Starting phenix.real_space_refine on Sat Mar 7 10:06:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p5w_13203/03_2026/7p5w_13203.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p5w_13203/03_2026/7p5w_13203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p5w_13203/03_2026/7p5w_13203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p5w_13203/03_2026/7p5w_13203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p5w_13203/03_2026/7p5w_13203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p5w_13203/03_2026/7p5w_13203.map" } resolution = 3.5 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= 0.003 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: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 26730 2.51 5 N 6960 2.21 5 O 7386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41250 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "E" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "F" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 953 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 9.40, per 1000 atoms: 0.23 Number of scatterers: 41250 At special positions: 0 Unit cell: (187.488, 180.978, 188.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 7386 8.00 N 6960 7.00 C 26730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 40 sheets defined 44.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.285A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 146 Proline residue: A 126 - end of helix removed outlier: 5.270A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.027A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.506A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 287 removed outlier: 4.563A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 353 through 360 removed outlier: 4.397A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.111A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.696A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.518A pdb=" N GLU A 507 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 534 through 543 removed outlier: 4.947A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.553A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.503A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.846A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 806 removed outlier: 3.873A pdb=" N LYS A 799 " --> pdb=" O PRO A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 4.051A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 146 Proline residue: B 126 - end of helix removed outlier: 5.285A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.993A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 344 Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.980A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.038A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 420 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.908A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 629 through 636 removed outlier: 3.752A pdb=" N ILE B 632 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 636 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.650A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 659 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 655 through 659' Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.854A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.501A pdb=" N CYS B 730 " --> pdb=" O LEU B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 753 removed outlier: 3.617A pdb=" N GLU B 752 " --> pdb=" O ARG B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.639A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 795 No H-bonds generated for 'chain 'B' and resid 793 through 795' Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.502A pdb=" N GLU B 800 " --> pdb=" O PRO B 796 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 801 " --> pdb=" O GLU B 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.530A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 146 Proline residue: C 126 - end of helix removed outlier: 5.284A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.098A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 166 " --> pdb=" O LYS C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 287 removed outlier: 4.623A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 344 Processing helix chain 'C' and resid 353 through 360 removed outlier: 4.358A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.114A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.520A pdb=" N PHE C 443 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 495 Processing helix chain 'C' and resid 504 through 508 removed outlier: 3.543A pdb=" N GLU C 507 " --> pdb=" O ASP C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 534 through 543 removed outlier: 5.027A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 608 through 613 Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.515A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.510A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.517A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 4.050A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.825A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 806 removed outlier: 3.863A pdb=" N LYS C 799 " --> pdb=" O PRO C 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.089A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.502A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.301A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.026A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 166 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 344 Processing helix chain 'D' and resid 353 through 360 removed outlier: 3.904A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.053A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 411 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 535 through 542 removed outlier: 3.945A pdb=" N GLY D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 629 through 636 removed outlier: 3.642A pdb=" N ILE D 632 " --> pdb=" O ILE D 629 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 660 removed outlier: 3.670A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D 659 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.862A pdb=" N CYS D 684 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 707 Processing helix chain 'D' and resid 726 through 730 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.759A pdb=" N VAL D 750 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU D 752 " --> pdb=" O ARG D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 Processing helix chain 'D' and resid 787 through 792 removed outlier: 3.614A pdb=" N SER D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 805 removed outlier: 4.211A pdb=" N LYS D 799 " --> pdb=" O PRO D 795 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 801 " --> pdb=" O GLU D 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.219A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 146 Proline residue: E 126 - end of helix removed outlier: 5.257A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.053A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 287 removed outlier: 4.612A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 344 Processing helix chain 'E' and resid 353 through 360 removed outlier: 4.368A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.135A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.571A pdb=" N PHE E 443 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 484 through 495 Processing helix chain 'E' and resid 504 through 508 removed outlier: 3.504A pdb=" N GLU E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 534 through 543 removed outlier: 4.979A pdb=" N GLY E 539 " --> pdb=" O VAL E 536 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 608 through 613 Processing helix chain 'E' and resid 629 through 638 removed outlier: 3.506A pdb=" N ILE E 632 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 Processing helix chain 'E' and resid 679 through 684 Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.505A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY E 705 " --> pdb=" O ALA E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 729 Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.938A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY E 751 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 806 removed outlier: 3.835A pdb=" N LYS E 799 " --> pdb=" O PRO E 795 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.039A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 146 Proline residue: F 126 - end of helix removed outlier: 5.299A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.032A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 Processing helix chain 'F' and resid 233 through 255 Processing helix chain 'F' and resid 259 through 286 Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 344 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.943A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.043A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 412 through 420 Processing helix chain 'F' and resid 441 through 445 Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 484 through 494 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 535 through 542 removed outlier: 3.821A pdb=" N GLY F 539 " --> pdb=" O VAL F 536 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG F 541 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 567 through 569 No H-bonds generated for 'chain 'F' and resid 567 through 569' Processing helix chain 'F' and resid 629 through 636 removed outlier: 3.745A pdb=" N ILE F 632 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE F 633 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 636 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.659A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 655 through 659' Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.878A pdb=" N CYS F 684 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 707 Processing helix chain 'F' and resid 726 through 730 Processing helix chain 'F' and resid 749 through 753 removed outlier: 3.560A pdb=" N GLU F 752 " --> pdb=" O ARG F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 775 removed outlier: 3.531A pdb=" N GLU F 775 " --> pdb=" O GLU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 removed outlier: 3.582A pdb=" N SER F 792 " --> pdb=" O GLU F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 793 through 795 No H-bonds generated for 'chain 'F' and resid 793 through 795' Processing helix chain 'F' and resid 796 through 806 removed outlier: 4.152A pdb=" N ARG F 801 " --> pdb=" O GLU F 797 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.902A pdb=" N LYS K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.632A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.847A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.583A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.502A pdb=" N THR J 91 " --> pdb=" O PRO J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 3.521A pdb=" N LEU A 498 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 549 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.792A pdb=" N VAL A 459 " --> pdb=" O LYS A 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.844A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 712 through 714 removed outlier: 7.001A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.610A pdb=" N LEU B 428 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS B 452 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 430 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLU B 454 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 432 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 459 through 461 Processing sheet with id=AA9, first strand: chain 'B' and resid 712 through 714 removed outlier: 6.900A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB2, first strand: chain 'C' and resid 421 through 422 removed outlier: 6.268A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU C 549 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.744A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.947A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 712 through 714 removed outlier: 7.055A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.662A pdb=" N LEU D 428 " --> pdb=" O VAL D 450 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LYS D 452 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 430 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU D 454 " --> pdb=" O LEU D 430 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 432 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 620 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 619 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 459 through 461 Processing sheet with id=AB9, first strand: chain 'D' and resid 712 through 714 removed outlier: 7.047A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.280A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU E 549 " --> pdb=" O SER E 573 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 459 through 461 removed outlier: 6.738A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.865A pdb=" N ILE E 619 " --> pdb=" O LYS E 645 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 712 through 714 removed outlier: 7.227A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AC7, first strand: chain 'F' and resid 421 through 422 removed outlier: 6.593A pdb=" N LEU F 428 " --> pdb=" O VAL F 450 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 430 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU F 454 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU F 432 " --> pdb=" O GLU F 454 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR F 477 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU F 453 " --> pdb=" O TYR F 477 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 549 " --> pdb=" O SER F 573 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASN F 575 " --> pdb=" O LEU F 549 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU F 551 " --> pdb=" O ASN F 575 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP F 620 " --> pdb=" O LEU F 596 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE F 619 " --> pdb=" O LYS F 645 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 459 through 461 Processing sheet with id=AC9, first strand: chain 'F' and resid 712 through 714 removed outlier: 7.038A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE F 759 " --> pdb=" O VAL F 785 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.601A pdb=" N VAL K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.660A pdb=" N SER K 120 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.558A pdb=" N VAL L 79 " --> pdb=" O CYS L 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.602A pdb=" N SER L 120 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.527A pdb=" N VAL G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.634A pdb=" N SER G 120 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.590A pdb=" N VAL H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.556A pdb=" N SER H 120 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.556A pdb=" N SER H 120 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 98 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 110 " --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 13 removed outlier: 3.579A pdb=" N SER I 120 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.585A pdb=" N VAL J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 11 through 13 removed outlier: 3.622A pdb=" N SER J 120 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) 1753 hydrogen bonds defined for protein. 4521 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: 10.59 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13065 1.34 - 1.46: 9636 1.46 - 1.58: 19263 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 42204 Sorted by residual: bond pdb=" C ALA C 485 " pdb=" N PRO C 486 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.71e+00 bond pdb=" C ALA E 485 " pdb=" N PRO E 486 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.52e+00 bond pdb=" C ALA A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.12e+00 bond pdb=" CA VAL B 742 " pdb=" CB VAL B 742 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.05e+00 bond pdb=" C GLN L 39 " pdb=" N ALA L 40 " ideal model delta sigma weight residual 1.331 1.310 0.021 2.07e-02 2.33e+03 1.04e+00 ... (remaining 42199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 56146 1.40 - 2.81: 915 2.81 - 4.21: 149 4.21 - 5.61: 28 5.61 - 7.02: 2 Bond angle restraints: 57240 Sorted by residual: angle pdb=" N VAL B 591 " pdb=" CA VAL B 591 " pdb=" C VAL B 591 " ideal model delta sigma weight residual 113.71 110.68 3.03 9.50e-01 1.11e+00 1.02e+01 angle pdb=" C THR H 104 " pdb=" N THR H 105 " pdb=" CA THR H 105 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.77e+00 angle pdb=" C THR K 104 " pdb=" N THR K 105 " pdb=" CA THR K 105 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.55e+00 angle pdb=" C THR G 104 " pdb=" N THR G 105 " pdb=" CA THR G 105 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.51e+00 angle pdb=" C THR L 104 " pdb=" N THR L 105 " pdb=" CA THR L 105 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.23e+00 ... (remaining 57235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 23495 16.76 - 33.51: 1391 33.51 - 50.27: 397 50.27 - 67.03: 76 67.03 - 83.79: 3 Dihedral angle restraints: 25362 sinusoidal: 10476 harmonic: 14886 Sorted by residual: dihedral pdb=" CA TRP L 33 " pdb=" C TRP L 33 " pdb=" N MET L 34 " pdb=" CA MET L 34 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP J 33 " pdb=" C TRP J 33 " pdb=" N MET J 34 " pdb=" CA MET J 34 " ideal model delta harmonic sigma weight residual -180.00 -160.53 -19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TRP H 33 " pdb=" C TRP H 33 " pdb=" N MET H 34 " pdb=" CA MET H 34 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 25359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3668 0.027 - 0.054: 1873 0.054 - 0.081: 649 0.081 - 0.108: 222 0.108 - 0.135: 86 Chirality restraints: 6498 Sorted by residual: chirality pdb=" CA ILE F 438 " pdb=" N ILE F 438 " pdb=" C ILE F 438 " pdb=" CB ILE F 438 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL L 93 " pdb=" N VAL L 93 " pdb=" C VAL L 93 " pdb=" CB VAL L 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE F 674 " pdb=" N ILE F 674 " pdb=" C ILE F 674 " pdb=" CB ILE F 674 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 6495 not shown) Planarity restraints: 7122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 795 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 796 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 796 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 796 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 795 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO D 796 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 796 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 796 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 795 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO F 796 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO F 796 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 796 " 0.017 5.00e-02 4.00e+02 ... (remaining 7119 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 791 2.68 - 3.24: 41445 3.24 - 3.79: 67004 3.79 - 4.35: 90060 4.35 - 4.90: 146018 Nonbonded interactions: 345318 Sorted by model distance: nonbonded pdb=" OH TYR B 513 " pdb=" O VAL B 536 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR H 101 " pdb=" O GLN H 107 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR L 101 " pdb=" O GLN L 107 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR J 101 " pdb=" O GLN J 107 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR D 513 " pdb=" O VAL D 536 " model vdw 2.153 3.040 ... (remaining 345313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 38.860 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.120 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.002 0.044 42228 Z= 0.120 Angle : 0.488 7.016 57288 Z= 0.276 Chirality : 0.039 0.135 6498 Planarity : 0.003 0.033 7122 Dihedral : 11.731 83.787 15642 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.75 % Allowed : 7.44 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4980 helix: 0.24 (0.12), residues: 2007 sheet: -0.64 (0.19), residues: 879 loop : -0.36 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 492 TYR 0.011 0.001 TYR C 332 PHE 0.010 0.001 PHE D 146 TRP 0.015 0.001 TRP G 33 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00234 (42204) covalent geometry : angle 0.48747 (57240) SS BOND : bond 0.00127 ( 24) SS BOND : angle 0.92759 ( 48) hydrogen bonds : bond 0.15400 ( 1748) hydrogen bonds : angle 5.84068 ( 4521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 768 time to evaluate : 1.529 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7331 (t0) cc_final: 0.6982 (t0) REVERT: A 238 GLU cc_start: 0.7627 (tt0) cc_final: 0.7228 (tm-30) REVERT: A 288 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 415 LYS cc_start: 0.5880 (tttt) cc_final: 0.5612 (tptt) REVERT: A 471 LEU cc_start: 0.7565 (tp) cc_final: 0.7117 (pt) REVERT: A 495 LEU cc_start: 0.4085 (tp) cc_final: 0.3767 (tp) REVERT: A 562 VAL cc_start: 0.7636 (t) cc_final: 0.7418 (t) REVERT: A 603 LEU cc_start: 0.5794 (mt) cc_final: 0.5090 (mt) REVERT: A 700 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.4941 (mp) REVERT: A 744 GLN cc_start: 0.4746 (mp10) cc_final: 0.4463 (pm20) REVERT: B 104 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8737 (t70) REVERT: B 160 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6819 (mm) REVERT: B 238 GLU cc_start: 0.6119 (tt0) cc_final: 0.5736 (pp20) REVERT: B 250 PHE cc_start: 0.5013 (t80) cc_final: 0.4624 (t80) REVERT: B 472 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7474 (tttp) REVERT: B 545 ARG cc_start: 0.6288 (mmm160) cc_final: 0.5927 (mmm160) REVERT: B 687 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5783 (mt) REVERT: B 706 LEU cc_start: 0.8130 (mt) cc_final: 0.7829 (mm) REVERT: B 715 VAL cc_start: 0.6141 (OUTLIER) cc_final: 0.5889 (t) REVERT: C 235 LYS cc_start: 0.7340 (mptt) cc_final: 0.6784 (tptp) REVERT: C 253 HIS cc_start: 0.5367 (OUTLIER) cc_final: 0.4986 (t-90) REVERT: C 473 GLU cc_start: 0.5388 (mt-10) cc_final: 0.5090 (mp0) REVERT: C 755 ASN cc_start: 0.6566 (t0) cc_final: 0.5336 (m110) REVERT: D 19 ILE cc_start: 0.8490 (pt) cc_final: 0.7971 (mp) REVERT: D 250 PHE cc_start: 0.4833 (t80) cc_final: 0.4357 (t80) REVERT: D 321 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7893 (mt) REVERT: D 354 GLU cc_start: 0.4781 (OUTLIER) cc_final: 0.4143 (tp30) REVERT: D 545 ARG cc_start: 0.6254 (mmm160) cc_final: 0.5796 (mmm160) REVERT: D 706 LEU cc_start: 0.7343 (mt) cc_final: 0.6920 (mp) REVERT: D 711 GLN cc_start: 0.4251 (mt0) cc_final: 0.4048 (mm-40) REVERT: D 715 VAL cc_start: 0.6913 (OUTLIER) cc_final: 0.6646 (t) REVERT: D 794 LEU cc_start: 0.1294 (OUTLIER) cc_final: 0.1091 (pp) REVERT: E 243 LEU cc_start: 0.8041 (tp) cc_final: 0.7829 (tp) REVERT: E 344 LEU cc_start: 0.7019 (mt) cc_final: 0.6420 (pp) REVERT: E 468 LEU cc_start: 0.4897 (mt) cc_final: 0.4682 (mp) REVERT: E 473 GLU cc_start: 0.5592 (mt-10) cc_final: 0.5327 (mp0) REVERT: E 540 LEU cc_start: 0.7185 (tp) cc_final: 0.6954 (tp) REVERT: E 592 ASN cc_start: 0.5740 (m-40) cc_final: 0.5467 (p0) REVERT: E 603 LEU cc_start: 0.5623 (mt) cc_final: 0.5364 (mt) REVERT: E 755 ASN cc_start: 0.4595 (t0) cc_final: 0.4300 (m-40) REVERT: E 761 LEU cc_start: 0.1846 (OUTLIER) cc_final: 0.1518 (mp) REVERT: F 29 ASP cc_start: 0.7493 (t0) cc_final: 0.7144 (m-30) REVERT: F 160 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7036 (mm) REVERT: F 250 PHE cc_start: 0.4981 (t80) cc_final: 0.4613 (t80) REVERT: F 275 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7202 (t80) REVERT: F 321 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7958 (mt) REVERT: F 423 ASN cc_start: 0.4965 (p0) cc_final: 0.4082 (p0) REVERT: F 450 VAL cc_start: 0.6550 (t) cc_final: 0.6042 (t) REVERT: F 468 LEU cc_start: 0.5098 (mt) cc_final: 0.4871 (mt) REVERT: F 471 LEU cc_start: 0.7118 (tp) cc_final: 0.6918 (pp) REVERT: F 488 LEU cc_start: 0.6833 (tp) cc_final: 0.6416 (pp) REVERT: F 546 LEU cc_start: 0.6094 (tp) cc_final: 0.5757 (mt) REVERT: F 548 VAL cc_start: 0.5496 (t) cc_final: 0.5075 (t) REVERT: F 673 LYS cc_start: 0.5136 (mptt) cc_final: 0.4778 (pttt) REVERT: F 701 PRO cc_start: 0.4088 (Cg_exo) cc_final: 0.3830 (Cg_endo) REVERT: F 706 LEU cc_start: 0.8317 (mt) cc_final: 0.8068 (mm) REVERT: F 708 GLN cc_start: 0.4462 (OUTLIER) cc_final: 0.4147 (mm110) REVERT: K 33 TRP cc_start: 0.2384 (OUTLIER) cc_final: 0.0796 (m100) REVERT: K 34 MET cc_start: 0.6861 (tpp) cc_final: 0.6495 (mmp) REVERT: K 36 TRP cc_start: 0.3327 (m100) cc_final: 0.3053 (m100) REVERT: K 37 TYR cc_start: 0.3590 (OUTLIER) cc_final: 0.3259 (m-80) REVERT: K 73 ASP cc_start: 0.5837 (m-30) cc_final: 0.4864 (m-30) REVERT: K 86 LEU cc_start: -0.2610 (OUTLIER) cc_final: -0.3202 (mt) REVERT: K 95 TYR cc_start: 0.4890 (m-10) cc_final: 0.4603 (m-80) REVERT: K 96 CYS cc_start: -0.0159 (OUTLIER) cc_final: -0.0540 (p) REVERT: K 98 VAL cc_start: 0.4399 (OUTLIER) cc_final: 0.3734 (p) REVERT: K 107 GLN cc_start: 0.6729 (tt0) cc_final: 0.6481 (tp40) REVERT: L 3 GLN cc_start: 0.6653 (pp30) cc_final: 0.5813 (mp-120) REVERT: L 5 VAL cc_start: 0.6520 (t) cc_final: 0.6270 (m) REVERT: L 29 VAL cc_start: 0.4267 (OUTLIER) cc_final: 0.3946 (p) REVERT: L 89 GLU cc_start: 0.3378 (pp20) cc_final: 0.2996 (pt0) REVERT: L 113 GLN cc_start: 0.5765 (mm-40) cc_final: 0.4703 (mt0) REVERT: L 116 GLN cc_start: 0.6034 (mt0) cc_final: 0.5613 (tm-30) REVERT: G 33 TRP cc_start: 0.1637 (OUTLIER) cc_final: 0.0076 (m100) REVERT: G 34 MET cc_start: 0.6877 (tpp) cc_final: 0.6469 (mmp) REVERT: G 35 TRP cc_start: 0.4909 (OUTLIER) cc_final: 0.4672 (m-10) REVERT: G 59 TRP cc_start: 0.4977 (m100) cc_final: 0.4776 (m100) REVERT: G 95 TYR cc_start: 0.4787 (m-80) cc_final: 0.4314 (m-80) REVERT: G 96 CYS cc_start: 0.0140 (OUTLIER) cc_final: -0.0179 (p) REVERT: H 4 LEU cc_start: -0.0818 (mp) cc_final: -0.1156 (mm) REVERT: H 29 VAL cc_start: 0.3099 (OUTLIER) cc_final: 0.2877 (p) REVERT: H 37 TYR cc_start: 0.4830 (OUTLIER) cc_final: 0.1878 (t80) REVERT: H 101 THR cc_start: 0.5294 (OUTLIER) cc_final: 0.5082 (m) REVERT: H 113 GLN cc_start: 0.6920 (mm-40) cc_final: 0.6177 (mm-40) REVERT: I 33 TRP cc_start: 0.2158 (OUTLIER) cc_final: 0.0693 (m100) REVERT: I 34 MET cc_start: 0.6521 (tpp) cc_final: 0.6298 (mmp) REVERT: I 35 TRP cc_start: 0.5426 (OUTLIER) cc_final: 0.4711 (m-10) REVERT: I 86 LEU cc_start: -0.5362 (OUTLIER) cc_final: -0.5819 (mt) REVERT: I 96 CYS cc_start: -0.0340 (OUTLIER) cc_final: -0.0885 (p) REVERT: I 98 VAL cc_start: 0.4783 (OUTLIER) cc_final: 0.4213 (p) outliers start: 172 outliers final: 40 residues processed: 919 average time/residue: 0.2723 time to fit residues: 399.9909 Evaluate side-chains 447 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 374 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 673 LYS Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 708 GLN Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 37 TYR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 37 TYR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 718 ASN C 288 ASN D 404 GLN ** D 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 GLN D 696 ASN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 288 ASN F 105 GLN ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 617 GLN F 650 HIS ** F 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 718 ASN K 74 ASN K 107 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN G 74 ASN G 97 ASN G 107 GLN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN I 84 ASN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 106 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.177128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.150156 restraints weight = 83916.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.146383 restraints weight = 123166.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.143408 restraints weight = 98690.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.142865 restraints weight = 92946.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.141935 restraints weight = 77623.023| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 42228 Z= 0.261 Angle : 0.686 10.572 57288 Z= 0.357 Chirality : 0.047 0.246 6498 Planarity : 0.005 0.072 7122 Dihedral : 6.900 59.645 5631 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.30 % Allowed : 12.11 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4980 helix: -0.36 (0.11), residues: 2070 sheet: -0.74 (0.18), residues: 894 loop : -0.62 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 345 TYR 0.031 0.002 TYR B 106 PHE 0.025 0.002 PHE B 443 TRP 0.025 0.002 TRP H 33 HIS 0.012 0.002 HIS E 253 Details of bonding type rmsd covalent geometry : bond 0.00612 (42204) covalent geometry : angle 0.68494 (57240) SS BOND : bond 0.00856 ( 24) SS BOND : angle 1.48231 ( 48) hydrogen bonds : bond 0.04349 ( 1748) hydrogen bonds : angle 5.19630 ( 4521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 408 time to evaluate : 1.544 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 17 TYR cc_start: 0.6501 (m-10) cc_final: 0.6184 (m-10) REVERT: A 29 ASP cc_start: 0.7195 (t0) cc_final: 0.6905 (t0) REVERT: A 353 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.5932 (t80) REVERT: A 375 MET cc_start: 0.8029 (mtt) cc_final: 0.7726 (mtm) REVERT: A 475 TRP cc_start: 0.6587 (m-10) cc_final: 0.5596 (m-10) REVERT: A 658 ILE cc_start: 0.4853 (mm) cc_final: 0.4643 (mm) REVERT: A 800 GLU cc_start: 0.2090 (OUTLIER) cc_final: 0.1729 (tp30) REVERT: B 160 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7201 (mt) REVERT: B 250 PHE cc_start: 0.5257 (t80) cc_final: 0.4902 (t80) REVERT: B 478 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7620 (m-70) REVERT: B 715 VAL cc_start: 0.5013 (OUTLIER) cc_final: 0.4797 (t) REVERT: C 353 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.5050 (t80) REVERT: C 475 TRP cc_start: 0.6226 (m-10) cc_final: 0.5672 (m-10) REVERT: C 755 ASN cc_start: 0.5147 (t0) cc_final: 0.4478 (m110) REVERT: D 19 ILE cc_start: 0.8566 (pt) cc_final: 0.8159 (mp) REVERT: D 250 PHE cc_start: 0.5028 (t80) cc_final: 0.4650 (t80) REVERT: D 337 MET cc_start: 0.7283 (mmm) cc_final: 0.7041 (mmm) REVERT: D 354 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5700 (tp30) REVERT: D 715 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6519 (t) REVERT: E 243 LEU cc_start: 0.8602 (tp) cc_final: 0.8281 (mp) REVERT: E 321 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7978 (tp) REVERT: E 353 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.5427 (t80) REVERT: F 160 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7413 (mm) REVERT: F 250 PHE cc_start: 0.5102 (t80) cc_final: 0.4580 (t80) REVERT: F 275 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7342 (t80) REVERT: F 321 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8282 (mt) REVERT: F 378 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7395 (mp) REVERT: F 468 LEU cc_start: 0.4377 (mt) cc_final: 0.4135 (mt) REVERT: F 521 LEU cc_start: 0.7302 (tp) cc_final: 0.6972 (tp) REVERT: F 549 LEU cc_start: 0.6911 (tp) cc_final: 0.6289 (tp) REVERT: F 706 LEU cc_start: 0.7463 (mt) cc_final: 0.7259 (mm) REVERT: K 33 TRP cc_start: 0.2512 (OUTLIER) cc_final: 0.0914 (m100) REVERT: K 37 TYR cc_start: 0.4169 (OUTLIER) cc_final: 0.3963 (m-80) REVERT: K 86 LEU cc_start: -0.0831 (OUTLIER) cc_final: -0.1760 (mt) REVERT: K 96 CYS cc_start: -0.0130 (OUTLIER) cc_final: -0.0406 (p) REVERT: K 98 VAL cc_start: 0.3861 (OUTLIER) cc_final: 0.3252 (p) REVERT: L 89 GLU cc_start: 0.2866 (pp20) cc_final: 0.2626 (pt0) REVERT: G 33 TRP cc_start: 0.1624 (OUTLIER) cc_final: 0.0178 (m100) REVERT: G 35 TRP cc_start: 0.4837 (OUTLIER) cc_final: 0.4606 (m-10) REVERT: G 82 GLN cc_start: 0.4885 (tp40) cc_final: 0.3757 (tm-30) REVERT: G 95 TYR cc_start: 0.2873 (m-80) cc_final: 0.2571 (m-80) REVERT: H 4 LEU cc_start: -0.0858 (mp) cc_final: -0.1187 (mm) REVERT: H 113 GLN cc_start: 0.5391 (mm-40) cc_final: 0.4646 (mm-40) REVERT: I 33 TRP cc_start: 0.1836 (OUTLIER) cc_final: 0.0547 (m100) REVERT: I 86 LEU cc_start: -0.3427 (OUTLIER) cc_final: -0.4426 (mt) REVERT: I 90 ASP cc_start: 0.3429 (OUTLIER) cc_final: 0.3222 (m-30) REVERT: I 98 VAL cc_start: 0.4557 (OUTLIER) cc_final: 0.3857 (p) REVERT: J 83 MET cc_start: 0.2776 (OUTLIER) cc_final: 0.0893 (pmm) REVERT: J 89 GLU cc_start: 0.3314 (OUTLIER) cc_final: 0.2974 (pm20) REVERT: J 108 TYR cc_start: 0.6053 (m-10) cc_final: 0.5287 (m-10) REVERT: J 113 GLN cc_start: 0.6082 (mm110) cc_final: 0.5443 (pt0) outliers start: 197 outliers final: 99 residues processed: 584 average time/residue: 0.2375 time to fit residues: 232.8935 Evaluate side-chains 419 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 293 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 687 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 721 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 96 CYS Chi-restraints excluded: chain K residue 98 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 430 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 221 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 409 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 479 optimal weight: 5.9990 chunk 414 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 442 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 288 ASN A 478 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 ASN F 711 GLN K 82 GLN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.177551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.151561 restraints weight = 83651.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.147875 restraints weight = 123730.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.146148 restraints weight = 90595.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.145588 restraints weight = 89309.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.144593 restraints weight = 78222.851| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 42228 Z= 0.190 Angle : 0.596 9.727 57288 Z= 0.312 Chirality : 0.043 0.205 6498 Planarity : 0.004 0.071 7122 Dihedral : 6.292 59.503 5594 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.25 % Allowed : 14.31 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.12), residues: 4980 helix: -0.33 (0.11), residues: 2052 sheet: -0.73 (0.18), residues: 897 loop : -0.60 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 762 TYR 0.017 0.002 TYR E 332 PHE 0.024 0.002 PHE E 699 TRP 0.027 0.002 TRP L 47 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00437 (42204) covalent geometry : angle 0.59533 (57240) SS BOND : bond 0.00346 ( 24) SS BOND : angle 1.19083 ( 48) hydrogen bonds : bond 0.03849 ( 1748) hydrogen bonds : angle 5.04337 ( 4521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 327 time to evaluate : 1.618 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.6339 (m-10) cc_final: 0.6125 (m-10) REVERT: A 29 ASP cc_start: 0.7192 (t0) cc_final: 0.6919 (t0) REVERT: A 353 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6035 (t80) REVERT: A 375 MET cc_start: 0.8016 (mtt) cc_final: 0.7664 (mtm) REVERT: A 414 ASP cc_start: 0.4842 (OUTLIER) cc_final: 0.4424 (t70) REVERT: A 658 ILE cc_start: 0.4813 (mm) cc_final: 0.4568 (mm) REVERT: A 800 GLU cc_start: 0.1996 (OUTLIER) cc_final: 0.1707 (tp30) REVERT: B 160 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7299 (mm) REVERT: B 250 PHE cc_start: 0.5299 (t80) cc_final: 0.4939 (t80) REVERT: B 478 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7508 (m170) REVERT: B 493 GLU cc_start: 0.6087 (pp20) cc_final: 0.5476 (pp20) REVERT: B 549 LEU cc_start: 0.7014 (tp) cc_final: 0.6766 (mm) REVERT: B 715 VAL cc_start: 0.5085 (OUTLIER) cc_final: 0.4862 (t) REVERT: C 353 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.5150 (t80) REVERT: C 475 TRP cc_start: 0.6280 (m-10) cc_final: 0.5357 (m-10) REVERT: C 761 LEU cc_start: 0.1973 (OUTLIER) cc_final: 0.1579 (mt) REVERT: D 19 ILE cc_start: 0.8610 (pt) cc_final: 0.8158 (mp) REVERT: D 250 PHE cc_start: 0.5036 (t80) cc_final: 0.4550 (t80) REVERT: D 354 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5685 (tp30) REVERT: D 448 LEU cc_start: 0.6717 (tp) cc_final: 0.6287 (tp) REVERT: D 715 VAL cc_start: 0.6790 (OUTLIER) cc_final: 0.6453 (t) REVERT: E 243 LEU cc_start: 0.8478 (tp) cc_final: 0.7734 (mp) REVERT: E 353 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.5536 (t80) REVERT: F 160 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7366 (mm) REVERT: F 275 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7425 (t80) REVERT: F 321 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8337 (mt) REVERT: K 33 TRP cc_start: 0.2607 (OUTLIER) cc_final: 0.0832 (m100) REVERT: K 37 TYR cc_start: 0.4222 (OUTLIER) cc_final: 0.3878 (m-80) REVERT: K 86 LEU cc_start: -0.0791 (OUTLIER) cc_final: -0.1818 (mt) REVERT: L 118 THR cc_start: 0.4436 (OUTLIER) cc_final: 0.4177 (m) REVERT: G 33 TRP cc_start: 0.1780 (OUTLIER) cc_final: 0.0241 (m100) REVERT: H 4 LEU cc_start: -0.0982 (mp) cc_final: -0.1294 (mt) REVERT: H 113 GLN cc_start: 0.5228 (mm-40) cc_final: 0.4540 (mm-40) REVERT: I 33 TRP cc_start: 0.2247 (OUTLIER) cc_final: 0.0853 (m100) REVERT: I 86 LEU cc_start: -0.3338 (OUTLIER) cc_final: -0.4397 (mt) REVERT: I 87 LYS cc_start: 0.3209 (mttt) cc_final: 0.2833 (mtpp) REVERT: J 83 MET cc_start: 0.2558 (OUTLIER) cc_final: 0.0822 (pmm) REVERT: J 113 GLN cc_start: 0.6099 (mm110) cc_final: 0.5580 (tm-30) outliers start: 195 outliers final: 107 residues processed: 497 average time/residue: 0.2243 time to fit residues: 191.3991 Evaluate side-chains 408 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 279 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 427 LYS Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 275 PHE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 535 ILE Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 263 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 434 optimal weight: 8.9990 chunk 157 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 426 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN C 755 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.177813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.151407 restraints weight = 82874.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.147149 restraints weight = 120004.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.144442 restraints weight = 98970.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.144148 restraints weight = 87948.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.143497 restraints weight = 72438.731| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 42228 Z= 0.166 Angle : 0.576 8.749 57288 Z= 0.300 Chirality : 0.042 0.212 6498 Planarity : 0.004 0.050 7122 Dihedral : 6.108 59.338 5583 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.93 % Allowed : 15.21 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.12), residues: 4980 helix: -0.40 (0.11), residues: 2094 sheet: -0.74 (0.18), residues: 918 loop : -0.70 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 762 TYR 0.024 0.002 TYR G 110 PHE 0.019 0.002 PHE K 27 TRP 0.026 0.002 TRP A 647 HIS 0.008 0.001 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00384 (42204) covalent geometry : angle 0.57503 (57240) SS BOND : bond 0.00383 ( 24) SS BOND : angle 1.13306 ( 48) hydrogen bonds : bond 0.03634 ( 1748) hydrogen bonds : angle 4.95746 ( 4521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 304 time to evaluate : 1.523 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: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7173 (t0) cc_final: 0.6901 (t0) REVERT: A 353 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6311 (t80) REVERT: A 375 MET cc_start: 0.8022 (mtt) cc_final: 0.7732 (mtm) REVERT: A 658 ILE cc_start: 0.4823 (mm) cc_final: 0.4551 (mm) REVERT: B 160 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7190 (mm) REVERT: B 250 PHE cc_start: 0.5283 (t80) cc_final: 0.4929 (t80) REVERT: B 478 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7512 (m170) REVERT: B 493 GLU cc_start: 0.6175 (pp20) cc_final: 0.5550 (pp20) REVERT: B 715 VAL cc_start: 0.5259 (OUTLIER) cc_final: 0.5050 (t) REVERT: C 353 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.5574 (t80) REVERT: C 475 TRP cc_start: 0.6314 (m-10) cc_final: 0.5380 (m-10) REVERT: C 761 LEU cc_start: 0.1987 (OUTLIER) cc_final: 0.1620 (mt) REVERT: D 19 ILE cc_start: 0.8665 (pt) cc_final: 0.8215 (mp) REVERT: D 250 PHE cc_start: 0.5128 (t80) cc_final: 0.4600 (t80) REVERT: D 354 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5667 (tp30) REVERT: D 375 MET cc_start: 0.7608 (mtt) cc_final: 0.7361 (mtm) REVERT: D 448 LEU cc_start: 0.6809 (tp) cc_final: 0.6301 (tp) REVERT: D 474 LEU cc_start: 0.7601 (pt) cc_final: 0.7003 (tp) REVERT: D 715 VAL cc_start: 0.6964 (OUTLIER) cc_final: 0.6650 (t) REVERT: E 243 LEU cc_start: 0.8420 (tp) cc_final: 0.7721 (mp) REVERT: E 337 MET cc_start: 0.7477 (mmm) cc_final: 0.7162 (mmm) REVERT: E 353 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.5528 (t80) REVERT: E 500 ILE cc_start: 0.5166 (OUTLIER) cc_final: 0.4956 (mp) REVERT: E 520 GLU cc_start: 0.5046 (OUTLIER) cc_final: 0.4691 (pt0) REVERT: F 160 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7288 (mm) REVERT: F 321 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8330 (mt) REVERT: F 345 ARG cc_start: 0.5682 (OUTLIER) cc_final: 0.5438 (mmt-90) REVERT: F 378 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7444 (mp) REVERT: K 33 TRP cc_start: 0.2244 (OUTLIER) cc_final: 0.0639 (m100) REVERT: K 86 LEU cc_start: -0.0897 (OUTLIER) cc_final: -0.1855 (mt) REVERT: K 95 TYR cc_start: 0.3339 (m-80) cc_final: 0.2979 (m-80) REVERT: G 33 TRP cc_start: 0.1503 (OUTLIER) cc_final: 0.0287 (m100) REVERT: H 4 LEU cc_start: -0.0940 (mp) cc_final: -0.1188 (mt) REVERT: H 113 GLN cc_start: 0.5465 (mm-40) cc_final: 0.4701 (mm-40) REVERT: I 33 TRP cc_start: 0.1685 (OUTLIER) cc_final: 0.0608 (m100) REVERT: I 86 LEU cc_start: -0.3582 (OUTLIER) cc_final: -0.4513 (mt) REVERT: I 87 LYS cc_start: 0.3355 (mttt) cc_final: 0.3067 (mtpp) outliers start: 180 outliers final: 111 residues processed: 466 average time/residue: 0.2222 time to fit residues: 177.9555 Evaluate side-chains 403 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 272 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 500 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 520 GLU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 345 ARG Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 145 optimal weight: 0.5980 chunk 485 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 459 optimal weight: 4.9990 chunk 354 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 186 optimal weight: 0.0870 chunk 337 optimal weight: 9.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 764 ASN ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.178662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.153282 restraints weight = 82735.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.149844 restraints weight = 119510.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.146724 restraints weight = 98020.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.146266 restraints weight = 93912.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.145578 restraints weight = 75027.661| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42228 Z= 0.126 Angle : 0.548 9.911 57288 Z= 0.285 Chirality : 0.041 0.155 6498 Planarity : 0.004 0.102 7122 Dihedral : 5.940 59.586 5577 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.38 % Allowed : 16.21 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4980 helix: -0.31 (0.11), residues: 2103 sheet: -0.74 (0.18), residues: 918 loop : -0.70 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 685 TYR 0.017 0.001 TYR K 110 PHE 0.023 0.001 PHE C 699 TRP 0.027 0.002 TRP A 647 HIS 0.006 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00284 (42204) covalent geometry : angle 0.54740 (57240) SS BOND : bond 0.00243 ( 24) SS BOND : angle 0.98030 ( 48) hydrogen bonds : bond 0.03394 ( 1748) hydrogen bonds : angle 4.80798 ( 4521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 315 time to evaluate : 1.512 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: symmetry clash REVERT: A 29 ASP cc_start: 0.7079 (t0) cc_final: 0.6817 (t0) REVERT: A 353 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.6270 (t80) REVERT: A 414 ASP cc_start: 0.4790 (OUTLIER) cc_final: 0.4436 (t70) REVERT: A 658 ILE cc_start: 0.4776 (mm) cc_final: 0.4517 (mm) REVERT: B 160 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7175 (mm) REVERT: B 250 PHE cc_start: 0.5681 (t80) cc_final: 0.5223 (t80) REVERT: B 468 LEU cc_start: 0.4890 (mt) cc_final: 0.4631 (mt) REVERT: B 478 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7196 (m170) REVERT: B 493 GLU cc_start: 0.6088 (pp20) cc_final: 0.5516 (pp20) REVERT: C 353 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5627 (t80) REVERT: C 475 TRP cc_start: 0.6096 (m-10) cc_final: 0.5197 (m-10) REVERT: C 761 LEU cc_start: 0.1916 (OUTLIER) cc_final: 0.1572 (mt) REVERT: D 19 ILE cc_start: 0.8666 (pt) cc_final: 0.8343 (mp) REVERT: D 250 PHE cc_start: 0.5268 (t80) cc_final: 0.4752 (t80) REVERT: D 354 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: D 448 LEU cc_start: 0.6697 (tp) cc_final: 0.6212 (tp) REVERT: D 715 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6679 (t) REVERT: E 243 LEU cc_start: 0.8312 (tp) cc_final: 0.7663 (mp) REVERT: E 337 MET cc_start: 0.7088 (mmm) cc_final: 0.6866 (mmm) REVERT: E 353 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5679 (t80) REVERT: F 160 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7435 (mm) REVERT: K 33 TRP cc_start: 0.1693 (OUTLIER) cc_final: 0.0313 (m100) REVERT: K 86 LEU cc_start: -0.0962 (OUTLIER) cc_final: -0.1987 (mt) REVERT: K 95 TYR cc_start: 0.3253 (m-80) cc_final: 0.2993 (m-80) REVERT: L 113 GLN cc_start: 0.4317 (pm20) cc_final: 0.2956 (mm-40) REVERT: G 33 TRP cc_start: 0.1475 (OUTLIER) cc_final: 0.0235 (m100) REVERT: H 4 LEU cc_start: -0.1254 (mp) cc_final: -0.2168 (mm) REVERT: H 83 MET cc_start: 0.3540 (mpp) cc_final: 0.3265 (tpp) REVERT: I 33 TRP cc_start: 0.1548 (OUTLIER) cc_final: 0.0679 (m100) REVERT: I 87 LYS cc_start: 0.3322 (mttt) cc_final: 0.3042 (mtpp) REVERT: I 98 VAL cc_start: 0.4529 (OUTLIER) cc_final: 0.3945 (p) REVERT: I 108 TYR cc_start: 0.3154 (OUTLIER) cc_final: 0.2485 (t80) REVERT: J 83 MET cc_start: 0.2825 (OUTLIER) cc_final: 0.1198 (pmm) outliers start: 155 outliers final: 101 residues processed: 452 average time/residue: 0.2246 time to fit residues: 174.3120 Evaluate side-chains 394 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 276 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 343 optimal weight: 4.9990 chunk 463 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 334 optimal weight: 0.9990 chunk 462 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 457 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 HIS F 377 HIS ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.177920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.150778 restraints weight = 83050.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.148022 restraints weight = 123878.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.145105 restraints weight = 90193.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.144739 restraints weight = 91407.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.144120 restraints weight = 72873.618| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 42228 Z= 0.154 Angle : 0.568 14.446 57288 Z= 0.294 Chirality : 0.042 0.188 6498 Planarity : 0.003 0.054 7122 Dihedral : 5.861 59.506 5570 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.90 % Allowed : 16.12 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4980 helix: -0.34 (0.11), residues: 2085 sheet: -0.72 (0.18), residues: 918 loop : -0.76 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 685 TYR 0.026 0.001 TYR G 110 PHE 0.020 0.001 PHE C 699 TRP 0.029 0.002 TRP A 647 HIS 0.010 0.001 HIS F 155 Details of bonding type rmsd covalent geometry : bond 0.00357 (42204) covalent geometry : angle 0.56723 (57240) SS BOND : bond 0.00307 ( 24) SS BOND : angle 0.86502 ( 48) hydrogen bonds : bond 0.03473 ( 1748) hydrogen bonds : angle 4.80871 ( 4521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 301 time to evaluate : 1.538 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: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7117 (t0) cc_final: 0.6847 (t0) REVERT: A 353 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6342 (t80) REVERT: A 414 ASP cc_start: 0.4922 (OUTLIER) cc_final: 0.4430 (t70) REVERT: A 658 ILE cc_start: 0.4944 (mm) cc_final: 0.4565 (mm) REVERT: B 160 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7070 (mt) REVERT: B 250 PHE cc_start: 0.5507 (t80) cc_final: 0.5094 (t80) REVERT: B 468 LEU cc_start: 0.4762 (mt) cc_final: 0.4487 (mt) REVERT: B 478 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.7277 (m170) REVERT: B 493 GLU cc_start: 0.6243 (pp20) cc_final: 0.5702 (pp20) REVERT: C 353 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.5747 (t80) REVERT: C 475 TRP cc_start: 0.6131 (m-10) cc_final: 0.5229 (m-10) REVERT: C 761 LEU cc_start: 0.1807 (OUTLIER) cc_final: 0.1454 (mt) REVERT: D 19 ILE cc_start: 0.8811 (pt) cc_final: 0.8476 (mp) REVERT: D 250 PHE cc_start: 0.5180 (t80) cc_final: 0.4743 (t80) REVERT: D 354 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5824 (tp30) REVERT: D 448 LEU cc_start: 0.6619 (tp) cc_final: 0.6150 (tp) REVERT: D 478 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.6324 (m-70) REVERT: D 715 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6681 (t) REVERT: E 243 LEU cc_start: 0.8342 (tp) cc_final: 0.7688 (mp) REVERT: E 353 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5731 (t80) REVERT: E 685 ARG cc_start: 0.6877 (mpt180) cc_final: 0.5787 (mmt180) REVERT: F 160 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7397 (mt) REVERT: F 378 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7260 (mp) REVERT: F 478 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.6461 (m-70) REVERT: K 86 LEU cc_start: -0.1042 (OUTLIER) cc_final: -0.2178 (mt) REVERT: G 33 TRP cc_start: 0.1442 (OUTLIER) cc_final: 0.0125 (m100) REVERT: G 108 TYR cc_start: 0.4407 (OUTLIER) cc_final: 0.3937 (t80) REVERT: H 83 MET cc_start: 0.3562 (mpp) cc_final: 0.3167 (tpp) REVERT: I 33 TRP cc_start: 0.1343 (OUTLIER) cc_final: 0.0423 (m100) REVERT: I 87 LYS cc_start: 0.3478 (mttt) cc_final: 0.3163 (mtpp) REVERT: I 108 TYR cc_start: 0.3508 (OUTLIER) cc_final: 0.2928 (t80) REVERT: J 83 MET cc_start: 0.3069 (OUTLIER) cc_final: 0.1338 (pmm) REVERT: J 84 ASN cc_start: 0.5618 (m-40) cc_final: 0.5417 (m-40) outliers start: 179 outliers final: 126 residues processed: 459 average time/residue: 0.2223 time to fit residues: 176.1153 Evaluate side-chains 413 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 268 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 HIS Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 650 HIS Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 68 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 408 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 299 optimal weight: 0.6980 chunk 270 optimal weight: 9.9990 chunk 221 optimal weight: 0.1980 chunk 421 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 344 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 HIS ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 84 ASN ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.177097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.150852 restraints weight = 82977.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.146973 restraints weight = 121648.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.143980 restraints weight = 96829.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.143675 restraints weight = 91121.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.142988 restraints weight = 71177.197| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42228 Z= 0.186 Angle : 0.598 10.607 57288 Z= 0.310 Chirality : 0.043 0.185 6498 Planarity : 0.004 0.050 7122 Dihedral : 5.973 59.149 5570 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.06 % Allowed : 16.97 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4980 helix: -0.30 (0.12), residues: 2010 sheet: -0.78 (0.18), residues: 915 loop : -0.70 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.030 0.002 TYR K 110 PHE 0.027 0.002 PHE E 443 TRP 0.037 0.002 TRP A 647 HIS 0.016 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00434 (42204) covalent geometry : angle 0.59800 (57240) SS BOND : bond 0.00381 ( 24) SS BOND : angle 0.93152 ( 48) hydrogen bonds : bond 0.03586 ( 1748) hydrogen bonds : angle 4.90281 ( 4521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 300 time to evaluate : 1.561 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.7126 (t0) cc_final: 0.6849 (t0) REVERT: A 234 LYS cc_start: 0.6410 (tppt) cc_final: 0.5850 (tptt) REVERT: A 321 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7550 (mp) REVERT: A 343 MET cc_start: 0.6164 (mtp) cc_final: 0.5634 (mtp) REVERT: A 353 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6373 (t80) REVERT: A 375 MET cc_start: 0.7694 (mtp) cc_final: 0.7431 (mtp) REVERT: A 414 ASP cc_start: 0.4986 (OUTLIER) cc_final: 0.4434 (t70) REVERT: A 727 LEU cc_start: 0.3948 (OUTLIER) cc_final: 0.3518 (tp) REVERT: B 160 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7235 (mm) REVERT: B 250 PHE cc_start: 0.5426 (t80) cc_final: 0.5073 (t80) REVERT: B 478 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.7241 (m-70) REVERT: B 493 GLU cc_start: 0.6247 (pp20) cc_final: 0.5678 (pp20) REVERT: C 353 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.5815 (t80) REVERT: C 475 TRP cc_start: 0.6147 (m-10) cc_final: 0.5240 (m-10) REVERT: C 520 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4962 (pt0) REVERT: C 761 LEU cc_start: 0.2121 (OUTLIER) cc_final: 0.1702 (mt) REVERT: D 19 ILE cc_start: 0.8829 (pt) cc_final: 0.8571 (mp) REVERT: D 250 PHE cc_start: 0.5319 (t80) cc_final: 0.4926 (t80) REVERT: D 354 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5892 (tp30) REVERT: D 448 LEU cc_start: 0.6918 (tp) cc_final: 0.6408 (tp) REVERT: D 478 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.6381 (m-70) REVERT: D 715 VAL cc_start: 0.6843 (OUTLIER) cc_final: 0.6487 (t) REVERT: E 243 LEU cc_start: 0.8351 (tp) cc_final: 0.7678 (mp) REVERT: E 321 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7847 (tp) REVERT: E 337 MET cc_start: 0.7053 (mmm) cc_final: 0.6851 (mmm) REVERT: E 353 PHE cc_start: 0.6740 (OUTLIER) cc_final: 0.5974 (t80) REVERT: E 685 ARG cc_start: 0.6879 (mpt180) cc_final: 0.6169 (mmt180) REVERT: F 160 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7154 (mt) REVERT: F 378 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7449 (mp) REVERT: F 478 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6442 (m-70) REVERT: K 33 TRP cc_start: 0.1134 (OUTLIER) cc_final: 0.0300 (m100) REVERT: K 86 LEU cc_start: -0.0852 (OUTLIER) cc_final: -0.1895 (mt) REVERT: G 27 PHE cc_start: 0.0507 (p90) cc_final: 0.0090 (p90) REVERT: G 33 TRP cc_start: 0.1468 (OUTLIER) cc_final: 0.0064 (m100) REVERT: H 19 ARG cc_start: 0.3910 (mmm160) cc_final: 0.3400 (mmm160) REVERT: H 83 MET cc_start: 0.3561 (mpp) cc_final: 0.3074 (tpp) REVERT: I 33 TRP cc_start: 0.1375 (OUTLIER) cc_final: 0.0536 (m100) REVERT: I 87 LYS cc_start: 0.3637 (mttt) cc_final: 0.3321 (mtpp) REVERT: I 108 TYR cc_start: 0.4034 (OUTLIER) cc_final: 0.3457 (t80) REVERT: J 31 GLN cc_start: 0.0504 (tm-30) cc_final: 0.0240 (tp-100) REVERT: J 83 MET cc_start: 0.3170 (OUTLIER) cc_final: 0.1432 (pmm) REVERT: J 84 ASN cc_start: 0.5497 (m-40) cc_final: 0.5268 (m-40) outliers start: 186 outliers final: 140 residues processed: 466 average time/residue: 0.2315 time to fit residues: 186.6851 Evaluate side-chains 445 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 282 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 HIS Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 33 TRP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 108 TYR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 185 optimal weight: 0.9990 chunk 231 optimal weight: 0.6980 chunk 455 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 758 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 155 HIS ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.180781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.153759 restraints weight = 84602.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.151955 restraints weight = 128072.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.150230 restraints weight = 85631.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.149555 restraints weight = 88961.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.148967 restraints weight = 82166.384| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42228 Z= 0.117 Angle : 0.552 10.759 57288 Z= 0.286 Chirality : 0.041 0.162 6498 Planarity : 0.003 0.064 7122 Dihedral : 5.778 59.499 5569 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.51 % Allowed : 17.65 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.12), residues: 4980 helix: -0.20 (0.12), residues: 2031 sheet: -0.76 (0.18), residues: 915 loop : -0.63 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 492 TYR 0.028 0.001 TYR G 110 PHE 0.018 0.001 PHE A 443 TRP 0.039 0.002 TRP A 647 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00263 (42204) covalent geometry : angle 0.55197 (57240) SS BOND : bond 0.00212 ( 24) SS BOND : angle 0.74177 ( 48) hydrogen bonds : bond 0.03287 ( 1748) hydrogen bonds : angle 4.72731 ( 4521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 304 time to evaluate : 1.613 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 29 ASP cc_start: 0.7089 (t0) cc_final: 0.6828 (t0) REVERT: A 234 LYS cc_start: 0.6329 (tppt) cc_final: 0.5187 (tptt) REVERT: A 353 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6309 (t80) REVERT: A 375 MET cc_start: 0.7559 (mtp) cc_final: 0.7313 (mtp) REVERT: A 414 ASP cc_start: 0.4705 (OUTLIER) cc_final: 0.4348 (t70) REVERT: B 160 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6996 (mm) REVERT: B 250 PHE cc_start: 0.5678 (t80) cc_final: 0.5251 (t80) REVERT: B 468 LEU cc_start: 0.4780 (mt) cc_final: 0.4521 (mt) REVERT: B 478 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6980 (m-70) REVERT: B 493 GLU cc_start: 0.6376 (pp20) cc_final: 0.5827 (pp20) REVERT: C 353 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5958 (t80) REVERT: C 475 TRP cc_start: 0.6067 (m-10) cc_final: 0.5226 (m-10) REVERT: C 520 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.5137 (tt0) REVERT: C 761 LEU cc_start: 0.2011 (OUTLIER) cc_final: 0.1640 (mt) REVERT: D 19 ILE cc_start: 0.8779 (pt) cc_final: 0.8541 (mp) REVERT: D 250 PHE cc_start: 0.5266 (t80) cc_final: 0.4929 (t80) REVERT: D 354 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5606 (tp30) REVERT: D 448 LEU cc_start: 0.6589 (tp) cc_final: 0.6133 (tp) REVERT: D 474 LEU cc_start: 0.7442 (pt) cc_final: 0.6846 (tp) REVERT: D 478 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6242 (m-70) REVERT: D 715 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6650 (t) REVERT: E 243 LEU cc_start: 0.8213 (tp) cc_final: 0.7598 (mp) REVERT: E 443 PHE cc_start: 0.4066 (m-80) cc_final: 0.3582 (m-80) REVERT: F 160 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7128 (mt) REVERT: F 478 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6409 (m-70) REVERT: K 86 LEU cc_start: -0.1002 (OUTLIER) cc_final: -0.2044 (mt) REVERT: G 33 TRP cc_start: 0.1308 (OUTLIER) cc_final: 0.0205 (m100) REVERT: G 108 TYR cc_start: 0.4849 (OUTLIER) cc_final: 0.4350 (t80) REVERT: H 19 ARG cc_start: 0.3949 (mmm160) cc_final: 0.3535 (mmm160) REVERT: H 83 MET cc_start: 0.3546 (mpp) cc_final: 0.2766 (tpp) REVERT: I 33 TRP cc_start: 0.0437 (OUTLIER) cc_final: 0.0051 (m100) REVERT: I 87 LYS cc_start: 0.3607 (mttt) cc_final: 0.3312 (mtpp) REVERT: I 108 TYR cc_start: 0.3902 (OUTLIER) cc_final: 0.3316 (t80) REVERT: J 83 MET cc_start: 0.3122 (OUTLIER) cc_final: 0.1405 (pmm) REVERT: J 84 ASN cc_start: 0.5520 (m-40) cc_final: 0.5173 (m-40) outliers start: 161 outliers final: 114 residues processed: 446 average time/residue: 0.2286 time to fit residues: 176.6809 Evaluate side-chains 404 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 272 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 HIS Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 590 MET Chi-restraints excluded: chain F residue 650 HIS Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 1 optimal weight: 0.6980 chunk 446 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 335 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 489 optimal weight: 6.9990 chunk 368 optimal weight: 2.9990 chunk 416 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN B 712 ASN B 737 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 649 ASN ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.176952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.149969 restraints weight = 83301.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.146130 restraints weight = 123440.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.143435 restraints weight = 93856.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.143230 restraints weight = 89596.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.142249 restraints weight = 81846.089| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 42228 Z= 0.179 Angle : 0.596 10.627 57288 Z= 0.308 Chirality : 0.043 0.293 6498 Planarity : 0.004 0.055 7122 Dihedral : 5.789 58.686 5565 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.32 % Allowed : 17.98 % Favored : 78.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 4980 helix: -0.31 (0.12), residues: 2013 sheet: -0.81 (0.18), residues: 915 loop : -0.69 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 685 TYR 0.024 0.002 TYR G 110 PHE 0.032 0.002 PHE E 353 TRP 0.039 0.002 TRP K 59 HIS 0.006 0.001 HIS F 104 Details of bonding type rmsd covalent geometry : bond 0.00417 (42204) covalent geometry : angle 0.59560 (57240) SS BOND : bond 0.00345 ( 24) SS BOND : angle 0.91765 ( 48) hydrogen bonds : bond 0.03512 ( 1748) hydrogen bonds : angle 4.81421 ( 4521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 278 time to evaluate : 1.607 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: symmetry clash REVERT: A 29 ASP cc_start: 0.7185 (t0) cc_final: 0.6918 (t0) REVERT: A 234 LYS cc_start: 0.6362 (tppt) cc_final: 0.5536 (ttpp) REVERT: A 353 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6354 (t80) REVERT: A 375 MET cc_start: 0.7757 (mtp) cc_final: 0.7366 (mtp) REVERT: A 414 ASP cc_start: 0.5031 (OUTLIER) cc_final: 0.4427 (t70) REVERT: B 160 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7025 (mm) REVERT: B 250 PHE cc_start: 0.5505 (t80) cc_final: 0.5087 (t80) REVERT: B 468 LEU cc_start: 0.4864 (mt) cc_final: 0.4605 (mt) REVERT: B 478 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7079 (m-70) REVERT: B 493 GLU cc_start: 0.6476 (pp20) cc_final: 0.5911 (pp20) REVERT: C 353 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5957 (t80) REVERT: C 475 TRP cc_start: 0.6184 (m-10) cc_final: 0.5315 (m-10) REVERT: C 520 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.5146 (tt0) REVERT: C 761 LEU cc_start: 0.2176 (OUTLIER) cc_final: 0.1774 (mt) REVERT: D 250 PHE cc_start: 0.5231 (t80) cc_final: 0.4844 (t80) REVERT: D 354 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5886 (tp30) REVERT: D 448 LEU cc_start: 0.6618 (tp) cc_final: 0.6142 (tp) REVERT: D 478 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6339 (m-70) REVERT: D 715 VAL cc_start: 0.6969 (OUTLIER) cc_final: 0.6604 (t) REVERT: E 243 LEU cc_start: 0.8331 (tp) cc_final: 0.7682 (mp) REVERT: F 160 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6965 (mt) REVERT: F 478 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6449 (m-70) REVERT: K 86 LEU cc_start: -0.1051 (OUTLIER) cc_final: -0.2087 (mt) REVERT: G 33 TRP cc_start: 0.1003 (OUTLIER) cc_final: 0.0190 (m100) REVERT: G 101 THR cc_start: 0.2927 (m) cc_final: 0.2693 (m) REVERT: G 108 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.4623 (t80) REVERT: H 19 ARG cc_start: 0.3910 (mmm160) cc_final: 0.3520 (mmm160) REVERT: H 83 MET cc_start: 0.3367 (mpp) cc_final: 0.2674 (tpp) REVERT: I 33 TRP cc_start: 0.1095 (OUTLIER) cc_final: 0.0483 (m100) REVERT: I 87 LYS cc_start: 0.3564 (mttt) cc_final: 0.3275 (mtpp) REVERT: I 108 TYR cc_start: 0.4190 (OUTLIER) cc_final: 0.3549 (t80) REVERT: J 83 MET cc_start: 0.2972 (OUTLIER) cc_final: 0.1297 (pmm) REVERT: J 84 ASN cc_start: 0.5631 (m-40) cc_final: 0.5313 (m-40) REVERT: J 89 GLU cc_start: 0.2862 (pm20) cc_final: 0.2628 (pm20) outliers start: 152 outliers final: 118 residues processed: 414 average time/residue: 0.2293 time to fit residues: 165.3107 Evaluate side-chains 408 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 272 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 HIS Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 590 MET Chi-restraints excluded: chain F residue 650 HIS Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain I residue 108 TYR Chi-restraints excluded: chain J residue 35 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 219 optimal weight: 0.4980 chunk 414 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 390 optimal weight: 0.9980 chunk 399 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 404 optimal weight: 8.9990 chunk 491 optimal weight: 8.9990 chunk 322 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 437 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN C 155 HIS C 740 ASN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.177125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.149459 restraints weight = 82723.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.146000 restraints weight = 126822.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.143673 restraints weight = 90366.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.143610 restraints weight = 85442.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.142974 restraints weight = 71358.005| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 42228 Z= 0.162 Angle : 0.595 10.342 57288 Z= 0.307 Chirality : 0.042 0.262 6498 Planarity : 0.004 0.059 7122 Dihedral : 5.717 58.568 5563 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.16 % Allowed : 18.39 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 4980 helix: -0.36 (0.11), residues: 2031 sheet: -0.83 (0.18), residues: 915 loop : -0.76 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 685 TYR 0.022 0.002 TYR G 110 PHE 0.022 0.002 PHE E 353 TRP 0.042 0.002 TRP K 59 HIS 0.006 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.00375 (42204) covalent geometry : angle 0.59461 (57240) SS BOND : bond 0.00310 ( 24) SS BOND : angle 0.87521 ( 48) hydrogen bonds : bond 0.03435 ( 1748) hydrogen bonds : angle 4.80414 ( 4521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 282 time to evaluate : 1.685 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 29 ASP cc_start: 0.7128 (t0) cc_final: 0.6866 (t0) REVERT: A 234 LYS cc_start: 0.6308 (tppt) cc_final: 0.5500 (ttpp) REVERT: A 353 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 375 MET cc_start: 0.7727 (mtp) cc_final: 0.7331 (mtp) REVERT: A 414 ASP cc_start: 0.4996 (OUTLIER) cc_final: 0.4451 (t70) REVERT: B 160 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7101 (mm) REVERT: B 250 PHE cc_start: 0.5416 (t80) cc_final: 0.5083 (t80) REVERT: B 478 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.7078 (m-70) REVERT: B 493 GLU cc_start: 0.6444 (pp20) cc_final: 0.5851 (pp20) REVERT: C 353 PHE cc_start: 0.6543 (OUTLIER) cc_final: 0.5978 (t80) REVERT: C 475 TRP cc_start: 0.6134 (m-10) cc_final: 0.5201 (m-10) REVERT: C 520 GLU cc_start: 0.5461 (OUTLIER) cc_final: 0.5137 (tt0) REVERT: C 761 LEU cc_start: 0.1928 (OUTLIER) cc_final: 0.1540 (mt) REVERT: D 250 PHE cc_start: 0.5237 (t80) cc_final: 0.4884 (t80) REVERT: D 448 LEU cc_start: 0.6509 (tp) cc_final: 0.6028 (tp) REVERT: D 478 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.6188 (m-70) REVERT: D 590 MET cc_start: 0.4432 (OUTLIER) cc_final: 0.4175 (ttt) REVERT: D 715 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6761 (t) REVERT: E 243 LEU cc_start: 0.8189 (tp) cc_final: 0.7600 (mp) REVERT: E 443 PHE cc_start: 0.3900 (m-80) cc_final: 0.3333 (m-10) REVERT: E 626 LEU cc_start: 0.4070 (mm) cc_final: 0.3787 (mt) REVERT: E 685 ARG cc_start: 0.5882 (mpt180) cc_final: 0.5370 (mmp80) REVERT: F 160 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6936 (mt) REVERT: F 478 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6390 (m-70) REVERT: K 86 LEU cc_start: -0.1040 (OUTLIER) cc_final: -0.1463 (pp) REVERT: G 33 TRP cc_start: 0.0914 (OUTLIER) cc_final: 0.0210 (m100) REVERT: G 101 THR cc_start: 0.3077 (m) cc_final: 0.2829 (m) REVERT: G 108 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.4760 (t80) REVERT: H 19 ARG cc_start: 0.3943 (mmm160) cc_final: 0.3601 (mmm160) REVERT: H 83 MET cc_start: 0.3309 (mpp) cc_final: 0.2535 (tpp) REVERT: H 113 GLN cc_start: 0.5146 (pm20) cc_final: 0.2775 (tp-100) REVERT: I 33 TRP cc_start: 0.0923 (OUTLIER) cc_final: 0.0424 (m100) REVERT: I 87 LYS cc_start: 0.3395 (mttt) cc_final: 0.3168 (mtpp) REVERT: J 83 MET cc_start: 0.2976 (OUTLIER) cc_final: 0.1266 (pmm) REVERT: J 84 ASN cc_start: 0.5610 (m-40) cc_final: 0.5271 (m-40) REVERT: J 89 GLU cc_start: 0.2867 (pm20) cc_final: 0.2612 (pm20) REVERT: J 113 GLN cc_start: 0.4888 (pp30) cc_final: 0.4420 (mm-40) outliers start: 145 outliers final: 114 residues processed: 413 average time/residue: 0.2287 time to fit residues: 163.0506 Evaluate side-chains 402 residues out of total 4584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 271 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 478 HIS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 650 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 380 ASP Chi-restraints excluded: chain C residue 478 HIS Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 698 THR Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 787 GLU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain D residue 590 MET Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 380 ASP Chi-restraints excluded: chain E residue 427 LYS Chi-restraints excluded: chain E residue 441 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 478 HIS Chi-restraints excluded: chain E residue 583 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 456 ILE Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 478 HIS Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 508 ILE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 687 LEU Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 745 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain L residue 96 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 TRP Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 35 TRP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 33 TRP Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 460 optimal weight: 0.0970 chunk 99 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 364 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 306 optimal weight: 0.6980 chunk 82 optimal weight: 0.0570 chunk 300 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 399 optimal weight: 10.0000 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN B 737 HIS C 155 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 HIS ** F 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 ASN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.178555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.152168 restraints weight = 83296.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.148298 restraints weight = 120684.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.145930 restraints weight = 87812.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.145537 restraints weight = 81439.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.144854 restraints weight = 66674.223| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42228 Z= 0.110 Angle : 0.571 10.483 57288 Z= 0.293 Chirality : 0.041 0.246 6498 Planarity : 0.003 0.057 7122 Dihedral : 5.504 59.917 5561 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.62 % Allowed : 18.87 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 4980 helix: -0.25 (0.12), residues: 2049 sheet: -0.80 (0.18), residues: 909 loop : -0.68 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 19 TYR 0.019 0.001 TYR G 110 PHE 0.023 0.001 PHE E 275 TRP 0.041 0.002 TRP A 647 HIS 0.005 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00244 (42204) covalent geometry : angle 0.57038 (57240) SS BOND : bond 0.00189 ( 24) SS BOND : angle 0.73098 ( 48) hydrogen bonds : bond 0.03246 ( 1748) hydrogen bonds : angle 4.67003 ( 4521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7116.06 seconds wall clock time: 124 minutes 25.80 seconds (7465.80 seconds total)