Starting phenix.real_space_refine on Mon Jul 6 13:05:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vcx_31899/07_2026/7vcx_31899.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 36 5.49 5 Mg 12 5.21 5 S 198 5.16 5 C 22146 2.51 5 N 6276 2.21 5 O 6822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35490 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5851 Classifications: {'peptide': 746} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 704} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 7.77, per 1000 atoms: 0.22 Number of scatterers: 35490 At special positions: 0 Unit cell: (182.52, 173.88, 104.76, 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 198 16.00 P 36 15.00 Mg 12 11.99 O 6822 8.00 N 6276 7.00 C 22146 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8364 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 30 sheets defined 51.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 91 Processing helix chain 'A' and resid 134 through 139 removed outlier: 4.047A pdb=" N TYR A 138 " --> pdb=" O TYR A 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 134 through 139' Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.651A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.929A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.911A pdb=" N GLY A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.563A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.119A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.636A pdb=" N SER A 352 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.849A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 448 through 456 removed outlier: 4.036A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.722A pdb=" N ASP A 478 " --> pdb=" O THR A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.781A pdb=" N LYS A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.237A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.676A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 removed outlier: 3.596A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.757A pdb=" N ASN A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 removed outlier: 4.503A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 611 removed outlier: 4.069A pdb=" N ASP A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 removed outlier: 3.688A pdb=" N LYS A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.794A pdb=" N ARG A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.501A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.649A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 716 Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.701A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 762 removed outlier: 4.121A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 134 through 139 removed outlier: 4.047A pdb=" N TYR B 138 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 139' Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.651A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.929A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.911A pdb=" N GLY B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 278 through 296 removed outlier: 3.562A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.120A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.637A pdb=" N SER B 352 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.849A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 430 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 448 through 456 removed outlier: 4.036A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.721A pdb=" N ASP B 478 " --> pdb=" O THR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.781A pdb=" N LYS B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.236A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 507 " --> pdb=" O PHE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.676A pdb=" N LEU B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 3.597A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 removed outlier: 3.756A pdb=" N ASN B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 586 removed outlier: 4.502A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 611 removed outlier: 4.069A pdb=" N ASP B 598 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.689A pdb=" N LYS B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.793A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.501A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.649A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 716 Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.702A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 762 removed outlier: 4.120A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 134 through 139 removed outlier: 4.047A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 139' Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.651A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.929A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.911A pdb=" N GLY C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 296 removed outlier: 3.562A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.119A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.636A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG C 358 " --> pdb=" O PRO C 355 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.850A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 430 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 448 through 456 removed outlier: 4.036A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.721A pdb=" N ASP C 478 " --> pdb=" O THR C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.781A pdb=" N LYS C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.236A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 507 " --> pdb=" O PHE C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.676A pdb=" N LEU C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.597A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 569 removed outlier: 3.757A pdb=" N ASN C 558 " --> pdb=" O GLU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 586 removed outlier: 4.503A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 611 removed outlier: 4.069A pdb=" N ASP C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.687A pdb=" N LYS C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.793A pdb=" N ARG C 635 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.501A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.648A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.701A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 762 removed outlier: 4.121A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 134 through 139 removed outlier: 4.047A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.651A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.929A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.911A pdb=" N GLY D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 278 through 296 removed outlier: 3.563A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.119A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.636A pdb=" N SER D 352 " --> pdb=" O ARG D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG D 358 " --> pdb=" O PRO D 355 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.849A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 430 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 448 through 456 removed outlier: 4.036A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.722A pdb=" N ASP D 478 " --> pdb=" O THR D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 494 removed outlier: 3.781A pdb=" N LYS D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.237A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 507 " --> pdb=" O PHE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.676A pdb=" N LEU D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 3.596A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 569 removed outlier: 3.757A pdb=" N ASN D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 586 removed outlier: 4.503A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 586 " --> pdb=" O ILE D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 611 removed outlier: 4.069A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 615 removed outlier: 3.688A pdb=" N LYS D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 612 through 615' Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.794A pdb=" N ARG D 635 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.501A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.649A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.701A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 762 removed outlier: 4.121A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.047A pdb=" N TYR E 138 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.651A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.929A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.911A pdb=" N GLY E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 278 through 296 removed outlier: 3.562A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.120A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 335 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.637A pdb=" N SER E 352 " --> pdb=" O ARG E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG E 358 " --> pdb=" O PRO E 355 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.849A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 430 Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 448 through 456 removed outlier: 4.036A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.721A pdb=" N ASP E 478 " --> pdb=" O THR E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 494 removed outlier: 3.781A pdb=" N LYS E 486 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.236A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 507 " --> pdb=" O PHE E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.676A pdb=" N LEU E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 550 removed outlier: 3.597A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 569 removed outlier: 3.756A pdb=" N ASN E 558 " --> pdb=" O GLU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 586 removed outlier: 4.502A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG E 586 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 611 removed outlier: 4.069A pdb=" N ASP E 598 " --> pdb=" O GLY E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 615 removed outlier: 3.689A pdb=" N LYS E 615 " --> pdb=" O SER E 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 612 through 615' Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.793A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.501A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.649A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 716 Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.702A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 762 removed outlier: 4.120A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.047A pdb=" N TYR F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.651A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.929A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.911A pdb=" N GLY F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 263 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 278 through 296 removed outlier: 3.562A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.119A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.636A pdb=" N SER F 352 " --> pdb=" O ARG F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.663A pdb=" N ARG F 358 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.850A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 430 Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 448 through 456 removed outlier: 4.036A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 removed outlier: 3.721A pdb=" N ASP F 478 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 494 removed outlier: 3.781A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 507 removed outlier: 4.236A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 507 " --> pdb=" O PHE F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.676A pdb=" N LEU F 527 " --> pdb=" O GLY F 523 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 550 removed outlier: 3.597A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 569 removed outlier: 3.757A pdb=" N ASN F 558 " --> pdb=" O GLU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 586 removed outlier: 4.503A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 611 removed outlier: 4.069A pdb=" N ASP F 598 " --> pdb=" O GLY F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 615 removed outlier: 3.687A pdb=" N LYS F 615 " --> pdb=" O SER F 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 612 through 615' Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.793A pdb=" N ARG F 635 " --> pdb=" O ALA F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.501A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.648A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.701A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 762 removed outlier: 4.121A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 9.127A pdb=" N LYS A 81 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER A 42 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 83 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 removed outlier: 7.070A pdb=" N LYS A 109 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 155 removed outlier: 5.801A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.479A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.608A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 9.129A pdb=" N LYS B 81 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER B 42 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 83 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 7.072A pdb=" N LYS B 109 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 155 removed outlier: 5.801A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.480A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.608A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 29 removed outlier: 9.128A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 83 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 110 removed outlier: 7.071A pdb=" N LYS C 109 " --> pdb=" O ILE C 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 155 removed outlier: 5.801A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.480A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.608A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 29 removed outlier: 9.127A pdb=" N LYS D 81 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER D 42 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG D 83 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 109 through 110 removed outlier: 7.070A pdb=" N LYS D 109 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 151 through 155 removed outlier: 5.801A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.479A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.608A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 29 removed outlier: 9.129A pdb=" N LYS E 81 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER E 42 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 83 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 109 through 110 removed outlier: 7.072A pdb=" N LYS E 109 " --> pdb=" O ILE E 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 151 through 155 removed outlier: 5.801A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.480A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.608A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 9.128A pdb=" N LYS F 81 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER F 42 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 109 through 110 removed outlier: 7.071A pdb=" N LYS F 109 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 151 through 155 removed outlier: 5.801A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.480A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 543 removed outlier: 6.608A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1524 hydrogen bonds defined for protein. 4446 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: 9.05 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12716 1.36 - 1.50: 11162 1.50 - 1.65: 11882 1.65 - 1.79: 210 1.79 - 1.94: 102 Bond restraints: 36072 Sorted by residual: bond pdb=" CG1 ILE B 380 " pdb=" CD1 ILE B 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CG1 ILE E 380 " pdb=" CD1 ILE E 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CG1 ILE C 380 " pdb=" CD1 ILE C 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CG1 ILE F 380 " pdb=" CD1 ILE F 380 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.48e+00 bond pdb=" CB GLN D 327 " pdb=" CG GLN D 327 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.44e+00 ... (remaining 36067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 45508 2.26 - 4.51: 2878 4.51 - 6.77: 274 6.77 - 9.02: 96 9.02 - 11.28: 30 Bond angle restraints: 48786 Sorted by residual: angle pdb=" CB ARG F 358 " pdb=" CG ARG F 358 " pdb=" CD ARG F 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG C 358 " pdb=" CG ARG C 358 " pdb=" CD ARG C 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG E 358 " pdb=" CG ARG E 358 " pdb=" CD ARG E 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG B 358 " pdb=" CG ARG B 358 " pdb=" CD ARG B 358 " ideal model delta sigma weight residual 111.30 100.15 11.15 2.30e+00 1.89e-01 2.35e+01 angle pdb=" CB ARG D 358 " pdb=" CG ARG D 358 " pdb=" CD ARG D 358 " ideal model delta sigma weight residual 111.30 100.17 11.13 2.30e+00 1.89e-01 2.34e+01 ... (remaining 48781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.67: 19398 10.67 - 21.33: 2262 21.33 - 32.00: 468 32.00 - 42.67: 132 42.67 - 53.33: 72 Dihedral angle restraints: 22332 sinusoidal: 9438 harmonic: 12894 Sorted by residual: dihedral pdb=" CA MET C 550 " pdb=" C MET C 550 " pdb=" N TRP C 551 " pdb=" CA TRP C 551 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA MET F 550 " pdb=" C MET F 550 " pdb=" N TRP F 551 " pdb=" CA TRP F 551 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA MET E 550 " pdb=" C MET E 550 " pdb=" N TRP E 551 " pdb=" CA TRP E 551 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 22329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2694 0.044 - 0.088: 1762 0.088 - 0.132: 708 0.132 - 0.176: 266 0.176 - 0.219: 48 Chirality restraints: 5478 Sorted by residual: chirality pdb=" PA AGS F 901 " pdb=" O2A AGS F 901 " pdb=" O3A AGS F 901 " pdb=" O5' AGS F 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.96 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" PA AGS C 901 " pdb=" O2A AGS C 901 " pdb=" O3A AGS C 901 " pdb=" O5' AGS C 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.96 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" PA AGS D 901 " pdb=" O2A AGS D 901 " pdb=" O3A AGS D 901 " pdb=" O5' AGS D 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.96 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5475 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 516 " 0.023 2.00e-02 2.50e+03 2.03e-02 7.21e+00 pdb=" CG PHE F 516 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE F 516 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE F 516 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 516 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 516 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 516 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 516 " -0.023 2.00e-02 2.50e+03 2.03e-02 7.21e+00 pdb=" CG PHE C 516 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 516 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 516 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 516 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 516 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 516 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 105 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO C 106 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.037 5.00e-02 4.00e+02 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 360 2.63 - 3.20: 29536 3.20 - 3.77: 48888 3.77 - 4.33: 68554 4.33 - 4.90: 115876 Nonbonded interactions: 263214 Sorted by model distance: nonbonded pdb=" O1B AGS E 903 " pdb="MG MG E 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS B 903 " pdb="MG MG B 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS F 903 " pdb="MG MG F 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS C 903 " pdb="MG MG C 904 " model vdw 2.065 2.170 nonbonded pdb=" O1B AGS D 903 " pdb="MG MG D 904 " model vdw 2.065 2.170 ... (remaining 263209 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' selection = chain 'E' selection = chain 'F' } 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 35.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.016 0.114 36072 Z= 0.626 Angle : 1.216 11.281 48786 Z= 0.663 Chirality : 0.067 0.219 5478 Planarity : 0.009 0.067 6420 Dihedral : 10.016 53.335 13968 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.10), residues: 4452 helix: -2.31 (0.09), residues: 1992 sheet: -1.21 (0.16), residues: 666 loop : -2.48 (0.12), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 766 TYR 0.036 0.007 TYR C 203 PHE 0.047 0.005 PHE F 516 TRP 0.019 0.005 TRP D 454 HIS 0.012 0.003 HIS E 406 Details of bonding type rmsd/Z covalent geometry : bond 0.01580 / 0.63 (36072) covalent geometry : angle 1.21598 / 0.66 (48786) hydrogen bonds : bond 0.18554 / 11.91 ( 1524) hydrogen bonds : angle 5.72403 / 3.96 ( 4446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6604 (mtp) cc_final: 0.6281 (mtp) REVERT: A 307 ASP cc_start: 0.8420 (p0) cc_final: 0.8194 (p0) REVERT: A 344 MET cc_start: 0.8678 (mtp) cc_final: 0.8464 (mtm) REVERT: B 46 MET cc_start: 0.6564 (mtp) cc_final: 0.6295 (mtp) REVERT: B 332 MET cc_start: 0.8631 (mmm) cc_final: 0.8412 (mmm) REVERT: C 46 MET cc_start: 0.6466 (mtp) cc_final: 0.6208 (mtp) REVERT: D 46 MET cc_start: 0.6588 (mtp) cc_final: 0.6263 (mtp) REVERT: D 307 ASP cc_start: 0.8422 (p0) cc_final: 0.8196 (p0) REVERT: D 344 MET cc_start: 0.8675 (mtp) cc_final: 0.8462 (mtm) REVERT: E 46 MET cc_start: 0.6559 (mtp) cc_final: 0.6287 (mtp) REVERT: E 332 MET cc_start: 0.8609 (mmm) cc_final: 0.8391 (mmm) REVERT: F 46 MET cc_start: 0.6473 (mtp) cc_final: 0.6213 (mtp) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2904 time to fit residues: 215.7708 Evaluate side-chains 266 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.9980 chunk 424 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 103 GLN B 36 ASN B 90 ASN B 103 GLN B 351 ASN C 36 ASN C 90 ASN C 103 GLN C 351 ASN D 90 ASN D 103 GLN E 36 ASN E 90 ASN E 103 GLN E 351 ASN F 36 ASN F 90 ASN F 103 GLN F 351 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.173810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121719 restraints weight = 43905.708| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.52 r_work: 0.3089 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36072 Z= 0.122 Angle : 0.580 5.589 48786 Z= 0.302 Chirality : 0.044 0.154 5478 Planarity : 0.006 0.051 6420 Dihedral : 6.903 58.578 4980 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.84 % Allowed : 4.35 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.12), residues: 4452 helix: -0.12 (0.11), residues: 1992 sheet: -0.30 (0.18), residues: 612 loop : -1.92 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 239 TYR 0.012 0.001 TYR E 203 PHE 0.012 0.001 PHE B 152 TRP 0.013 0.002 TRP C 454 HIS 0.004 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (36072) covalent geometry : angle 0.58036 / 0.30 (48786) hydrogen bonds : bond 0.05387 / 3.55 ( 1524) hydrogen bonds : angle 4.22051 / 2.92 ( 4446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 334 time to evaluate : 1.360 Fit side-chains REVERT: A 46 MET cc_start: 0.6646 (mtp) cc_final: 0.6351 (mtp) REVERT: A 534 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: A 678 MET cc_start: 0.8275 (mmm) cc_final: 0.8067 (mmp) REVERT: B 46 MET cc_start: 0.6611 (mtp) cc_final: 0.6282 (mtp) REVERT: B 484 ASP cc_start: 0.7868 (p0) cc_final: 0.7649 (p0) REVERT: C 46 MET cc_start: 0.6479 (mtp) cc_final: 0.6166 (mtp) REVERT: C 484 ASP cc_start: 0.8008 (p0) cc_final: 0.7791 (p0) REVERT: C 693 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8312 (mtp85) REVERT: D 46 MET cc_start: 0.6645 (mtp) cc_final: 0.6347 (mtp) REVERT: D 534 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: D 678 MET cc_start: 0.8279 (mmm) cc_final: 0.8070 (mmp) REVERT: E 46 MET cc_start: 0.6608 (mtp) cc_final: 0.6278 (mtp) REVERT: E 484 ASP cc_start: 0.7858 (p0) cc_final: 0.7642 (p0) REVERT: F 46 MET cc_start: 0.6473 (mtp) cc_final: 0.6161 (mtp) REVERT: F 484 ASP cc_start: 0.8028 (p0) cc_final: 0.7801 (p0) REVERT: F 693 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8312 (mtp85) outliers start: 32 outliers final: 8 residues processed: 362 average time/residue: 0.2303 time to fit residues: 133.4152 Evaluate side-chains 260 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 369 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 433 optimal weight: 1.9990 chunk 193 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 440 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN C 398 GLN D 398 GLN F 398 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.172505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120479 restraints weight = 44064.360| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.49 r_work: 0.3065 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36072 Z= 0.156 Angle : 0.557 7.124 48786 Z= 0.283 Chirality : 0.044 0.137 5478 Planarity : 0.005 0.045 6420 Dihedral : 6.467 58.877 4980 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.94 % Allowed : 5.97 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4452 helix: 0.58 (0.12), residues: 2016 sheet: -0.25 (0.19), residues: 642 loop : -1.57 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.016 0.002 TYR B 495 PHE 0.014 0.002 PHE A 516 TRP 0.009 0.002 TRP C 454 HIS 0.002 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (36072) covalent geometry : angle 0.55670 / 0.28 (48786) hydrogen bonds : bond 0.05383 / 3.54 ( 1524) hydrogen bonds : angle 3.92801 / 2.72 ( 4446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 1.268 Fit side-chains REVERT: A 46 MET cc_start: 0.6502 (mtp) cc_final: 0.6236 (mtp) REVERT: A 398 GLN cc_start: 0.7782 (tt0) cc_final: 0.7573 (mm110) REVERT: A 453 ARG cc_start: 0.8069 (tpp-160) cc_final: 0.7794 (mmt-90) REVERT: A 611 MET cc_start: 0.8298 (tpp) cc_final: 0.8077 (tpt) REVERT: B 46 MET cc_start: 0.6601 (mtp) cc_final: 0.6282 (mtp) REVERT: C 46 MET cc_start: 0.6529 (mtp) cc_final: 0.6298 (mtp) REVERT: D 46 MET cc_start: 0.6502 (mtp) cc_final: 0.6238 (mtp) REVERT: D 453 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.7774 (mmt-90) REVERT: D 611 MET cc_start: 0.8293 (tpp) cc_final: 0.8070 (tpt) REVERT: E 46 MET cc_start: 0.6606 (mtp) cc_final: 0.6284 (mtp) REVERT: F 46 MET cc_start: 0.6531 (mtp) cc_final: 0.6301 (mtp) REVERT: F 693 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8286 (mtp85) outliers start: 36 outliers final: 14 residues processed: 300 average time/residue: 0.2041 time to fit residues: 101.2383 Evaluate side-chains 266 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 410 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 86 optimal weight: 0.0470 chunk 424 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 407 optimal weight: 10.0000 chunk 392 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 379 optimal weight: 30.0000 overall best weight: 3.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 398 GLN E 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118233 restraints weight = 43951.800| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.46 r_work: 0.3028 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36072 Z= 0.211 Angle : 0.600 7.788 48786 Z= 0.304 Chirality : 0.046 0.141 5478 Planarity : 0.005 0.050 6420 Dihedral : 6.462 59.734 4980 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.07 % Allowed : 6.55 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.13), residues: 4452 helix: 0.81 (0.12), residues: 2016 sheet: -0.22 (0.19), residues: 642 loop : -1.45 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 567 TYR 0.022 0.002 TYR E 495 PHE 0.019 0.002 PHE D 267 TRP 0.008 0.002 TRP A 454 HIS 0.004 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.21 (36072) covalent geometry : angle 0.60013 / 0.30 (48786) hydrogen bonds : bond 0.06068 / 4.00 ( 1524) hydrogen bonds : angle 4.00232 / 2.76 ( 4446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6470 (mtp) cc_final: 0.6199 (mtp) REVERT: B 46 MET cc_start: 0.6558 (mtp) cc_final: 0.6230 (mtp) REVERT: C 46 MET cc_start: 0.6570 (mtp) cc_final: 0.6345 (mtp) REVERT: D 46 MET cc_start: 0.6475 (mtp) cc_final: 0.6209 (mtp) REVERT: E 46 MET cc_start: 0.6553 (mtp) cc_final: 0.6223 (mtp) REVERT: F 46 MET cc_start: 0.6571 (mtp) cc_final: 0.6345 (mtp) REVERT: F 693 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8249 (mtp85) outliers start: 41 outliers final: 23 residues processed: 302 average time/residue: 0.1953 time to fit residues: 98.4529 Evaluate side-chains 270 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 428 optimal weight: 2.9990 chunk 297 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 430 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 98 optimal weight: 0.0980 chunk 298 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 313 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119512 restraints weight = 44025.556| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.49 r_work: 0.3060 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36072 Z= 0.155 Angle : 0.541 7.290 48786 Z= 0.273 Chirality : 0.044 0.133 5478 Planarity : 0.004 0.043 6420 Dihedral : 6.331 59.366 4980 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.81 % Allowed : 7.91 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4452 helix: 1.08 (0.12), residues: 2016 sheet: -0.14 (0.19), residues: 642 loop : -1.25 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.012 0.002 TYR F 244 PHE 0.012 0.001 PHE E 516 TRP 0.009 0.001 TRP A 454 HIS 0.002 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (36072) covalent geometry : angle 0.54110 / 0.27 (48786) hydrogen bonds : bond 0.04996 / 3.29 ( 1524) hydrogen bonds : angle 3.83240 / 2.65 ( 4446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6573 (mtp) cc_final: 0.6310 (mtp) REVERT: A 614 LYS cc_start: 0.6749 (mmtm) cc_final: 0.6239 (mmmt) REVERT: B 46 MET cc_start: 0.6570 (mtp) cc_final: 0.6244 (mtp) REVERT: C 46 MET cc_start: 0.6542 (mtp) cc_final: 0.6304 (mtp) REVERT: D 46 MET cc_start: 0.6569 (mtp) cc_final: 0.6307 (mtp) REVERT: D 614 LYS cc_start: 0.6743 (mmtm) cc_final: 0.6233 (mmmt) REVERT: E 46 MET cc_start: 0.6567 (mtp) cc_final: 0.6239 (mtp) REVERT: F 46 MET cc_start: 0.6547 (mtp) cc_final: 0.6307 (mtp) REVERT: F 693 ARG cc_start: 0.8432 (tpp80) cc_final: 0.8227 (mtp85) outliers start: 31 outliers final: 23 residues processed: 276 average time/residue: 0.1991 time to fit residues: 94.3895 Evaluate side-chains 262 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 320 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.171377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118747 restraints weight = 44145.790| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.48 r_work: 0.3049 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36072 Z= 0.179 Angle : 0.555 6.536 48786 Z= 0.279 Chirality : 0.045 0.135 5478 Planarity : 0.004 0.042 6420 Dihedral : 6.300 59.290 4980 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.02 % Allowed : 8.60 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.13), residues: 4452 helix: 1.18 (0.12), residues: 2004 sheet: -0.13 (0.19), residues: 642 loop : -1.14 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 239 TYR 0.014 0.002 TYR F 244 PHE 0.014 0.002 PHE D 516 TRP 0.007 0.001 TRP D 454 HIS 0.006 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (36072) covalent geometry : angle 0.55542 / 0.28 (48786) hydrogen bonds : bond 0.05348 / 3.53 ( 1524) hydrogen bonds : angle 3.85344 / 2.66 ( 4446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6575 (mtp) cc_final: 0.6314 (mtp) REVERT: A 614 LYS cc_start: 0.6814 (mmtm) cc_final: 0.6275 (mmmt) REVERT: B 46 MET cc_start: 0.6631 (mtp) cc_final: 0.6333 (mtp) REVERT: C 46 MET cc_start: 0.6550 (mtp) cc_final: 0.6298 (mtp) REVERT: C 442 MET cc_start: 0.7219 (ttm) cc_final: 0.6903 (tmm) REVERT: D 46 MET cc_start: 0.6576 (mtp) cc_final: 0.6316 (mtp) REVERT: D 614 LYS cc_start: 0.6809 (mmtm) cc_final: 0.6269 (mmmt) REVERT: E 46 MET cc_start: 0.6627 (mtp) cc_final: 0.6332 (mtp) REVERT: F 46 MET cc_start: 0.6547 (mtp) cc_final: 0.6292 (mtp) REVERT: F 442 MET cc_start: 0.7203 (ttm) cc_final: 0.6897 (tmm) outliers start: 39 outliers final: 27 residues processed: 273 average time/residue: 0.1998 time to fit residues: 93.3169 Evaluate side-chains 264 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 668 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 126 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 318 optimal weight: 0.6980 chunk 437 optimal weight: 6.9990 chunk 341 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 322 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120548 restraints weight = 43993.068| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.39 r_work: 0.3067 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36072 Z= 0.141 Angle : 0.520 6.602 48786 Z= 0.262 Chirality : 0.044 0.132 5478 Planarity : 0.004 0.043 6420 Dihedral : 6.227 59.741 4980 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.84 % Allowed : 9.04 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.13), residues: 4452 helix: 1.31 (0.12), residues: 2010 sheet: -0.06 (0.19), residues: 642 loop : -1.08 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 239 TYR 0.012 0.001 TYR C 244 PHE 0.012 0.001 PHE B 516 TRP 0.009 0.001 TRP C 454 HIS 0.003 0.001 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (36072) covalent geometry : angle 0.51988 / 0.26 (48786) hydrogen bonds : bond 0.04738 / 3.13 ( 1524) hydrogen bonds : angle 3.75244 / 2.59 ( 4446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 1.454 Fit side-chains REVERT: A 46 MET cc_start: 0.6561 (mtp) cc_final: 0.6303 (mtp) REVERT: A 614 LYS cc_start: 0.7047 (mmtm) cc_final: 0.6583 (mmmt) REVERT: B 484 ASP cc_start: 0.7758 (p0) cc_final: 0.7386 (m-30) REVERT: C 46 MET cc_start: 0.6570 (mtp) cc_final: 0.6325 (mtp) REVERT: C 442 MET cc_start: 0.7296 (ttm) cc_final: 0.6955 (tmm) REVERT: C 484 ASP cc_start: 0.7925 (p0) cc_final: 0.7600 (m-30) REVERT: D 46 MET cc_start: 0.6560 (mtp) cc_final: 0.6307 (mtp) REVERT: D 614 LYS cc_start: 0.7051 (mmtm) cc_final: 0.6582 (mmmt) REVERT: E 484 ASP cc_start: 0.7746 (p0) cc_final: 0.7379 (m-30) REVERT: F 46 MET cc_start: 0.6568 (mtp) cc_final: 0.6319 (mtp) REVERT: F 442 MET cc_start: 0.7289 (ttm) cc_final: 0.6950 (tmm) REVERT: F 484 ASP cc_start: 0.7912 (p0) cc_final: 0.7593 (m-30) outliers start: 32 outliers final: 28 residues processed: 268 average time/residue: 0.2018 time to fit residues: 93.2271 Evaluate side-chains 258 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 416 optimal weight: 0.3980 chunk 232 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 435 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 285 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 HIS C 103 GLN C 340 HIS E 340 HIS F 103 GLN F 340 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118610 restraints weight = 44188.588| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.73 r_work: 0.3005 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 36072 Z= 0.238 Angle : 0.617 8.852 48786 Z= 0.309 Chirality : 0.046 0.139 5478 Planarity : 0.005 0.042 6420 Dihedral : 6.395 58.988 4980 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.84 % Allowed : 9.43 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4452 helix: 1.12 (0.12), residues: 2004 sheet: -0.14 (0.19), residues: 642 loop : -1.13 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 239 TYR 0.017 0.002 TYR C 244 PHE 0.018 0.002 PHE D 516 TRP 0.007 0.002 TRP E 476 HIS 0.004 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.24 (36072) covalent geometry : angle 0.61673 / 0.31 (48786) hydrogen bonds : bond 0.06218 / 4.10 ( 1524) hydrogen bonds : angle 3.95034 / 2.73 ( 4446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 1.296 Fit side-chains REVERT: A 46 MET cc_start: 0.6456 (mtp) cc_final: 0.6192 (mtp) REVERT: B 46 MET cc_start: 0.6758 (ttm) cc_final: 0.5704 (mtp) REVERT: B 484 ASP cc_start: 0.8033 (p0) cc_final: 0.7697 (m-30) REVERT: C 46 MET cc_start: 0.6520 (mtp) cc_final: 0.6269 (mtp) REVERT: C 442 MET cc_start: 0.7246 (ttm) cc_final: 0.6874 (tmm) REVERT: C 484 ASP cc_start: 0.8021 (p0) cc_final: 0.7621 (m-30) REVERT: C 614 LYS cc_start: 0.6922 (mmtm) cc_final: 0.6717 (mmmt) REVERT: D 46 MET cc_start: 0.6452 (mtp) cc_final: 0.6187 (mtp) REVERT: E 46 MET cc_start: 0.6752 (ttm) cc_final: 0.5691 (mtp) REVERT: E 484 ASP cc_start: 0.8036 (p0) cc_final: 0.7702 (m-30) REVERT: F 46 MET cc_start: 0.6517 (mtp) cc_final: 0.6264 (mtp) REVERT: F 442 MET cc_start: 0.7245 (ttm) cc_final: 0.6872 (tmm) REVERT: F 484 ASP cc_start: 0.8018 (p0) cc_final: 0.7617 (m-30) REVERT: F 614 LYS cc_start: 0.6920 (mmtm) cc_final: 0.6716 (mmmt) outliers start: 32 outliers final: 30 residues processed: 272 average time/residue: 0.2029 time to fit residues: 94.1771 Evaluate side-chains 266 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 303 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 0.0060 chunk 286 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 345 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.172347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119544 restraints weight = 44104.098| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.69 r_work: 0.3028 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 36072 Z= 0.177 Angle : 0.562 8.490 48786 Z= 0.281 Chirality : 0.045 0.137 5478 Planarity : 0.004 0.042 6420 Dihedral : 6.371 59.504 4980 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.89 % Allowed : 9.56 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4452 helix: 1.25 (0.12), residues: 1998 sheet: -0.08 (0.19), residues: 642 loop : -1.05 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 239 TYR 0.014 0.002 TYR C 244 PHE 0.014 0.001 PHE B 516 TRP 0.007 0.001 TRP D 454 HIS 0.003 0.001 HIS C 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (36072) covalent geometry : angle 0.56241 / 0.28 (48786) hydrogen bonds : bond 0.05299 / 3.50 ( 1524) hydrogen bonds : angle 3.85317 / 2.67 ( 4446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 1.406 Fit side-chains REVERT: A 46 MET cc_start: 0.6461 (mtp) cc_final: 0.6200 (mtp) REVERT: A 344 MET cc_start: 0.9286 (mtp) cc_final: 0.9022 (mtm) REVERT: B 46 MET cc_start: 0.6799 (ttm) cc_final: 0.5731 (mtp) REVERT: B 484 ASP cc_start: 0.7952 (p0) cc_final: 0.7622 (m-30) REVERT: C 46 MET cc_start: 0.6592 (mtp) cc_final: 0.6318 (mtp) REVERT: C 442 MET cc_start: 0.7082 (ttm) cc_final: 0.6753 (tmm) REVERT: C 484 ASP cc_start: 0.7954 (p0) cc_final: 0.7569 (m-30) REVERT: C 614 LYS cc_start: 0.7028 (mmtm) cc_final: 0.6739 (mmmt) REVERT: D 46 MET cc_start: 0.6459 (mtp) cc_final: 0.6196 (mtp) REVERT: D 344 MET cc_start: 0.9287 (mtp) cc_final: 0.9020 (mtm) REVERT: E 46 MET cc_start: 0.6799 (ttm) cc_final: 0.5731 (mtp) REVERT: E 484 ASP cc_start: 0.7963 (p0) cc_final: 0.7626 (m-30) REVERT: F 46 MET cc_start: 0.6587 (mtp) cc_final: 0.6310 (mtp) REVERT: F 442 MET cc_start: 0.7084 (ttm) cc_final: 0.6752 (tmm) REVERT: F 484 ASP cc_start: 0.7958 (p0) cc_final: 0.7571 (m-30) REVERT: F 614 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6726 (mmmt) outliers start: 34 outliers final: 32 residues processed: 268 average time/residue: 0.1912 time to fit residues: 88.7939 Evaluate side-chains 268 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 356 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 268 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 391 optimal weight: 0.1980 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121925 restraints weight = 44178.293| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.66 r_work: 0.3075 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36072 Z= 0.109 Angle : 0.505 9.093 48786 Z= 0.251 Chirality : 0.043 0.130 5478 Planarity : 0.004 0.043 6420 Dihedral : 6.194 59.708 4980 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.63 % Allowed : 10.04 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4452 helix: 1.44 (0.12), residues: 2010 sheet: 0.20 (0.20), residues: 636 loop : -0.89 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 239 TYR 0.010 0.001 TYR F 244 PHE 0.010 0.001 PHE C 152 TRP 0.010 0.001 TRP C 454 HIS 0.002 0.000 HIS B 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (36072) covalent geometry : angle 0.50517 / 0.25 (48786) hydrogen bonds : bond 0.03968 / 2.62 ( 1524) hydrogen bonds : angle 3.65178 / 2.53 ( 4446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8904 Ramachandran restraints generated. 4452 Oldfield, 0 Emsley, 4452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 1.413 Fit side-chains REVERT: A 46 MET cc_start: 0.6486 (mtp) cc_final: 0.6227 (mtp) REVERT: B 46 MET cc_start: 0.6810 (ttm) cc_final: 0.5730 (mtp) REVERT: B 484 ASP cc_start: 0.7950 (p0) cc_final: 0.7735 (m-30) REVERT: C 46 MET cc_start: 0.6536 (mtp) cc_final: 0.6261 (mtp) REVERT: C 442 MET cc_start: 0.7076 (ttm) cc_final: 0.6757 (tmm) REVERT: C 484 ASP cc_start: 0.7947 (p0) cc_final: 0.7596 (m-30) REVERT: D 46 MET cc_start: 0.6483 (mtp) cc_final: 0.6225 (mtp) REVERT: E 46 MET cc_start: 0.6811 (ttm) cc_final: 0.5723 (mtp) REVERT: E 484 ASP cc_start: 0.7959 (p0) cc_final: 0.7734 (m-30) REVERT: F 46 MET cc_start: 0.6532 (mtp) cc_final: 0.6254 (mtp) REVERT: F 442 MET cc_start: 0.7080 (ttm) cc_final: 0.6755 (tmm) REVERT: F 484 ASP cc_start: 0.7936 (p0) cc_final: 0.7589 (m-30) outliers start: 24 outliers final: 22 residues processed: 266 average time/residue: 0.1863 time to fit residues: 85.1980 Evaluate side-chains 256 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 705 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 276 optimal weight: 3.9990 chunk 135 optimal weight: 0.0060 chunk 348 optimal weight: 1.9990 chunk 406 optimal weight: 0.7980 chunk 266 optimal weight: 0.0870 chunk 156 optimal weight: 0.0270 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 164 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 367 optimal weight: 0.9990 overall best weight: 0.3232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 HIS C 90 ASN D 384 HIS F 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.177736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126861 restraints weight = 43957.975| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.52 r_work: 0.3158 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 36072 Z= 0.084 Angle : 0.474 11.761 48786 Z= 0.234 Chirality : 0.042 0.127 5478 Planarity : 0.004 0.044 6420 Dihedral : 5.928 58.629 4980 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.42 % Allowed : 10.35 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4452 helix: 1.72 (0.12), residues: 2004 sheet: 0.46 (0.20), residues: 636 loop : -0.75 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 159 TYR 0.006 0.001 TYR E 203 PHE 0.011 0.001 PHE E 563 TRP 0.013 0.001 TRP C 454 HIS 0.008 0.000 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.08 (36072) covalent geometry : angle 0.47410 / 0.23 (48786) hydrogen bonds : bond 0.02967 / 1.96 ( 1524) hydrogen bonds : angle 3.47401 / 2.41 ( 4446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7402.27 seconds wall clock time: 127 minutes 42.84 seconds (7662.84 seconds total)