.7427 (mp0) REVERT: C 634 GLN cc_start: 0.9106 (mp10) cc_final: 0.8718 (mp10) REVERT: D 26 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (mtm180) REVERT: D 30 GLU cc_start: 0.8748 (tp30) cc_final: 0.8411 (tp30) REVERT: D 168 GLU cc_start: 0.8733 (pt0) cc_final: 0.8393 (tp30) REVERT: D 300 GLU cc_start: 0.7442 (mp0) cc_final: 0.7135 (mp0) REVERT: D 634 GLN cc_start: 0.9090 (mp10) cc_final: 0.8697 (mp10) outliers start: 26 outliers final: 18 residues processed: 183 average time/residue: 1.4853 time to fit residues: 306.8578 Evaluate side-chains 184 residues out of total 2348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER 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 167 THR 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 112 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 168 GLU 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 167 THR Chi-restraints excluded: chain D residue 204 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 48 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 178 optimal weight: 50.0000 chunk 200 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 40.0000 chunk 237 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.153185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.092501 restraints weight = 36078.423| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.46 r_work: 0.2898 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22640 Z= 0.168 Angle : 0.517 8.955 30760 Z= 0.274 Chirality : 0.045 0.181 3616 Planarity : 0.003 0.034 3920 Dihedral : 7.434 112.453 3284 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.15 % Allowed : 17.33 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 2884 helix: 1.79 (0.16), residues: 1108 sheet: 0.26 (0.23), residues: 520 loop : -1.33 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 15 HIS 0.004 0.001 HIS B 18 PHE 0.014 0.001 PHE B 43 TYR 0.010 0.001 TYR D 116 ARG 0.009 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 998) hydrogen bonds : angle 4.33356 ( 2802) covalent geometry : bond 0.00403 (22640) covalent geometry : angle 0.51727 (30760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15891.16 seconds wall clock time: 277 minutes 52.99 seconds (16672.99 seconds total)