Starting phenix.real_space_refine on Tue Sep 15 00:41:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.map" model { file = "/net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftn_3299/09_2026/5ftn_3299.cif" } resolution = 3.3 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= 0.006 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 192 5.16 5 C 21882 2.51 5 N 6144 2.21 5 O 6690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34956 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5762 Classifications: {'peptide': 737} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 697} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 6.77, per 1000 atoms: 0.19 Number of scatterers: 34956 At special positions: 0 Unit cell: (165.62, 171.028, 123.032, 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 192 16.00 P 36 15.00 Mg 12 11.99 O 6690 8.00 N 6144 7.00 C 21882 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 24 sheets defined 46.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.623A pdb=" N GLU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.960A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.819A pdb=" N GLU A 132 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.718A pdb=" N PHE A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.788A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.611A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.627A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 4.347A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.645A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.418A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.754A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.586A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.717A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.500A pdb=" N ARG A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.159A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.539A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 507 removed outlier: 3.595A pdb=" N GLU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 500 - end of helix removed outlier: 4.368A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.639A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 550 removed outlier: 4.063A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.904A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 removed outlier: 4.171A pdb=" N ILE A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.659A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 3.909A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 3.654A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 743 removed outlier: 4.080A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.830A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.624A pdb=" N GLU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.960A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.819A pdb=" N GLU B 132 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.718A pdb=" N PHE B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.788A pdb=" N GLU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.612A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.627A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.348A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.645A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.418A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.754A pdb=" N ILE B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.585A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.717A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.733A pdb=" N LYS B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 4.159A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 removed outlier: 3.539A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 507 removed outlier: 3.595A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 500 - end of helix removed outlier: 4.368A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 504 " --> pdb=" O PRO B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.639A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 550 removed outlier: 4.063A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.903A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 removed outlier: 4.170A pdb=" N ILE B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.658A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 677 removed outlier: 3.909A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 3.654A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 4.079A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 761 removed outlier: 3.830A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.624A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.960A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.820A pdb=" N GLU C 132 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.718A pdb=" N PHE C 139 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 199 removed outlier: 3.788A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 220 removed outlier: 3.612A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.627A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.348A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.645A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.418A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.753A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.586A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.716A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 removed outlier: 3.500A pdb=" N ARG C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 425 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 4.158A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.539A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 507 removed outlier: 3.596A pdb=" N GLU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Proline residue: C 500 - end of helix removed outlier: 4.368A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.639A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 4.063A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.904A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 removed outlier: 4.171A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.659A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 677 removed outlier: 3.909A pdb=" N LEU C 675 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 3.654A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 4.080A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 761 removed outlier: 3.830A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.623A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.960A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.819A pdb=" N GLU D 132 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.718A pdb=" N PHE D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 199 removed outlier: 3.788A pdb=" N GLU D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 removed outlier: 3.611A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.627A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.347A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.645A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 287 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.418A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.754A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.586A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.717A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.500A pdb=" N ARG D 424 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 425 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 4.159A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 removed outlier: 3.539A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 507 removed outlier: 3.595A pdb=" N GLU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Proline residue: D 500 - end of helix removed outlier: 4.368A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU D 504 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.639A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 550 removed outlier: 4.063A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 553 No H-bonds generated for 'chain 'D' and resid 551 through 553' Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.904A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 removed outlier: 4.170A pdb=" N ILE D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.659A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 removed outlier: 3.909A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 3.654A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 4.080A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 761 removed outlier: 3.831A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.624A pdb=" N GLU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.960A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.820A pdb=" N GLU E 132 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.718A pdb=" N PHE E 139 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.788A pdb=" N GLU E 195 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 220 removed outlier: 3.612A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.626A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.348A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.645A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.417A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.754A pdb=" N ILE E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.586A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.717A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 425 removed outlier: 3.501A pdb=" N ARG E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 425 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 4.159A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.539A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 507 removed outlier: 3.594A pdb=" N GLU E 491 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Proline residue: E 500 - end of helix removed outlier: 4.368A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.639A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 550 removed outlier: 4.063A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 553 No H-bonds generated for 'chain 'E' and resid 551 through 553' Processing helix chain 'E' and resid 556 through 569 removed outlier: 3.903A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 584 removed outlier: 4.171A pdb=" N ILE E 582 " --> pdb=" O GLU E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 610 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.659A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 677 removed outlier: 3.909A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 removed outlier: 3.654A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 704 " --> pdb=" O ARG E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 removed outlier: 4.080A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 761 removed outlier: 3.830A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.624A pdb=" N GLU F 48 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 removed outlier: 3.960A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.820A pdb=" N GLU F 132 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.719A pdb=" N PHE F 139 " --> pdb=" O LYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 199 removed outlier: 3.788A pdb=" N GLU F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 220 removed outlier: 3.612A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.627A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.348A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.644A pdb=" N LEU F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.418A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 333 removed outlier: 3.754A pdb=" N ILE F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.586A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.716A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.500A pdb=" N ARG F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 removed outlier: 4.159A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 removed outlier: 3.539A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 507 removed outlier: 3.596A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Proline residue: F 500 - end of helix removed outlier: 4.368A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F 504 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.639A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 550 removed outlier: 4.063A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 553 No H-bonds generated for 'chain 'F' and resid 551 through 553' Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.904A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 removed outlier: 4.171A pdb=" N ILE F 582 " --> pdb=" O GLU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 610 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.658A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 677 removed outlier: 3.910A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 removed outlier: 3.655A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 4.080A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 removed outlier: 3.831A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.907A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.765A pdb=" N LEU A 117 " --> pdb=" O LYS A 164 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 265 through 270 Processing sheet with id=AD, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.561A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.907A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.765A pdb=" N LEU B 117 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 265 through 270 Processing sheet with id=BD, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.562A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.907A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.765A pdb=" N LEU C 117 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 265 through 270 Processing sheet with id=CD, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.562A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.907A pdb=" N LEU D 26 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 117 through 118 removed outlier: 3.765A pdb=" N LEU D 117 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 265 through 270 Processing sheet with id=DD, first strand: chain 'D' and resid 538 through 543 removed outlier: 3.561A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.906A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.765A pdb=" N LEU E 117 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 265 through 270 Processing sheet with id=ED, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.561A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 25 through 26 removed outlier: 3.907A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 117 through 118 removed outlier: 3.765A pdb=" N LEU F 117 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing sheet with id=FC, first strand: chain 'F' and resid 265 through 270 Processing sheet with id=FD, first strand: chain 'F' and resid 538 through 543 removed outlier: 3.561A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3405 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: 6.29 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 13719 1.39 - 1.56: 21435 1.56 - 1.73: 72 1.73 - 1.90: 288 1.90 - 2.07: 12 Bond restraints: 35526 Sorted by residual: bond pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 AGS E 901 " pdb=" C5 AGS E 901 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.92e+01 bond pdb=" C4 AGS C 902 " pdb=" C5 AGS C 902 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS F 902 " pdb=" C5 AGS F 902 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 AGS A 902 " pdb=" C5 AGS A 902 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.85e+01 ... (remaining 35521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 46421 2.95 - 5.90: 1399 5.90 - 8.85: 174 8.85 - 11.79: 36 11.79 - 14.74: 24 Bond angle restraints: 48054 Sorted by residual: angle pdb=" C5 AGS F 901 " pdb=" C4 AGS F 901 " pdb=" N3 AGS F 901 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS C 901 " pdb=" C4 AGS C 901 " pdb=" N3 AGS C 901 " ideal model delta sigma weight residual 126.80 118.63 8.17 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS C 902 " pdb=" C4 AGS C 902 " pdb=" N3 AGS C 902 " ideal model delta sigma weight residual 126.80 118.64 8.16 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS A 901 " pdb=" C4 AGS A 901 " pdb=" N3 AGS A 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N3 AGS D 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 ... (remaining 48049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 20628 15.89 - 31.78: 1002 31.78 - 47.68: 246 47.68 - 63.57: 30 63.57 - 79.46: 30 Dihedral angle restraints: 21936 sinusoidal: 9216 harmonic: 12720 Sorted by residual: dihedral pdb=" CA ALA D 142 " pdb=" C ALA D 142 " pdb=" N TYR D 143 " pdb=" CA TYR D 143 " ideal model delta harmonic sigma weight residual -180.00 -133.07 -46.93 0 5.00e+00 4.00e-02 8.81e+01 dihedral pdb=" CA ALA A 142 " pdb=" C ALA A 142 " pdb=" N TYR A 143 " pdb=" CA TYR A 143 " ideal model delta harmonic sigma weight residual 180.00 -133.07 -46.93 0 5.00e+00 4.00e-02 8.81e+01 dihedral pdb=" CA ALA B 142 " pdb=" C ALA B 142 " pdb=" N TYR B 143 " pdb=" CA TYR B 143 " ideal model delta harmonic sigma weight residual -180.00 -133.08 -46.92 0 5.00e+00 4.00e-02 8.81e+01 ... (remaining 21933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4037 0.070 - 0.141: 1234 0.141 - 0.211: 129 0.211 - 0.282: 24 0.282 - 0.352: 12 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CA LYS E 20 " pdb=" N LYS E 20 " pdb=" C LYS E 20 " pdb=" CB LYS E 20 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS F 20 " pdb=" N LYS F 20 " pdb=" C LYS F 20 " pdb=" CB LYS F 20 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA LYS A 20 " pdb=" N LYS A 20 " pdb=" C LYS A 20 " pdb=" CB LYS A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 5433 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 169 " 0.051 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO B 170 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 169 " -0.051 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO D 170 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 169 " 0.051 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 170 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.042 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 7372 2.77 - 3.30: 34560 3.30 - 3.83: 55172 3.83 - 4.37: 68689 4.37 - 4.90: 109631 Nonbonded interactions: 275424 Sorted by model distance: nonbonded pdb=" NE1 TRP E 476 " pdb=" OE1 GLU E 534 " model vdw 2.234 3.120 nonbonded pdb=" NE1 TRP B 476 " pdb=" OE1 GLU B 534 " model vdw 2.234 3.120 nonbonded pdb=" NE1 TRP C 476 " pdb=" OE1 GLU C 534 " model vdw 2.234 3.120 nonbonded pdb=" NE1 TRP F 476 " pdb=" OE1 GLU F 534 " model vdw 2.234 3.120 nonbonded pdb=" NE1 TRP A 476 " pdb=" OE1 GLU A 534 " model vdw 2.234 3.120 ... (remaining 275419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.040 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.012 0.123 35526 Z= 0.573 Angle : 1.271 14.743 48054 Z= 0.780 Chirality : 0.067 0.352 5436 Planarity : 0.008 0.076 6288 Dihedral : 10.983 79.460 13692 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.39 % Favored : 91.66 % Rotamer: Outliers : 0.32 % Allowed : 2.24 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.72 % 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: -4.38 (0.10), residues: 4398 helix: -3.94 (0.08), residues: 1728 sheet: -1.22 (0.21), residues: 390 loop : -2.31 (0.11), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 766 TYR 0.029 0.004 TYR E 203 PHE 0.028 0.004 PHE B 290 TRP 0.029 0.006 TRP A 551 HIS 0.010 0.002 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.01173 / 0.57 (35526) covalent geometry : angle 1.27131 / 0.78 (48054) hydrogen bonds : bond 0.31955 / 21.28 ( 1189) hydrogen bonds : angle 9.97759 / 6.85 ( 3405) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 798 time to evaluate : 1.300 Fit side-chains REVERT: A 46 MET cc_start: 0.2840 (mtp) cc_final: 0.2455 (mmm) REVERT: A 88 VAL cc_start: 0.4687 (m) cc_final: 0.4452 (m) REVERT: A 204 ASP cc_start: 0.8349 (m-30) cc_final: 0.7846 (p0) REVERT: A 217 LYS cc_start: 0.8964 (mttt) cc_final: 0.8644 (mtpt) REVERT: A 221 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 273 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 320 VAL cc_start: 0.7659 (t) cc_final: 0.7456 (p) REVERT: A 484 ASP cc_start: 0.7891 (p0) cc_final: 0.7635 (p0) REVERT: A 560 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7391 (mtt180) REVERT: A 584 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7149 (tppt) REVERT: A 603 GLN cc_start: 0.8081 (tp40) cc_final: 0.7748 (tt0) REVERT: A 650 GLU cc_start: 0.7535 (pm20) cc_final: 0.7201 (tt0) REVERT: A 651 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7692 (mmmt) REVERT: A 764 GLN cc_start: 0.8020 (mp10) cc_final: 0.7418 (mt0) REVERT: B 46 MET cc_start: 0.2607 (mtp) cc_final: 0.2245 (mmm) REVERT: B 88 VAL cc_start: 0.4727 (m) cc_final: 0.4451 (m) REVERT: B 204 ASP cc_start: 0.8300 (m-30) cc_final: 0.7837 (p0) REVERT: B 217 LYS cc_start: 0.8991 (mttt) cc_final: 0.8689 (mtpt) REVERT: B 273 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 335 LEU cc_start: 0.7518 (mt) cc_final: 0.7315 (mt) REVERT: B 484 ASP cc_start: 0.7850 (p0) cc_final: 0.7516 (p0) REVERT: B 508 MET cc_start: 0.7221 (ptm) cc_final: 0.6559 (ptm) REVERT: B 560 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7132 (mtt180) REVERT: B 584 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7178 (tppt) REVERT: B 603 GLN cc_start: 0.8135 (tp40) cc_final: 0.7835 (mt0) REVERT: B 650 GLU cc_start: 0.7540 (pm20) cc_final: 0.7211 (tt0) REVERT: B 651 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7724 (mmmt) REVERT: B 764 GLN cc_start: 0.8042 (mp10) cc_final: 0.7445 (mt0) REVERT: C 46 MET cc_start: 0.2703 (mtp) cc_final: 0.2263 (mmm) REVERT: C 88 VAL cc_start: 0.4662 (m) cc_final: 0.4309 (m) REVERT: C 204 ASP cc_start: 0.8345 (m-30) cc_final: 0.7937 (p0) REVERT: C 217 LYS cc_start: 0.9011 (mttt) cc_final: 0.8715 (mtpt) REVERT: C 273 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 320 VAL cc_start: 0.7695 (t) cc_final: 0.7477 (p) REVERT: C 484 ASP cc_start: 0.7976 (p0) cc_final: 0.7750 (p0) REVERT: C 560 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7092 (mtt180) REVERT: C 584 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7046 (tppt) REVERT: C 603 GLN cc_start: 0.8109 (tp40) cc_final: 0.7859 (mt0) REVERT: C 650 GLU cc_start: 0.7541 (pm20) cc_final: 0.7224 (tt0) REVERT: C 651 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7759 (mmmt) REVERT: C 764 GLN cc_start: 0.8103 (mp10) cc_final: 0.7544 (mt0) REVERT: D 46 MET cc_start: 0.2833 (mtp) cc_final: 0.2435 (mmm) REVERT: D 88 VAL cc_start: 0.4684 (m) cc_final: 0.4445 (m) REVERT: D 204 ASP cc_start: 0.8347 (m-30) cc_final: 0.7850 (p0) REVERT: D 217 LYS cc_start: 0.8964 (mttt) cc_final: 0.8643 (mtpt) REVERT: D 221 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 273 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 320 VAL cc_start: 0.7669 (t) cc_final: 0.7466 (p) REVERT: D 484 ASP cc_start: 0.7895 (p0) cc_final: 0.7640 (p0) REVERT: D 560 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7395 (mtt180) REVERT: D 584 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7145 (tppt) REVERT: D 603 GLN cc_start: 0.8080 (tp40) cc_final: 0.7742 (tt0) REVERT: D 650 GLU cc_start: 0.7537 (pm20) cc_final: 0.7198 (tt0) REVERT: D 651 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7696 (mmmt) REVERT: D 764 GLN cc_start: 0.8013 (mp10) cc_final: 0.7417 (mt0) REVERT: E 46 MET cc_start: 0.2505 (mtp) cc_final: 0.2146 (mmm) REVERT: E 88 VAL cc_start: 0.4731 (m) cc_final: 0.4471 (m) REVERT: E 204 ASP cc_start: 0.8304 (m-30) cc_final: 0.7840 (p0) REVERT: E 217 LYS cc_start: 0.9000 (mttt) cc_final: 0.8751 (mtpt) REVERT: E 219 MET cc_start: 0.8212 (mtt) cc_final: 0.8010 (mtt) REVERT: E 273 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 335 LEU cc_start: 0.7514 (mt) cc_final: 0.7304 (mt) REVERT: E 484 ASP cc_start: 0.7826 (p0) cc_final: 0.7512 (p0) REVERT: E 508 MET cc_start: 0.7204 (ptm) cc_final: 0.6552 (ptm) REVERT: E 560 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7386 (mtt180) REVERT: E 584 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7154 (tppt) REVERT: E 603 GLN cc_start: 0.8146 (tp40) cc_final: 0.7849 (mt0) REVERT: E 650 GLU cc_start: 0.7543 (pm20) cc_final: 0.7217 (tt0) REVERT: E 651 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7740 (mmmt) REVERT: E 764 GLN cc_start: 0.8047 (mp10) cc_final: 0.7446 (mt0) REVERT: F 46 MET cc_start: 0.2698 (mtp) cc_final: 0.2269 (mmm) REVERT: F 88 VAL cc_start: 0.4663 (m) cc_final: 0.4300 (m) REVERT: F 204 ASP cc_start: 0.8338 (m-30) cc_final: 0.7938 (p0) REVERT: F 217 LYS cc_start: 0.9016 (mttt) cc_final: 0.8719 (mtpt) REVERT: F 229 LEU cc_start: 0.8638 (mt) cc_final: 0.8388 (mt) REVERT: F 273 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7622 (tm-30) REVERT: F 484 ASP cc_start: 0.7974 (p0) cc_final: 0.7750 (p0) REVERT: F 560 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7092 (mtt180) REVERT: F 584 LYS cc_start: 0.7719 (ttmt) cc_final: 0.7055 (tppt) REVERT: F 603 GLN cc_start: 0.8104 (tp40) cc_final: 0.7870 (mt0) REVERT: F 650 GLU cc_start: 0.7547 (pm20) cc_final: 0.7224 (tt0) REVERT: F 651 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7762 (mmmt) REVERT: F 764 GLN cc_start: 0.8097 (mp10) cc_final: 0.7503 (mt0) outliers start: 12 outliers final: 6 residues processed: 810 average time/residue: 0.2402 time to fit residues: 298.6137 Evaluate side-chains 443 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 437 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN B 327 GLN C 327 GLN D 327 GLN E 327 GLN F 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131874 restraints weight = 52732.142| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.68 r_work: 0.3324 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35526 Z= 0.214 Angle : 0.886 10.080 48054 Z= 0.466 Chirality : 0.051 0.189 5436 Planarity : 0.008 0.092 6288 Dihedral : 8.736 51.795 4902 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.91 % Favored : 91.54 % Rotamer: Outliers : 1.92 % Allowed : 7.51 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.29 % 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: -2.70 (0.11), residues: 4398 helix: -1.99 (0.10), residues: 1764 sheet: -0.40 (0.23), residues: 408 loop : -1.84 (0.12), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 653 TYR 0.022 0.003 TYR A 755 PHE 0.014 0.002 PHE E 506 TRP 0.010 0.002 TRP F 551 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (35526) covalent geometry : angle 0.88650 / 0.47 (48054) hydrogen bonds : bond 0.06147 / 4.17 ( 1189) hydrogen bonds : angle 5.80838 / 4.03 ( 3405) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 461 time to evaluate : 1.285 Fit side-chains REVERT: A 46 MET cc_start: 0.3015 (mtp) cc_final: 0.2370 (tpt) REVERT: A 204 ASP cc_start: 0.8251 (m-30) cc_final: 0.7944 (p0) REVERT: A 560 ARG cc_start: 0.7422 (ttm110) cc_final: 0.6995 (mtt180) REVERT: A 584 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7133 (tptm) REVERT: A 651 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7760 (mmmt) REVERT: A 764 GLN cc_start: 0.8002 (mp10) cc_final: 0.7696 (mt0) REVERT: B 46 MET cc_start: 0.2977 (mtp) cc_final: 0.2358 (tpt) REVERT: B 204 ASP cc_start: 0.8090 (m-30) cc_final: 0.7876 (p0) REVERT: B 205 ASP cc_start: 0.7566 (m-30) cc_final: 0.7355 (m-30) REVERT: B 273 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 560 ARG cc_start: 0.7437 (ttm110) cc_final: 0.7014 (mtt180) REVERT: B 584 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7063 (tptm) REVERT: B 651 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7822 (mmmt) REVERT: B 764 GLN cc_start: 0.7972 (mp10) cc_final: 0.7624 (mt0) REVERT: C 46 MET cc_start: 0.3089 (mtp) cc_final: 0.2435 (tpt) REVERT: C 204 ASP cc_start: 0.8249 (m-30) cc_final: 0.7974 (p0) REVERT: C 273 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 542 ILE cc_start: 0.8760 (mp) cc_final: 0.8455 (tt) REVERT: C 560 ARG cc_start: 0.7346 (ttm110) cc_final: 0.7020 (mtt180) REVERT: C 584 LYS cc_start: 0.7766 (ttmt) cc_final: 0.7271 (tppt) REVERT: C 651 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7793 (mmmt) REVERT: D 46 MET cc_start: 0.3021 (mtp) cc_final: 0.2374 (tpt) REVERT: D 204 ASP cc_start: 0.8253 (m-30) cc_final: 0.7948 (p0) REVERT: D 560 ARG cc_start: 0.7432 (ttm110) cc_final: 0.7003 (mtt180) REVERT: D 584 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7130 (tptm) REVERT: D 651 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7762 (mmmt) REVERT: E 46 MET cc_start: 0.2955 (mtp) cc_final: 0.2333 (tpt) REVERT: E 204 ASP cc_start: 0.8092 (m-30) cc_final: 0.7850 (p0) REVERT: E 273 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 560 ARG cc_start: 0.7483 (ttm110) cc_final: 0.6972 (mtt180) REVERT: E 584 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7069 (tptm) REVERT: E 651 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7819 (mmmt) REVERT: E 764 GLN cc_start: 0.7958 (mp10) cc_final: 0.7614 (mt0) REVERT: F 46 MET cc_start: 0.3147 (mtp) cc_final: 0.2481 (tpt) REVERT: F 204 ASP cc_start: 0.8251 (m-30) cc_final: 0.7972 (p0) REVERT: F 273 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7624 (tm-30) REVERT: F 542 ILE cc_start: 0.8761 (mp) cc_final: 0.8457 (tt) REVERT: F 560 ARG cc_start: 0.7365 (ttm110) cc_final: 0.7039 (mtt180) REVERT: F 584 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7283 (tppt) REVERT: F 651 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7810 (mmmt) outliers start: 72 outliers final: 56 residues processed: 511 average time/residue: 0.2231 time to fit residues: 180.7177 Evaluate side-chains 406 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 88 optimal weight: 9.9990 chunk 373 optimal weight: 0.0570 chunk 220 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 221 optimal weight: 30.0000 chunk 389 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 235 optimal weight: 0.4980 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.177297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134707 restraints weight = 52653.415| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.73 r_work: 0.3341 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35526 Z= 0.141 Angle : 0.731 8.568 48054 Z= 0.378 Chirality : 0.047 0.195 5436 Planarity : 0.007 0.074 6288 Dihedral : 8.100 53.861 4902 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.37 % Favored : 92.09 % Rotamer: Outliers : 3.01 % Allowed : 10.52 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.61 (0.12), residues: 4398 helix: -0.73 (0.11), residues: 1794 sheet: -0.93 (0.22), residues: 558 loop : -1.32 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 653 TYR 0.014 0.002 TYR A 755 PHE 0.012 0.001 PHE F 139 TRP 0.007 0.001 TRP B 551 HIS 0.005 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (35526) covalent geometry : angle 0.73092 / 0.38 (48054) hydrogen bonds : bond 0.04116 / 2.79 ( 1189) hydrogen bonds : angle 4.90941 / 3.42 ( 3405) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 401 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.3149 (mtp) cc_final: 0.2468 (tpt) REVERT: A 203 TYR cc_start: 0.7712 (m-10) cc_final: 0.7274 (m-10) REVERT: A 368 ASP cc_start: 0.7911 (t70) cc_final: 0.7708 (t70) REVERT: A 560 ARG cc_start: 0.7284 (ttm110) cc_final: 0.7000 (mtp180) REVERT: A 584 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7203 (tppt) REVERT: A 651 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7729 (mmmt) REVERT: B 46 MET cc_start: 0.3080 (mtp) cc_final: 0.2433 (tpt) REVERT: B 204 ASP cc_start: 0.8115 (m-30) cc_final: 0.7912 (p0) REVERT: B 225 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7535 (mtp180) REVERT: B 294 GLU cc_start: 0.7987 (tt0) cc_final: 0.7663 (mt-10) REVERT: B 504 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7350 (tp) REVERT: B 560 ARG cc_start: 0.7347 (ttm110) cc_final: 0.6900 (mtt180) REVERT: B 584 LYS cc_start: 0.7860 (ttmt) cc_final: 0.6963 (tptm) REVERT: B 651 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7873 (mmmt) REVERT: C 46 MET cc_start: 0.3109 (mtp) cc_final: 0.2443 (tpt) REVERT: C 203 TYR cc_start: 0.7816 (m-10) cc_final: 0.7425 (m-10) REVERT: C 225 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7755 (mtp180) REVERT: C 491 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7732 (mt-10) REVERT: C 542 ILE cc_start: 0.8758 (mp) cc_final: 0.8434 (tt) REVERT: C 560 ARG cc_start: 0.7364 (ttm110) cc_final: 0.7066 (mtt180) REVERT: C 584 LYS cc_start: 0.7740 (ttmt) cc_final: 0.6931 (tptm) REVERT: C 651 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7759 (mmmt) REVERT: D 46 MET cc_start: 0.3189 (mtp) cc_final: 0.2506 (tpt) REVERT: D 203 TYR cc_start: 0.7707 (m-10) cc_final: 0.7265 (m-10) REVERT: D 368 ASP cc_start: 0.7914 (t70) cc_final: 0.7709 (t70) REVERT: D 560 ARG cc_start: 0.7296 (ttm110) cc_final: 0.7011 (mtp180) REVERT: D 584 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7217 (tppt) REVERT: D 651 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7733 (mmmt) REVERT: E 46 MET cc_start: 0.3061 (mtp) cc_final: 0.2428 (tpt) REVERT: E 203 TYR cc_start: 0.7745 (m-10) cc_final: 0.7283 (m-10) REVERT: E 204 ASP cc_start: 0.8179 (m-30) cc_final: 0.7946 (p0) REVERT: E 225 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7505 (mtp180) REVERT: E 498 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7325 (mp0) REVERT: E 504 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7344 (tp) REVERT: E 560 ARG cc_start: 0.7393 (ttm110) cc_final: 0.6945 (mtt180) REVERT: E 584 LYS cc_start: 0.7777 (ttmt) cc_final: 0.6888 (tptm) REVERT: E 651 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7861 (mmmt) REVERT: E 692 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8193 (mm-40) REVERT: E 764 GLN cc_start: 0.7954 (mp10) cc_final: 0.7708 (mt0) REVERT: F 46 MET cc_start: 0.3082 (mtp) cc_final: 0.2423 (tpt) REVERT: F 203 TYR cc_start: 0.7833 (m-10) cc_final: 0.7440 (m-10) REVERT: F 225 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7754 (mtp180) REVERT: F 491 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7715 (mt-10) REVERT: F 542 ILE cc_start: 0.8732 (mp) cc_final: 0.8426 (tt) REVERT: F 560 ARG cc_start: 0.7368 (ttm110) cc_final: 0.7095 (mtt180) REVERT: F 584 LYS cc_start: 0.7741 (ttmt) cc_final: 0.6928 (tptm) REVERT: F 651 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7761 (mmmt) outliers start: 113 outliers final: 66 residues processed: 491 average time/residue: 0.2118 time to fit residues: 170.3030 Evaluate side-chains 410 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 342 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 357 optimal weight: 2.9990 chunk 105 optimal weight: 0.0070 chunk 126 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 251 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 396 optimal weight: 1.9990 chunk 312 optimal weight: 20.0000 chunk 188 optimal weight: 0.7980 chunk 358 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 overall best weight: 2.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 589 ASN B 764 GLN D 589 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.177502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134585 restraints weight = 52560.104| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.64 r_work: 0.3350 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35526 Z= 0.136 Angle : 0.697 8.483 48054 Z= 0.357 Chirality : 0.047 0.209 5436 Planarity : 0.006 0.075 6288 Dihedral : 7.690 51.118 4902 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.46 % Favored : 91.86 % Rotamer: Outliers : 3.35 % Allowed : 10.94 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.10 (0.13), residues: 4398 helix: -0.14 (0.12), residues: 1782 sheet: -0.64 (0.22), residues: 558 loop : -1.22 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 653 TYR 0.014 0.002 TYR F 203 PHE 0.013 0.001 PHE D 163 TRP 0.012 0.002 TRP F 551 HIS 0.006 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (35526) covalent geometry : angle 0.69723 / 0.36 (48054) hydrogen bonds : bond 0.03647 / 2.47 ( 1189) hydrogen bonds : angle 4.61247 / 3.20 ( 3405) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 391 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.3095 (mtp) cc_final: 0.2438 (tpt) REVERT: A 294 GLU cc_start: 0.7930 (tt0) cc_final: 0.7647 (mt-10) REVERT: A 498 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 560 ARG cc_start: 0.7278 (ttm110) cc_final: 0.7047 (mtp180) REVERT: A 584 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7245 (tppt) REVERT: A 651 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7724 (mmmt) REVERT: B 46 MET cc_start: 0.3149 (mtp) cc_final: 0.2582 (tpt) REVERT: B 204 ASP cc_start: 0.8116 (m-30) cc_final: 0.7913 (p0) REVERT: B 225 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7591 (mtp180) REVERT: B 294 GLU cc_start: 0.8015 (tt0) cc_final: 0.7696 (mt-10) REVERT: B 560 ARG cc_start: 0.7299 (ttm110) cc_final: 0.6990 (mtt180) REVERT: B 584 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7022 (tptm) REVERT: B 651 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7852 (mmmt) REVERT: C 46 MET cc_start: 0.3088 (mtp) cc_final: 0.2483 (tpt) REVERT: C 225 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7880 (mtp85) REVERT: C 491 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 560 ARG cc_start: 0.7337 (ttm110) cc_final: 0.7028 (mtt180) REVERT: C 584 LYS cc_start: 0.7775 (ttmt) cc_final: 0.6961 (tptm) REVERT: C 651 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7776 (mmmt) REVERT: D 46 MET cc_start: 0.3102 (mtp) cc_final: 0.2440 (tpt) REVERT: D 294 GLU cc_start: 0.7938 (tt0) cc_final: 0.7646 (mt-10) REVERT: D 560 ARG cc_start: 0.7268 (ttm110) cc_final: 0.7046 (mtp180) REVERT: D 584 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7250 (tppt) REVERT: D 651 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7717 (mmmt) REVERT: E 46 MET cc_start: 0.3131 (mtp) cc_final: 0.2567 (tpt) REVERT: E 204 ASP cc_start: 0.8231 (m-30) cc_final: 0.7982 (p0) REVERT: E 225 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7603 (mtp180) REVERT: E 294 GLU cc_start: 0.7975 (tt0) cc_final: 0.7716 (mt-10) REVERT: E 560 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6982 (mtt180) REVERT: E 584 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7018 (tptm) REVERT: E 651 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7872 (mmmt) REVERT: F 46 MET cc_start: 0.3019 (mtp) cc_final: 0.2442 (tpt) REVERT: F 225 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7874 (mtp180) REVERT: F 491 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7674 (mt-10) REVERT: F 560 ARG cc_start: 0.7297 (ttm110) cc_final: 0.7028 (mtt180) REVERT: F 584 LYS cc_start: 0.7808 (ttmt) cc_final: 0.6978 (tptm) REVERT: F 651 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7771 (mmmt) outliers start: 126 outliers final: 76 residues processed: 490 average time/residue: 0.2184 time to fit residues: 172.9753 Evaluate side-chains 418 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 341 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 501 ASP Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 119 optimal weight: 10.0000 chunk 380 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 391 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 216 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 589 ASN B 603 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 ASN E 589 ASN E 603 GLN E 764 GLN ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 589 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134143 restraints weight = 52641.935| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.60 r_work: 0.3338 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35526 Z= 0.147 Angle : 0.702 11.735 48054 Z= 0.355 Chirality : 0.047 0.186 5436 Planarity : 0.006 0.073 6288 Dihedral : 7.593 51.934 4902 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.53 % Favored : 91.79 % Rotamer: Outliers : 3.97 % Allowed : 11.58 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.93 (0.13), residues: 4398 helix: 0.07 (0.12), residues: 1794 sheet: -0.18 (0.23), residues: 504 loop : -1.29 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 653 TYR 0.009 0.002 TYR C 173 PHE 0.010 0.001 PHE C 267 TRP 0.012 0.002 TRP E 551 HIS 0.006 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (35526) covalent geometry : angle 0.70225 / 0.35 (48054) hydrogen bonds : bond 0.03728 / 2.52 ( 1189) hydrogen bonds : angle 4.48274 / 3.10 ( 3405) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 379 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.7998 (tt0) cc_final: 0.7688 (mt-10) REVERT: A 560 ARG cc_start: 0.7329 (ttm110) cc_final: 0.7077 (mtp180) REVERT: A 584 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7129 (tptm) REVERT: A 651 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7707 (mmmt) REVERT: B 204 ASP cc_start: 0.8123 (m-30) cc_final: 0.7916 (p0) REVERT: B 294 GLU cc_start: 0.8097 (tt0) cc_final: 0.7818 (mt-10) REVERT: B 560 ARG cc_start: 0.7378 (ttm110) cc_final: 0.7053 (mtt180) REVERT: B 584 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7109 (tptm) REVERT: B 651 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7844 (mmmt) REVERT: C 491 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7638 (mt-10) REVERT: C 560 ARG cc_start: 0.7328 (ttm110) cc_final: 0.7092 (mtt180) REVERT: C 584 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7040 (tptm) REVERT: C 651 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7802 (mmmt) REVERT: D 294 GLU cc_start: 0.7993 (tt0) cc_final: 0.7704 (mt-10) REVERT: D 560 ARG cc_start: 0.7330 (ttm110) cc_final: 0.7084 (mtp180) REVERT: D 584 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7140 (tptm) REVERT: D 651 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7710 (mmmt) REVERT: E 204 ASP cc_start: 0.8207 (m-30) cc_final: 0.7979 (p0) REVERT: E 294 GLU cc_start: 0.8106 (tt0) cc_final: 0.7838 (mt-10) REVERT: E 560 ARG cc_start: 0.7406 (ttm110) cc_final: 0.7095 (mtt180) REVERT: E 584 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7117 (tptm) REVERT: E 651 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7837 (mmmt) REVERT: F 225 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7795 (mtp180) REVERT: F 491 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7656 (mt-10) REVERT: F 560 ARG cc_start: 0.7329 (ttm110) cc_final: 0.7102 (mtt180) REVERT: F 584 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7034 (tptm) REVERT: F 651 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7804 (mmmt) outliers start: 149 outliers final: 112 residues processed: 492 average time/residue: 0.2062 time to fit residues: 166.1135 Evaluate side-chains 460 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 348 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 501 ASP Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 534 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 281 optimal weight: 0.4980 chunk 263 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 398 optimal weight: 6.9990 chunk 421 optimal weight: 0.9980 chunk 176 optimal weight: 0.0270 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 130 optimal weight: 0.3980 overall best weight: 1.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 603 GLN A 764 GLN D 603 GLN D 764 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.177980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134817 restraints weight = 52440.780| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.65 r_work: 0.3361 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35526 Z= 0.115 Angle : 0.646 8.560 48054 Z= 0.328 Chirality : 0.045 0.172 5436 Planarity : 0.006 0.070 6288 Dihedral : 7.274 52.031 4902 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.46 % Favored : 91.86 % Rotamer: Outliers : 2.88 % Allowed : 12.49 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.60 (0.13), residues: 4398 helix: 0.40 (0.13), residues: 1794 sheet: -0.08 (0.23), residues: 504 loop : -1.15 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 86 TYR 0.012 0.001 TYR B 244 PHE 0.010 0.001 PHE B 163 TRP 0.010 0.001 TRP E 551 HIS 0.007 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (35526) covalent geometry : angle 0.64599 / 0.33 (48054) hydrogen bonds : bond 0.03062 / 2.08 ( 1189) hydrogen bonds : angle 4.23799 / 2.93 ( 3405) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 393 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.3188 (mtp) cc_final: 0.2552 (tpt) REVERT: A 294 GLU cc_start: 0.7931 (tt0) cc_final: 0.7638 (mt-10) REVERT: A 584 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7206 (tppt) REVERT: A 651 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7693 (mmmt) REVERT: B 46 MET cc_start: 0.3090 (mtp) cc_final: 0.2481 (tpt) REVERT: B 229 LEU cc_start: 0.8294 (mm) cc_final: 0.7978 (mt) REVERT: B 294 GLU cc_start: 0.7987 (tt0) cc_final: 0.7734 (mt-10) REVERT: B 560 ARG cc_start: 0.7284 (ttm110) cc_final: 0.7057 (mtt180) REVERT: B 584 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7063 (tptm) REVERT: B 651 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7771 (mmmt) REVERT: C 46 MET cc_start: 0.3007 (mtp) cc_final: 0.2401 (tpt) REVERT: C 491 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7557 (mt-10) REVERT: C 498 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: C 584 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7063 (tptm) REVERT: C 651 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7772 (mmmt) REVERT: D 46 MET cc_start: 0.3205 (mtp) cc_final: 0.2559 (tpt) REVERT: D 294 GLU cc_start: 0.7920 (tt0) cc_final: 0.7637 (mt-10) REVERT: D 404 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6942 (m90) REVERT: D 584 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7229 (tppt) REVERT: D 651 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7702 (mmmt) REVERT: E 46 MET cc_start: 0.3085 (mtp) cc_final: 0.2486 (tpt) REVERT: E 229 LEU cc_start: 0.8292 (mm) cc_final: 0.7977 (mt) REVERT: E 294 GLU cc_start: 0.8048 (tt0) cc_final: 0.7807 (mt-10) REVERT: E 560 ARG cc_start: 0.7327 (ttm110) cc_final: 0.7096 (mtt180) REVERT: E 584 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7066 (tptm) REVERT: E 651 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7790 (mmmt) REVERT: F 46 MET cc_start: 0.3014 (mtp) cc_final: 0.2412 (tpt) REVERT: F 491 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7538 (mt-10) REVERT: F 498 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: F 584 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7057 (tptm) REVERT: F 651 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7781 (mmmt) outliers start: 108 outliers final: 80 residues processed: 483 average time/residue: 0.2134 time to fit residues: 166.5150 Evaluate side-chains 437 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 354 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 763 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 354 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 420 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 96 optimal weight: 0.0060 chunk 33 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 overall best weight: 4.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132901 restraints weight = 52864.539| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.70 r_work: 0.3316 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 35526 Z= 0.159 Angle : 0.699 9.809 48054 Z= 0.353 Chirality : 0.047 0.179 5436 Planarity : 0.006 0.069 6288 Dihedral : 7.370 51.545 4902 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.64 % Favored : 91.68 % Rotamer: Outliers : 3.65 % Allowed : 12.86 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.67 (0.13), residues: 4398 helix: 0.37 (0.12), residues: 1794 sheet: -0.16 (0.23), residues: 486 loop : -1.21 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 653 TYR 0.011 0.002 TYR D 244 PHE 0.015 0.001 PHE D 363 TRP 0.014 0.002 TRP A 551 HIS 0.006 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (35526) covalent geometry : angle 0.69917 / 0.35 (48054) hydrogen bonds : bond 0.03726 / 2.51 ( 1189) hydrogen bonds : angle 4.29482 / 2.95 ( 3405) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 360 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8017 (tt0) cc_final: 0.7779 (mt-10) REVERT: A 389 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7488 (ttpt) REVERT: A 584 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7165 (tptm) REVERT: A 651 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7772 (mmmt) REVERT: B 229 LEU cc_start: 0.8295 (mm) cc_final: 0.7985 (mt) REVERT: B 294 GLU cc_start: 0.8194 (tt0) cc_final: 0.7871 (mt-10) REVERT: B 560 ARG cc_start: 0.7345 (ttm110) cc_final: 0.7097 (mtt180) REVERT: B 584 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7111 (tptm) REVERT: B 651 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7771 (mmmt) REVERT: C 131 PHE cc_start: 0.1120 (t80) cc_final: 0.0809 (t80) REVERT: C 327 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8277 (tm130) REVERT: C 491 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 498 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: C 584 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7107 (tptm) REVERT: C 651 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7788 (mmmt) REVERT: C 763 GLN cc_start: 0.7739 (mp10) cc_final: 0.7485 (mp10) REVERT: C 764 GLN cc_start: 0.8047 (mp10) cc_final: 0.7822 (mt0) REVERT: D 294 GLU cc_start: 0.7994 (tt0) cc_final: 0.7775 (mt-10) REVERT: D 584 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7165 (tptm) REVERT: D 651 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7771 (mmmt) REVERT: E 229 LEU cc_start: 0.8290 (mm) cc_final: 0.7981 (mt) REVERT: E 294 GLU cc_start: 0.8175 (tt0) cc_final: 0.7876 (mt-10) REVERT: E 560 ARG cc_start: 0.7378 (ttm110) cc_final: 0.7118 (mtt180) REVERT: E 584 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7105 (tptm) REVERT: E 651 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7870 (mmmt) REVERT: F 131 PHE cc_start: 0.1119 (t80) cc_final: 0.0812 (t80) REVERT: F 327 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8326 (tm130) REVERT: F 491 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7610 (mt-10) REVERT: F 498 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: F 584 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7136 (tptm) REVERT: F 651 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7791 (mmmt) REVERT: F 763 GLN cc_start: 0.7720 (mp10) cc_final: 0.7472 (mp10) REVERT: F 764 GLN cc_start: 0.8032 (mp10) cc_final: 0.7807 (mt0) outliers start: 137 outliers final: 113 residues processed: 466 average time/residue: 0.2044 time to fit residues: 156.8521 Evaluate side-chains 464 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 347 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 707 ILE Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 661 LEU Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 214 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 150 optimal weight: 40.0000 chunk 430 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 287 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 327 GLN D 327 GLN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN F 91 ASN F 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.173470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131624 restraints weight = 52942.829| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.67 r_work: 0.3298 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 35526 Z= 0.222 Angle : 0.781 10.829 48054 Z= 0.394 Chirality : 0.051 0.236 5436 Planarity : 0.007 0.071 6288 Dihedral : 7.771 51.525 4902 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.57 % Favored : 91.75 % Rotamer: Outliers : 3.73 % Allowed : 13.26 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.17 (0.13), residues: 4398 helix: -0.02 (0.12), residues: 1776 sheet: -0.57 (0.22), residues: 522 loop : -1.45 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 653 TYR 0.014 0.002 TYR E 110 PHE 0.016 0.002 PHE D 363 TRP 0.018 0.003 TRP E 551 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (35526) covalent geometry : angle 0.78091 / 0.39 (48054) hydrogen bonds : bond 0.04525 / 3.04 ( 1189) hydrogen bonds : angle 4.59443 / 3.16 ( 3405) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 334 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 LYS cc_start: 0.8030 (ttmt) cc_final: 0.7187 (tptm) REVERT: A 651 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7768 (mmmt) REVERT: B 229 LEU cc_start: 0.8331 (mm) cc_final: 0.8020 (mt) REVERT: B 584 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7149 (tptm) REVERT: B 651 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7796 (mmmt) REVERT: C 131 PHE cc_start: 0.1164 (t80) cc_final: 0.0806 (t80) REVERT: C 327 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: C 491 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7713 (mt-10) REVERT: C 498 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: C 584 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7204 (tptm) REVERT: C 651 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7811 (mmmt) REVERT: C 764 GLN cc_start: 0.8119 (mp10) cc_final: 0.7785 (mt0) REVERT: D 584 LYS cc_start: 0.8034 (ttmt) cc_final: 0.7191 (tptm) REVERT: D 651 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7776 (mmmt) REVERT: E 229 LEU cc_start: 0.8338 (mm) cc_final: 0.8024 (mt) REVERT: E 560 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7203 (mtt180) REVERT: E 584 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7142 (tptm) REVERT: E 651 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7836 (mmmt) REVERT: F 131 PHE cc_start: 0.1128 (t80) cc_final: 0.0759 (t80) REVERT: F 327 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: F 491 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7723 (mt-10) REVERT: F 498 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: F 584 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7206 (tptm) REVERT: F 651 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7818 (mmmt) REVERT: F 764 GLN cc_start: 0.8108 (mp10) cc_final: 0.7774 (mt0) outliers start: 140 outliers final: 119 residues processed: 448 average time/residue: 0.2037 time to fit residues: 151.4332 Evaluate side-chains 453 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 330 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 412 optimal weight: 6.9990 chunk 433 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 325 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 176 optimal weight: 0.0020 chunk 143 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 327 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133297 restraints weight = 52824.749| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.50 r_work: 0.3337 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35526 Z= 0.124 Angle : 0.668 9.630 48054 Z= 0.337 Chirality : 0.046 0.178 5436 Planarity : 0.005 0.069 6288 Dihedral : 7.388 51.925 4902 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.05 % Favored : 92.27 % Rotamer: Outliers : 3.09 % Allowed : 14.11 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.69 (0.13), residues: 4398 helix: 0.38 (0.12), residues: 1800 sheet: -0.24 (0.23), residues: 486 loop : -1.23 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 25 TYR 0.009 0.001 TYR F 203 PHE 0.009 0.001 PHE D 363 TRP 0.009 0.001 TRP E 551 HIS 0.007 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (35526) covalent geometry : angle 0.66802 / 0.34 (48054) hydrogen bonds : bond 0.03430 / 2.33 ( 1189) hydrogen bonds : angle 4.27808 / 2.95 ( 3405) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 347 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 404 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.6911 (m90) REVERT: A 584 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7177 (tptm) REVERT: A 651 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7781 (mmmt) REVERT: B 229 LEU cc_start: 0.8303 (mm) cc_final: 0.8019 (mt) REVERT: B 294 GLU cc_start: 0.8176 (tt0) cc_final: 0.7848 (mt-10) REVERT: B 584 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7124 (tptm) REVERT: B 651 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7738 (mmmt) REVERT: C 46 MET cc_start: 0.2936 (mtp) cc_final: 0.2252 (tpt) REVERT: C 84 MET cc_start: 0.3959 (mtt) cc_final: 0.3758 (ptt) REVERT: C 491 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 498 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: C 584 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7213 (tptm) REVERT: C 651 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7793 (mmmt) REVERT: C 764 GLN cc_start: 0.8076 (mp10) cc_final: 0.7782 (mt0) REVERT: D 404 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6899 (m90) REVERT: D 584 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7165 (tptm) REVERT: D 651 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7772 (mmmt) REVERT: E 229 LEU cc_start: 0.8295 (mm) cc_final: 0.8010 (mt) REVERT: E 584 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7111 (tptm) REVERT: E 651 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7812 (mmmt) REVERT: F 46 MET cc_start: 0.2898 (mtp) cc_final: 0.2259 (tpt) REVERT: F 491 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7511 (mt-10) REVERT: F 498 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: F 584 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7216 (tptm) REVERT: F 651 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7798 (mmmt) REVERT: F 764 GLN cc_start: 0.8067 (mp10) cc_final: 0.7773 (mt0) outliers start: 116 outliers final: 104 residues processed: 441 average time/residue: 0.1998 time to fit residues: 146.1289 Evaluate side-chains 448 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 340 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 362 optimal weight: 5.9990 chunk 428 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 402 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 301 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN D 327 GLN F 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.174612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132180 restraints weight = 52983.454| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.81 r_work: 0.3308 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35526 Z= 0.167 Angle : 0.705 10.194 48054 Z= 0.355 Chirality : 0.047 0.180 5436 Planarity : 0.006 0.070 6288 Dihedral : 7.431 51.523 4902 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.66 % Favored : 91.66 % Rotamer: Outliers : 3.14 % Allowed : 14.48 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.84 (0.13), residues: 4398 helix: 0.26 (0.12), residues: 1776 sheet: -0.41 (0.23), residues: 504 loop : -1.28 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 25 TYR 0.018 0.002 TYR B 244 PHE 0.012 0.002 PHE C 363 TRP 0.015 0.002 TRP D 551 HIS 0.006 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (35526) covalent geometry : angle 0.70483 / 0.36 (48054) hydrogen bonds : bond 0.03850 / 2.59 ( 1189) hydrogen bonds : angle 4.32564 / 2.98 ( 3405) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8796 Ramachandran restraints generated. 4398 Oldfield, 0 Emsley, 4398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 339 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.3601 (mtp) cc_final: 0.3339 (mmt) REVERT: A 404 HIS cc_start: 0.7356 (OUTLIER) cc_final: 0.6983 (m90) REVERT: A 584 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7188 (tptm) REVERT: A 651 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7802 (mmmt) REVERT: B 229 LEU cc_start: 0.8312 (mm) cc_final: 0.8031 (mt) REVERT: B 584 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7120 (tptm) REVERT: B 651 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7731 (mmmt) REVERT: C 46 MET cc_start: 0.2903 (mtp) cc_final: 0.2246 (tpt) REVERT: C 491 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7601 (mt-10) REVERT: C 498 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: C 584 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7216 (tptm) REVERT: C 651 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7804 (mmmt) REVERT: C 764 GLN cc_start: 0.8107 (mp10) cc_final: 0.7768 (mt0) REVERT: D 84 MET cc_start: 0.3621 (mtp) cc_final: 0.3345 (mmt) REVERT: D 404 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.7002 (m90) REVERT: D 584 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7181 (tptm) REVERT: D 651 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7798 (mmmt) REVERT: E 229 LEU cc_start: 0.8304 (mm) cc_final: 0.8025 (mt) REVERT: E 584 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7121 (tptm) REVERT: E 651 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7822 (mmmt) REVERT: F 84 MET cc_start: 0.3709 (ptt) cc_final: 0.2357 (mtp) REVERT: F 491 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7616 (mt-10) REVERT: F 498 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: F 584 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7192 (tptm) REVERT: F 651 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7803 (mmmt) REVERT: F 764 GLN cc_start: 0.8098 (mp10) cc_final: 0.7760 (mt0) outliers start: 118 outliers final: 111 residues processed: 433 average time/residue: 0.2030 time to fit residues: 145.4862 Evaluate side-chains 449 residues out of total 3762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 334 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 384 HIS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 664 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 501 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 664 SER Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 429 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 490 GLN Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 664 SER Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 384 HIS Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 448 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 600 VAL Chi-restraints excluded: chain F residue 664 SER Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 416 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132542 restraints weight = 52843.972| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.88 r_work: 0.3315 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35526 Z= 0.143 Angle : 0.677 9.935 48054 Z= 0.341 Chirality : 0.046 0.179 5436 Planarity : 0.006 0.070 6288 Dihedral : 7.354 51.781 4902 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.53 % Favored : 91.79 % Rotamer: Outliers : 3.22 % Allowed : 14.48 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.69 (0.13), residues: 4398 helix: 0.37 (0.12), residues: 1812 sheet: -0.27 (0.24), residues: 486 loop : -1.21 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 25 TYR 0.010 0.002 TYR C 244 PHE 0.010 0.001 PHE C 363 TRP 0.012 0.002 TRP A 551 HIS 0.006 0.001 HIS F 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (35526) covalent geometry : angle 0.67733 / 0.34 (48054) hydrogen bonds : bond 0.03580 / 2.42 ( 1189) hydrogen bonds : angle 4.23975 / 2.92 ( 3405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7497.25 seconds wall clock time: 129 minutes 8.05 seconds (7748.05 seconds total)