Starting phenix.real_space_refine on Fri Mar 6 23:32:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vcx_31899/03_2026/7vcx_31899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vcx_31899/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vcx_31899/03_2026/7vcx_31899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vcx_31899/03_2026/7vcx_31899.map" model { file = "/net/cci-nas-00/data/ceres_data/7vcx_31899/03_2026/7vcx_31899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vcx_31899/03_2026/7vcx_31899.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.82, per 1000 atoms: 0.19 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 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: 1.56 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: 8.87 Time building geometry restraints manager: 3.98 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 - 11.19: 19664 11.19 - 22.37: 2114 22.37 - 33.56: 476 33.56 - 44.74: 132 44.74 - 55.93: 78 Dihedral angle restraints: 22464 sinusoidal: 9570 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 22461 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: 0.10 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.510 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 10.491 55.929 14100 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 covalent geometry : bond 0.01580 (36072) covalent geometry : angle 1.21598 (48786) hydrogen bonds : bond 0.18554 ( 1524) hydrogen bonds : angle 5.72403 ( 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 : 1.352 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: 0.2984 time to fit residues: 219.8580 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 : 1.327 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4063 r_free = 0.4063 target = 0.174291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122063 restraints weight = 43897.715| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.50 r_work: 0.3097 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1961 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= 0.124 Angle : 0.577 5.429 48786 Z= 0.301 Chirality : 0.044 0.157 5478 Planarity : 0.006 0.052 6420 Dihedral : 8.305 58.175 5112 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.84 % Allowed : 4.40 % Favored : 94.76 % 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: -1.35 (0.12), residues: 4452 helix: -0.16 (0.11), residues: 1998 sheet: -0.29 (0.18), residues: 612 loop : -1.89 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 225 TYR 0.013 0.001 TYR E 203 PHE 0.013 0.001 PHE B 152 TRP 0.012 0.002 TRP A 454 HIS 0.004 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00269 (36072) covalent geometry : angle 0.57660 (48786) hydrogen bonds : bond 0.05263 ( 1524) hydrogen bonds : angle 4.19908 ( 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 368 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 336 time to evaluate : 1.476 Fit side-chains REVERT: A 46 MET cc_start: 0.6648 (mtp) cc_final: 0.6351 (mtp) REVERT: A 678 MET cc_start: 0.8284 (mmm) cc_final: 0.8078 (mmp) REVERT: B 46 MET cc_start: 0.6609 (mtp) cc_final: 0.6282 (mtp) REVERT: B 484 ASP cc_start: 0.7877 (p0) cc_final: 0.7654 (p0) REVERT: C 46 MET cc_start: 0.6473 (mtp) cc_final: 0.6165 (mtp) REVERT: C 484 ASP cc_start: 0.8008 (p0) cc_final: 0.7787 (p0) REVERT: C 693 ARG cc_start: 0.8527 (tpp80) cc_final: 0.8307 (mtp85) REVERT: D 46 MET cc_start: 0.6644 (mtp) cc_final: 0.6350 (mtp) REVERT: D 678 MET cc_start: 0.8281 (mmm) cc_final: 0.8073 (mmp) REVERT: E 46 MET cc_start: 0.6606 (mtp) cc_final: 0.6278 (mtp) REVERT: E 484 ASP cc_start: 0.7853 (p0) cc_final: 0.7639 (p0) REVERT: F 46 MET cc_start: 0.6473 (mtp) cc_final: 0.6165 (mtp) REVERT: F 484 ASP cc_start: 0.8028 (p0) cc_final: 0.7798 (p0) REVERT: F 693 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8303 (mtp85) outliers start: 32 outliers final: 8 residues processed: 364 average time/residue: 0.2422 time to fit residues: 141.2714 Evaluate side-chains 261 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 253 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 416 SER 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 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: 2.9990 chunk 23 optimal weight: 0.8980 chunk 369 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 433 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 365 optimal weight: 20.0000 chunk 440 optimal weight: 0.0010 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123198 restraints weight = 44080.895| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.51 r_work: 0.3122 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36072 Z= 0.101 Angle : 0.498 7.318 48786 Z= 0.254 Chirality : 0.043 0.143 5478 Planarity : 0.005 0.043 6420 Dihedral : 7.515 58.523 5112 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.68 % Allowed : 5.77 % Favored : 93.55 % 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: -0.39 (0.12), residues: 4452 helix: 0.69 (0.12), residues: 2016 sheet: -0.08 (0.19), residues: 642 loop : -1.39 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.012 0.001 TYR E 203 PHE 0.012 0.001 PHE C 152 TRP 0.012 0.002 TRP B 454 HIS 0.002 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00224 (36072) covalent geometry : angle 0.49843 (48786) hydrogen bonds : bond 0.04189 ( 1524) hydrogen bonds : angle 3.73260 ( 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: 26 poor density : 282 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6510 (mtp) cc_final: 0.6239 (mtp) REVERT: A 753 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8117 (ptp-170) REVERT: B 46 MET cc_start: 0.6602 (mtp) cc_final: 0.6284 (mtp) REVERT: C 46 MET cc_start: 0.6503 (mtp) cc_final: 0.6278 (mtp) REVERT: C 668 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8518 (mmtp) REVERT: D 46 MET cc_start: 0.6506 (mtp) cc_final: 0.6235 (mtp) REVERT: D 753 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8091 (ptp-170) REVERT: E 46 MET cc_start: 0.6611 (mtp) cc_final: 0.6291 (mtp) REVERT: F 46 MET cc_start: 0.6507 (mtp) cc_final: 0.6282 (mtp) REVERT: F 668 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8535 (mmtp) outliers start: 26 outliers final: 4 residues processed: 300 average time/residue: 0.2275 time to fit residues: 112.1345 Evaluate side-chains 257 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 249 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 ARG Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain F residue 96 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: 9.9990 chunk 310 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 424 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 407 optimal weight: 10.0000 chunk 392 optimal weight: 0.0870 chunk 362 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 379 optimal weight: 30.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN B 398 GLN C 398 GLN D 398 GLN E 398 GLN F 398 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117453 restraints weight = 44191.621| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.42 r_work: 0.3020 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 36072 Z= 0.274 Angle : 0.665 7.905 48786 Z= 0.336 Chirality : 0.048 0.148 5478 Planarity : 0.005 0.064 6420 Dihedral : 7.591 59.632 5112 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.05 % Allowed : 6.71 % Favored : 92.24 % 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: 0.76 (0.12), residues: 2010 sheet: -0.17 (0.19), residues: 636 loop : -1.41 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 567 TYR 0.030 0.003 TYR E 495 PHE 0.023 0.002 PHE D 267 TRP 0.010 0.002 TRP D 476 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00689 (36072) covalent geometry : angle 0.66533 (48786) hydrogen bonds : bond 0.06975 ( 1524) hydrogen bonds : angle 4.08633 ( 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 294 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6460 (mtp) cc_final: 0.6199 (mtp) REVERT: A 753 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8163 (ptp-170) REVERT: B 46 MET cc_start: 0.6541 (mtp) cc_final: 0.6214 (mtp) REVERT: C 46 MET cc_start: 0.6538 (mtp) cc_final: 0.6326 (mtp) REVERT: D 46 MET cc_start: 0.6465 (mtp) cc_final: 0.6207 (mtp) REVERT: D 753 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8174 (ptp-170) REVERT: E 46 MET cc_start: 0.6544 (mtp) cc_final: 0.6216 (mtp) REVERT: F 46 MET cc_start: 0.6540 (mtp) cc_final: 0.6328 (mtp) outliers start: 40 outliers final: 28 residues processed: 282 average time/residue: 0.2203 time to fit residues: 103.5015 Evaluate side-chains 280 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU 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 753 ARG Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 668 LYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 92 LEU 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 753 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 668 LYS Chi-restraints excluded: chain F residue 761 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 428 optimal weight: 1.9990 chunk 297 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 430 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 368 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 313 optimal weight: 0.0050 chunk 265 optimal weight: 8.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120525 restraints weight = 43870.211| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.51 r_work: 0.3068 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36072 Z= 0.128 Angle : 0.520 7.296 48786 Z= 0.264 Chirality : 0.043 0.133 5478 Planarity : 0.004 0.043 6420 Dihedral : 7.362 59.967 5112 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.94 % Allowed : 7.15 % Favored : 91.90 % 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: 1.13 (0.12), residues: 2016 sheet: -0.06 (0.19), residues: 642 loop : -1.19 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.011 0.001 TYR F 244 PHE 0.014 0.001 PHE F 230 TRP 0.009 0.001 TRP A 454 HIS 0.002 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00309 (36072) covalent geometry : angle 0.51974 (48786) hydrogen bonds : bond 0.04697 ( 1524) hydrogen bonds : angle 3.78969 ( 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: 36 poor density : 246 time to evaluate : 1.410 Fit side-chains REVERT: A 46 MET cc_start: 0.6578 (mtp) cc_final: 0.6311 (mtp) REVERT: B 614 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7768 (mmtm) REVERT: C 46 MET cc_start: 0.6526 (mtp) cc_final: 0.6297 (mtp) REVERT: D 46 MET cc_start: 0.6574 (mtp) cc_final: 0.6309 (mtp) REVERT: E 614 LYS cc_start: 0.7994 (mmpt) cc_final: 0.7766 (mmtm) REVERT: F 46 MET cc_start: 0.6533 (mtp) cc_final: 0.6302 (mtp) outliers start: 36 outliers final: 20 residues processed: 276 average time/residue: 0.2116 time to fit residues: 99.9556 Evaluate side-chains 254 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 94 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 668 LYS 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 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 94 VAL Chi-restraints excluded: chain F residue 96 LEU 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: 4.9990 chunk 15 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 441 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 166 optimal weight: 0.9980 chunk 340 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 320 optimal weight: 0.3980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120159 restraints weight = 44190.106| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.42 r_work: 0.3057 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2659 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= 0.162 Angle : 0.537 6.645 48786 Z= 0.270 Chirality : 0.044 0.134 5478 Planarity : 0.004 0.043 6420 Dihedral : 7.237 58.212 5112 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.28 % Allowed : 7.63 % Favored : 91.09 % 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: 0.14 (0.13), residues: 4452 helix: 1.20 (0.12), residues: 2016 sheet: -0.01 (0.19), residues: 642 loop : -1.12 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 225 TYR 0.013 0.002 TYR F 244 PHE 0.014 0.002 PHE B 516 TRP 0.007 0.001 TRP D 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00400 (36072) covalent geometry : angle 0.53681 (48786) hydrogen bonds : bond 0.05086 ( 1524) hydrogen bonds : angle 3.78156 ( 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 295 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 1.230 Fit side-chains REVERT: A 46 MET cc_start: 0.6564 (mtp) cc_final: 0.6310 (mtp) REVERT: B 46 MET cc_start: 0.6792 (ttm) cc_final: 0.5814 (mtp) REVERT: B 484 ASP cc_start: 0.7927 (p0) cc_final: 0.7571 (m-30) REVERT: C 46 MET cc_start: 0.6479 (mtp) cc_final: 0.6250 (mtp) REVERT: D 46 MET cc_start: 0.6563 (mtp) cc_final: 0.6310 (mtp) REVERT: E 46 MET cc_start: 0.6786 (ttm) cc_final: 0.5807 (mtp) REVERT: E 484 ASP cc_start: 0.7933 (p0) cc_final: 0.7575 (m-30) REVERT: F 46 MET cc_start: 0.6481 (mtp) cc_final: 0.6253 (mtp) outliers start: 49 outliers final: 36 residues processed: 284 average time/residue: 0.2069 time to fit residues: 100.2671 Evaluate side-chains 273 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 94 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 94 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 417 GLU 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 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 94 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 94 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU 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: 0.9990 chunk 234 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 318 optimal weight: 0.5980 chunk 437 optimal weight: 6.9990 chunk 341 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 322 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 340 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.171695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119558 restraints weight = 44222.074| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.42 r_work: 0.3051 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36072 Z= 0.174 Angle : 0.553 8.264 48786 Z= 0.276 Chirality : 0.045 0.135 5478 Planarity : 0.004 0.043 6420 Dihedral : 7.196 58.549 5112 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.23 % Allowed : 8.33 % Favored : 90.44 % 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: 0.21 (0.13), residues: 4452 helix: 1.23 (0.12), residues: 2004 sheet: 0.00 (0.19), residues: 642 loop : -1.03 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 225 TYR 0.014 0.002 TYR F 244 PHE 0.019 0.002 PHE F 230 TRP 0.007 0.001 TRP D 454 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00433 (36072) covalent geometry : angle 0.55312 (48786) hydrogen bonds : bond 0.05242 ( 1524) hydrogen bonds : angle 3.78873 ( 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 287 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 1.482 Fit side-chains REVERT: A 46 MET cc_start: 0.6519 (mtp) cc_final: 0.6261 (mtp) REVERT: B 46 MET cc_start: 0.6826 (ttm) cc_final: 0.5769 (mtp) REVERT: B 421 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7408 (tp40) REVERT: B 484 ASP cc_start: 0.7966 (p0) cc_final: 0.7650 (m-30) REVERT: C 46 MET cc_start: 0.6548 (mtp) cc_final: 0.6300 (mtp) REVERT: C 442 MET cc_start: 0.7296 (ttm) cc_final: 0.6962 (tmm) REVERT: C 484 ASP cc_start: 0.7953 (p0) cc_final: 0.7597 (m-30) REVERT: D 46 MET cc_start: 0.6518 (mtp) cc_final: 0.6261 (mtp) REVERT: E 46 MET cc_start: 0.6826 (ttm) cc_final: 0.5765 (mtp) REVERT: E 421 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7411 (tp40) REVERT: E 484 ASP cc_start: 0.7967 (p0) cc_final: 0.7654 (m-30) REVERT: F 46 MET cc_start: 0.6550 (mtp) cc_final: 0.6301 (mtp) REVERT: F 442 MET cc_start: 0.7277 (ttm) cc_final: 0.6954 (tmm) REVERT: F 484 ASP cc_start: 0.7960 (p0) cc_final: 0.7599 (m-30) outliers start: 47 outliers final: 35 residues processed: 277 average time/residue: 0.2005 time to fit residues: 96.6076 Evaluate side-chains 268 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 231 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain B residue 340 HIS Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 340 HIS 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 705 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 416 optimal weight: 0.2980 chunk 232 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 322 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 435 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 344 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS C 340 HIS E 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118517 restraints weight = 43832.488| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.59 r_work: 0.3008 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36072 Z= 0.219 Angle : 0.594 7.610 48786 Z= 0.297 Chirality : 0.046 0.138 5478 Planarity : 0.005 0.042 6420 Dihedral : 7.246 59.083 5112 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.05 % Allowed : 8.70 % Favored : 90.25 % 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: 0.12 (0.13), residues: 4452 helix: 1.18 (0.12), residues: 1998 sheet: 0.01 (0.19), residues: 636 loop : -1.11 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 567 TYR 0.016 0.002 TYR E 495 PHE 0.017 0.002 PHE D 516 TRP 0.006 0.002 TRP A 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00550 (36072) covalent geometry : angle 0.59371 (48786) hydrogen bonds : bond 0.05890 ( 1524) hydrogen bonds : angle 3.89123 ( 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 279 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 1.384 Fit side-chains REVERT: A 46 MET cc_start: 0.6490 (mtp) cc_final: 0.6228 (mtp) REVERT: B 46 MET cc_start: 0.6791 (ttm) cc_final: 0.5712 (mtp) REVERT: B 421 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: B 484 ASP cc_start: 0.7996 (p0) cc_final: 0.7647 (m-30) REVERT: C 46 MET cc_start: 0.6516 (mtp) cc_final: 0.6253 (mtp) REVERT: C 442 MET cc_start: 0.7239 (ttm) cc_final: 0.6880 (tmm) REVERT: C 484 ASP cc_start: 0.8020 (p0) cc_final: 0.7591 (m-30) REVERT: C 608 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8910 (mtp) REVERT: D 46 MET cc_start: 0.6483 (mtp) cc_final: 0.6223 (mtp) REVERT: E 46 MET cc_start: 0.6791 (ttm) cc_final: 0.5712 (mtp) REVERT: E 421 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7341 (tp40) REVERT: E 484 ASP cc_start: 0.8000 (p0) cc_final: 0.7651 (m-30) REVERT: F 46 MET cc_start: 0.6513 (mtp) cc_final: 0.6251 (mtp) REVERT: F 442 MET cc_start: 0.7233 (ttm) cc_final: 0.6877 (tmm) REVERT: F 484 ASP cc_start: 0.8004 (p0) cc_final: 0.7583 (m-30) REVERT: F 608 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8917 (mtp) outliers start: 40 outliers final: 34 residues processed: 269 average time/residue: 0.2025 time to fit residues: 93.0845 Evaluate side-chains 268 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 458 GLN Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 608 MET 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 458 GLN Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 608 MET 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: 6.9990 chunk 203 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 345 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119376 restraints weight = 43797.559| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.67 r_work: 0.3024 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 36072 Z= 0.185 Angle : 0.567 8.628 48786 Z= 0.283 Chirality : 0.045 0.136 5478 Planarity : 0.004 0.042 6420 Dihedral : 7.185 59.049 5112 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.00 % Allowed : 8.99 % Favored : 90.02 % 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: 0.20 (0.13), residues: 4452 helix: 1.24 (0.12), residues: 1998 sheet: 0.04 (0.19), residues: 636 loop : -1.06 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 239 TYR 0.014 0.002 TYR F 244 PHE 0.016 0.002 PHE E 516 TRP 0.007 0.001 TRP A 454 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00461 (36072) covalent geometry : angle 0.56671 (48786) hydrogen bonds : bond 0.05366 ( 1524) hydrogen bonds : angle 3.84819 ( 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 278 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 1.287 Fit side-chains REVERT: A 46 MET cc_start: 0.6489 (mtp) cc_final: 0.6233 (mtp) REVERT: B 46 MET cc_start: 0.6861 (ttm) cc_final: 0.5803 (mtp) REVERT: B 421 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7288 (tp40) REVERT: B 484 ASP cc_start: 0.7966 (p0) cc_final: 0.7634 (m-30) REVERT: C 46 MET cc_start: 0.6580 (mtp) cc_final: 0.6305 (mtp) REVERT: C 442 MET cc_start: 0.7078 (ttm) cc_final: 0.6757 (tmm) REVERT: C 484 ASP cc_start: 0.7968 (p0) cc_final: 0.7567 (m-30) REVERT: C 564 ASP cc_start: 0.8378 (m-30) cc_final: 0.8176 (m-30) REVERT: C 608 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8868 (mtp) REVERT: C 614 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7946 (mmtm) REVERT: D 46 MET cc_start: 0.6487 (mtp) cc_final: 0.6230 (mtp) REVERT: E 46 MET cc_start: 0.6858 (ttm) cc_final: 0.5797 (mtp) REVERT: E 421 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7293 (tp40) REVERT: E 484 ASP cc_start: 0.7971 (p0) cc_final: 0.7638 (m-30) REVERT: F 46 MET cc_start: 0.6578 (mtp) cc_final: 0.6301 (mtp) REVERT: F 442 MET cc_start: 0.7085 (ttm) cc_final: 0.6756 (tmm) REVERT: F 484 ASP cc_start: 0.7957 (p0) cc_final: 0.7561 (m-30) REVERT: F 564 ASP cc_start: 0.8396 (m-30) cc_final: 0.8192 (m-30) REVERT: F 614 LYS cc_start: 0.8191 (mmpt) cc_final: 0.7945 (mmtm) outliers start: 38 outliers final: 32 residues processed: 268 average time/residue: 0.1975 time to fit residues: 91.5635 Evaluate side-chains 273 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 94 VAL Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 608 MET 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 94 VAL Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 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 356 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 287 optimal weight: 6.9990 chunk 360 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 391 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119302 restraints weight = 44145.753| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.70 r_work: 0.3037 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36072 Z= 0.146 Angle : 0.534 9.412 48786 Z= 0.266 Chirality : 0.044 0.135 5478 Planarity : 0.004 0.043 6420 Dihedral : 7.075 59.005 5112 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.84 % Allowed : 9.12 % Favored : 90.04 % 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: 0.35 (0.13), residues: 4452 helix: 1.36 (0.12), residues: 1998 sheet: 0.08 (0.19), residues: 642 loop : -0.97 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 700 TYR 0.012 0.001 TYR F 244 PHE 0.013 0.001 PHE E 516 TRP 0.007 0.001 TRP C 454 HIS 0.002 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00361 (36072) covalent geometry : angle 0.53413 (48786) hydrogen bonds : bond 0.04774 ( 1524) hydrogen bonds : angle 3.75269 ( 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 275 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.342 Fit side-chains REVERT: A 46 MET cc_start: 0.6491 (mtp) cc_final: 0.6232 (mtp) REVERT: B 46 MET cc_start: 0.6862 (ttm) cc_final: 0.5802 (mtp) REVERT: B 421 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7215 (tp40) REVERT: B 484 ASP cc_start: 0.7940 (p0) cc_final: 0.7619 (m-30) REVERT: C 46 MET cc_start: 0.6577 (mtp) cc_final: 0.6306 (mtp) REVERT: C 442 MET cc_start: 0.6957 (ttm) cc_final: 0.6654 (tmm) REVERT: C 484 ASP cc_start: 0.7989 (p0) cc_final: 0.7596 (m-30) REVERT: C 564 ASP cc_start: 0.8394 (m-30) cc_final: 0.8167 (m-30) REVERT: C 614 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7917 (mmtm) REVERT: D 46 MET cc_start: 0.6486 (mtp) cc_final: 0.6229 (mtp) REVERT: E 46 MET cc_start: 0.6863 (ttm) cc_final: 0.5797 (mtp) REVERT: E 421 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7278 (tp40) REVERT: E 484 ASP cc_start: 0.7940 (p0) cc_final: 0.7617 (m-30) REVERT: F 46 MET cc_start: 0.6579 (mtp) cc_final: 0.6305 (mtp) REVERT: F 442 MET cc_start: 0.6961 (ttm) cc_final: 0.6657 (tmm) REVERT: F 484 ASP cc_start: 0.7975 (p0) cc_final: 0.7591 (m-30) REVERT: F 564 ASP cc_start: 0.8404 (m-30) cc_final: 0.8174 (m-30) REVERT: F 614 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7908 (mmtm) outliers start: 32 outliers final: 27 residues processed: 267 average time/residue: 0.2016 time to fit residues: 92.7310 Evaluate side-chains 266 residues out of total 3816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 96 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 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 94 VAL Chi-restraints excluded: chain E residue 421 GLN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 96 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 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: 0.3980 chunk 348 optimal weight: 0.0670 chunk 406 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 156 optimal weight: 0.0070 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS D 384 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123961 restraints weight = 43724.777| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.60 r_work: 0.3108 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3188 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= 0.088 Angle : 0.483 10.694 48786 Z= 0.239 Chirality : 0.042 0.130 5478 Planarity : 0.004 0.044 6420 Dihedral : 6.846 58.260 5112 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.37 % Allowed : 9.83 % Favored : 89.81 % 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: 0.66 (0.13), residues: 4452 helix: 1.60 (0.12), residues: 2004 sheet: 0.35 (0.20), residues: 636 loop : -0.84 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 487 TYR 0.007 0.001 TYR F 244 PHE 0.013 0.001 PHE C 563 TRP 0.010 0.001 TRP E 454 HIS 0.001 0.000 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00198 (36072) covalent geometry : angle 0.48261 (48786) hydrogen bonds : bond 0.03280 ( 1524) hydrogen bonds : angle 3.55409 ( 4446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7739.10 seconds wall clock time: 133 minutes 10.81 seconds (7990.81 seconds total)