Starting phenix.real_space_refine on Tue Aug 26 21:56:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gq5_34198/08_2025/8gq5_34198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gq5_34198/08_2025/8gq5_34198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gq5_34198/08_2025/8gq5_34198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gq5_34198/08_2025/8gq5_34198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gq5_34198/08_2025/8gq5_34198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gq5_34198/08_2025/8gq5_34198.map" } resolution = 2.7 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= 0.030 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 208 5.16 5 C 26720 2.51 5 N 7600 2.21 5 O 8064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42592 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "a" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "B" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "b" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "c" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "D" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "d" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "E" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "e" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "F" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "f" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "G" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "g" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "H" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "h" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "I" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "i" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "J" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "j" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "K" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "k" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "l" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "M" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "m" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "N" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "n" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "O" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "o" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "P" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1798 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "p" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Time building chain proxies: 8.21, per 1000 atoms: 0.19 Number of scatterers: 42592 At special positions: 0 Unit cell: (173.236, 173.236, 144.184, 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 208 16.00 O 8064 8.00 N 7600 7.00 C 26720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 96 " distance=2.02 Simple disulfide: pdb=" SG CYS c 23 " - pdb=" SG CYS c 96 " distance=2.03 Simple disulfide: pdb=" SG CYS d 23 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 96 " distance=2.03 Simple disulfide: pdb=" SG CYS f 23 " - pdb=" SG CYS f 96 " distance=2.02 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 96 " distance=2.03 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS i 23 " - pdb=" SG CYS i 96 " distance=2.02 Simple disulfide: pdb=" SG CYS j 23 " - pdb=" SG CYS j 96 " distance=2.02 Simple disulfide: pdb=" SG CYS k 23 " - pdb=" SG CYS k 96 " distance=2.02 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 96 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 96 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 96 " distance=2.02 Simple disulfide: pdb=" SG CYS o 23 " - pdb=" SG CYS o 96 " distance=2.02 Simple disulfide: pdb=" SG CYS p 23 " - pdb=" SG CYS p 96 " distance=2.02 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: 3.74 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... Secondary structure from input PDB file: 320 helices and 32 sheets defined 53.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.866A pdb=" N GLN A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 330' Processing helix chain 'A' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU A 334 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR A 475 " --> pdb=" O THR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 500' Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 32 Processing helix chain 'a' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS a 65 " --> pdb=" O ASP a 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU B 334 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 369 through 378 removed outlier: 4.044A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS B 430 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 500' Processing helix chain 'B' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU B 525 " --> pdb=" O GLN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS b 65 " --> pdb=" O ASP b 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 330' Processing helix chain 'C' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU C 334 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 413 through 425 Processing helix chain 'C' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR C 475 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS C 516 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU C 525 " --> pdb=" O GLN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 32 Processing helix chain 'c' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS c 65 " --> pdb=" O ASP c 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU D 334 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 368 Processing helix chain 'D' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS D 430 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 436 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR D 475 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG D 499 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 496 through 500' Processing helix chain 'D' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 4.287A pdb=" N HIS D 516 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU D 525 " --> pdb=" O GLN D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 32 Processing helix chain 'd' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS d 65 " --> pdb=" O ASP d 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 325 through 330' Processing helix chain 'E' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU E 334 " --> pdb=" O VAL E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 358 removed outlier: 4.031A pdb=" N GLN E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 413 through 425 Processing helix chain 'E' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS E 430 " --> pdb=" O SER E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG E 499 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 496 through 500' Processing helix chain 'E' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS E 516 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU E 525 " --> pdb=" O GLN E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 32 Processing helix chain 'e' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS e 65 " --> pdb=" O ASP e 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 330' Processing helix chain 'F' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU F 334 " --> pdb=" O VAL F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 358 removed outlier: 4.031A pdb=" N GLN F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 368 Processing helix chain 'F' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 426 through 430 removed outlier: 3.623A pdb=" N CYS F 430 " --> pdb=" O SER F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR F 475 " --> pdb=" O THR F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG F 499 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 518 removed outlier: 4.287A pdb=" N HIS F 516 " --> pdb=" O SER F 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 32 Processing helix chain 'f' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS f 65 " --> pdb=" O ASP f 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 325 through 330' Processing helix chain 'G' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU G 334 " --> pdb=" O VAL G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 358 removed outlier: 4.029A pdb=" N GLN G 342 " --> pdb=" O ARG G 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 368 Processing helix chain 'G' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 413 through 425 Processing helix chain 'G' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS G 430 " --> pdb=" O SER G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP G 454 " --> pdb=" O GLU G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR G 475 " --> pdb=" O THR G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG G 499 " --> pdb=" O PRO G 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 496 through 500' Processing helix chain 'G' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS G 516 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU G 525 " --> pdb=" O GLN G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 32 Processing helix chain 'g' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS g 65 " --> pdb=" O ASP g 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 325 through 330' Processing helix chain 'H' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU H 334 " --> pdb=" O VAL H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN H 342 " --> pdb=" O ARG H 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 368 Processing helix chain 'H' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 413 through 425 Processing helix chain 'H' and resid 426 through 430 removed outlier: 3.623A pdb=" N CYS H 430 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 436 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP H 454 " --> pdb=" O GLU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR H 475 " --> pdb=" O THR H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG H 499 " --> pdb=" O PRO H 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 496 through 500' Processing helix chain 'H' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS H 516 " --> pdb=" O SER H 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU H 525 " --> pdb=" O GLN H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET H 545 " --> pdb=" O ALA H 541 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS h 65 " --> pdb=" O ASP h 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG I 329 " --> pdb=" O ASP I 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU I 330 " --> pdb=" O ASP I 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 325 through 330' Processing helix chain 'I' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU I 334 " --> pdb=" O VAL I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN I 342 " --> pdb=" O ARG I 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 368 Processing helix chain 'I' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER I 373 " --> pdb=" O GLY I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 397 Processing helix chain 'I' and resid 413 through 425 Processing helix chain 'I' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS I 430 " --> pdb=" O SER I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 436 Processing helix chain 'I' and resid 439 through 444 Processing helix chain 'I' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP I 454 " --> pdb=" O GLU I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR I 475 " --> pdb=" O THR I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP I 490 " --> pdb=" O ASN I 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU I 494 " --> pdb=" O TRP I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG I 499 " --> pdb=" O PRO I 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN I 500 " --> pdb=" O ARG I 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 496 through 500' Processing helix chain 'I' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS I 508 " --> pdb=" O GLY I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS I 516 " --> pdb=" O SER I 513 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG I 517 " --> pdb=" O LEU I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU I 525 " --> pdb=" O GLN I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 32 Processing helix chain 'i' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS i 65 " --> pdb=" O ASP i 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 330 removed outlier: 3.904A pdb=" N ARG J 329 " --> pdb=" O ASP J 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU J 330 " --> pdb=" O ASP J 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 330' Processing helix chain 'J' and resid 331 through 336 removed outlier: 4.254A pdb=" N LEU J 334 " --> pdb=" O VAL J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN J 342 " --> pdb=" O ARG J 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 368 Processing helix chain 'J' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER J 373 " --> pdb=" O GLY J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 413 through 425 Processing helix chain 'J' and resid 426 through 428 No H-bonds generated for 'chain 'J' and resid 426 through 428' Processing helix chain 'J' and resid 429 through 436 Processing helix chain 'J' and resid 439 through 444 Processing helix chain 'J' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP J 454 " --> pdb=" O GLU J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR J 475 " --> pdb=" O THR J 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP J 490 " --> pdb=" O ASN J 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU J 494 " --> pdb=" O TRP J 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG J 499 " --> pdb=" O PRO J 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN J 500 " --> pdb=" O ARG J 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 496 through 500' Processing helix chain 'J' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS J 508 " --> pdb=" O GLY J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS J 516 " --> pdb=" O SER J 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG J 517 " --> pdb=" O LEU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU J 525 " --> pdb=" O GLN J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 32 Processing helix chain 'j' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS j 65 " --> pdb=" O ASP j 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG K 329 " --> pdb=" O ASP K 325 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU K 330 " --> pdb=" O ASP K 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 330' Processing helix chain 'K' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU K 334 " --> pdb=" O VAL K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN K 342 " --> pdb=" O ARG K 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 368 Processing helix chain 'K' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER K 373 " --> pdb=" O GLY K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 397 Processing helix chain 'K' and resid 413 through 425 Processing helix chain 'K' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS K 430 " --> pdb=" O SER K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 439 through 444 Processing helix chain 'K' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP K 454 " --> pdb=" O GLU K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR K 475 " --> pdb=" O THR K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP K 490 " --> pdb=" O ASN K 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU K 494 " --> pdb=" O TRP K 490 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG K 499 " --> pdb=" O PRO K 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN K 500 " --> pdb=" O ARG K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 496 through 500' Processing helix chain 'K' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS K 508 " --> pdb=" O GLY K 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 518 removed outlier: 4.285A pdb=" N HIS K 516 " --> pdb=" O SER K 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG K 517 " --> pdb=" O LEU K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU K 525 " --> pdb=" O GLN K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET K 545 " --> pdb=" O ALA K 541 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 32 Processing helix chain 'k' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS k 65 " --> pdb=" O ASP k 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG L 329 " --> pdb=" O ASP L 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU L 330 " --> pdb=" O ASP L 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 325 through 330' Processing helix chain 'L' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU L 334 " --> pdb=" O VAL L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 358 removed outlier: 4.031A pdb=" N GLN L 342 " --> pdb=" O ARG L 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 368 Processing helix chain 'L' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER L 373 " --> pdb=" O GLY L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 397 Processing helix chain 'L' and resid 413 through 425 Processing helix chain 'L' and resid 426 through 430 removed outlier: 3.623A pdb=" N CYS L 430 " --> pdb=" O SER L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 436 Processing helix chain 'L' and resid 439 through 444 Processing helix chain 'L' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP L 454 " --> pdb=" O GLU L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 475 removed outlier: 3.652A pdb=" N THR L 475 " --> pdb=" O THR L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP L 490 " --> pdb=" O ASN L 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU L 494 " --> pdb=" O TRP L 490 " (cutoff:3.500A) Processing helix chain 'L' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG L 499 " --> pdb=" O PRO L 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN L 500 " --> pdb=" O ARG L 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 496 through 500' Processing helix chain 'L' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS L 508 " --> pdb=" O GLY L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 518 removed outlier: 4.287A pdb=" N HIS L 516 " --> pdb=" O SER L 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG L 517 " --> pdb=" O LEU L 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU L 525 " --> pdb=" O GLN L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET L 545 " --> pdb=" O ALA L 541 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 32 Processing helix chain 'l' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS l 65 " --> pdb=" O ASP l 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG M 329 " --> pdb=" O ASP M 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU M 330 " --> pdb=" O ASP M 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 330' Processing helix chain 'M' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU M 334 " --> pdb=" O VAL M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN M 342 " --> pdb=" O ARG M 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU M 358 " --> pdb=" O ALA M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 368 Processing helix chain 'M' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER M 373 " --> pdb=" O GLY M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 397 Processing helix chain 'M' and resid 413 through 425 Processing helix chain 'M' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS M 430 " --> pdb=" O SER M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 436 Processing helix chain 'M' and resid 439 through 444 Processing helix chain 'M' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP M 454 " --> pdb=" O GLU M 450 " (cutoff:3.500A) Processing helix chain 'M' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR M 475 " --> pdb=" O THR M 471 " (cutoff:3.500A) Processing helix chain 'M' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP M 490 " --> pdb=" O ASN M 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU M 494 " --> pdb=" O TRP M 490 " (cutoff:3.500A) Processing helix chain 'M' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG M 499 " --> pdb=" O PRO M 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN M 500 " --> pdb=" O ARG M 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 496 through 500' Processing helix chain 'M' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS M 508 " --> pdb=" O GLY M 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS M 516 " --> pdb=" O SER M 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG M 517 " --> pdb=" O LEU M 514 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU M 525 " --> pdb=" O GLN M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET M 545 " --> pdb=" O ALA M 541 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 Processing helix chain 'm' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS m 65 " --> pdb=" O ASP m 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG N 329 " --> pdb=" O ASP N 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU N 330 " --> pdb=" O ASP N 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 325 through 330' Processing helix chain 'N' and resid 331 through 336 removed outlier: 4.252A pdb=" N LEU N 334 " --> pdb=" O VAL N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN N 342 " --> pdb=" O ARG N 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU N 358 " --> pdb=" O ALA N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 368 Processing helix chain 'N' and resid 369 through 378 removed outlier: 4.042A pdb=" N SER N 373 " --> pdb=" O GLY N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 397 Processing helix chain 'N' and resid 413 through 425 Processing helix chain 'N' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS N 430 " --> pdb=" O SER N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 431 through 436 Processing helix chain 'N' and resid 439 through 444 Processing helix chain 'N' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP N 454 " --> pdb=" O GLU N 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR N 475 " --> pdb=" O THR N 471 " (cutoff:3.500A) Processing helix chain 'N' and resid 486 through 495 removed outlier: 3.768A pdb=" N TRP N 490 " --> pdb=" O ASN N 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU N 494 " --> pdb=" O TRP N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 496 through 500 removed outlier: 3.635A pdb=" N ARG N 499 " --> pdb=" O PRO N 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN N 500 " --> pdb=" O ARG N 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 496 through 500' Processing helix chain 'N' and resid 501 through 508 removed outlier: 3.804A pdb=" N CYS N 508 " --> pdb=" O GLY N 504 " (cutoff:3.500A) Processing helix chain 'N' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS N 516 " --> pdb=" O SER N 513 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG N 517 " --> pdb=" O LEU N 514 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU N 525 " --> pdb=" O GLN N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET N 545 " --> pdb=" O ALA N 541 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 32 Processing helix chain 'n' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS n 65 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG O 329 " --> pdb=" O ASP O 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU O 330 " --> pdb=" O ASP O 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 325 through 330' Processing helix chain 'O' and resid 331 through 336 removed outlier: 4.254A pdb=" N LEU O 334 " --> pdb=" O VAL O 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN O 342 " --> pdb=" O ARG O 338 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU O 358 " --> pdb=" O ALA O 354 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 368 Processing helix chain 'O' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER O 373 " --> pdb=" O GLY O 369 " (cutoff:3.500A) Processing helix chain 'O' and resid 383 through 397 Processing helix chain 'O' and resid 413 through 425 Processing helix chain 'O' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS O 430 " --> pdb=" O SER O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 436 Processing helix chain 'O' and resid 439 through 444 Processing helix chain 'O' and resid 447 through 454 removed outlier: 3.621A pdb=" N ASP O 454 " --> pdb=" O GLU O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) Processing helix chain 'O' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP O 490 " --> pdb=" O ASN O 486 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU O 494 " --> pdb=" O TRP O 490 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 500 removed outlier: 3.635A pdb=" N ARG O 499 " --> pdb=" O PRO O 496 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN O 500 " --> pdb=" O ARG O 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 496 through 500' Processing helix chain 'O' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS O 508 " --> pdb=" O GLY O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 513 through 518 removed outlier: 4.285A pdb=" N HIS O 516 " --> pdb=" O SER O 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG O 517 " --> pdb=" O LEU O 514 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 526 removed outlier: 4.047A pdb=" N GLU O 525 " --> pdb=" O GLN O 521 " (cutoff:3.500A) Processing helix chain 'O' and resid 531 through 545 removed outlier: 3.699A pdb=" N MET O 545 " --> pdb=" O ALA O 541 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 32 Processing helix chain 'o' and resid 61 through 65 removed outlier: 3.777A pdb=" N LYS o 65 " --> pdb=" O ASP o 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 325 through 330 removed outlier: 3.903A pdb=" N ARG P 329 " --> pdb=" O ASP P 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU P 330 " --> pdb=" O ASP P 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 325 through 330' Processing helix chain 'P' and resid 331 through 336 removed outlier: 4.253A pdb=" N LEU P 334 " --> pdb=" O VAL P 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 358 removed outlier: 4.030A pdb=" N GLN P 342 " --> pdb=" O ARG P 338 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU P 358 " --> pdb=" O ALA P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 368 Processing helix chain 'P' and resid 369 through 378 removed outlier: 4.043A pdb=" N SER P 373 " --> pdb=" O GLY P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 383 through 397 Processing helix chain 'P' and resid 413 through 425 Processing helix chain 'P' and resid 426 through 430 removed outlier: 3.622A pdb=" N CYS P 430 " --> pdb=" O SER P 427 " (cutoff:3.500A) Processing helix chain 'P' and resid 431 through 436 Processing helix chain 'P' and resid 439 through 444 Processing helix chain 'P' and resid 447 through 454 removed outlier: 3.620A pdb=" N ASP P 454 " --> pdb=" O GLU P 450 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 475 removed outlier: 3.651A pdb=" N THR P 475 " --> pdb=" O THR P 471 " (cutoff:3.500A) Processing helix chain 'P' and resid 486 through 495 removed outlier: 3.767A pdb=" N TRP P 490 " --> pdb=" O ASN P 486 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU P 494 " --> pdb=" O TRP P 490 " (cutoff:3.500A) Processing helix chain 'P' and resid 496 through 500 removed outlier: 3.634A pdb=" N ARG P 499 " --> pdb=" O PRO P 496 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN P 500 " --> pdb=" O ARG P 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 496 through 500' Processing helix chain 'P' and resid 501 through 508 removed outlier: 3.803A pdb=" N CYS P 508 " --> pdb=" O GLY P 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 513 through 518 removed outlier: 4.286A pdb=" N HIS P 516 " --> pdb=" O SER P 513 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG P 517 " --> pdb=" O LEU P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 519 through 526 removed outlier: 4.048A pdb=" N GLU P 525 " --> pdb=" O GLN P 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 545 removed outlier: 3.700A pdb=" N MET P 545 " --> pdb=" O ALA P 541 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 32 Processing helix chain 'p' and resid 61 through 65 removed outlier: 3.778A pdb=" N LYS p 65 " --> pdb=" O ASP p 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET a 35 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL a 51 " --> pdb=" O MET a 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP a 37 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN a 59 " --> pdb=" O VAL a 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'b' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR b 78 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET b 35 " --> pdb=" O VAL b 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL b 51 " --> pdb=" O MET b 35 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP b 37 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN b 59 " --> pdb=" O VAL b 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 6 through 8 removed outlier: 3.702A pdb=" N THR c 78 " --> pdb=" O ASP c 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET c 35 " --> pdb=" O VAL c 51 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL c 51 " --> pdb=" O MET c 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP c 37 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN c 59 " --> pdb=" O VAL c 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR d 78 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'd' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET d 35 " --> pdb=" O VAL d 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL d 51 " --> pdb=" O MET d 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP d 37 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN d 59 " --> pdb=" O VAL d 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR e 78 " --> pdb=" O ASP e 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET e 35 " --> pdb=" O VAL e 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL e 51 " --> pdb=" O MET e 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP e 37 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN e 59 " --> pdb=" O VAL e 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR f 78 " --> pdb=" O ASP f 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET f 35 " --> pdb=" O VAL f 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL f 51 " --> pdb=" O MET f 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP f 37 " --> pdb=" O VAL f 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN f 59 " --> pdb=" O VAL f 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR g 78 " --> pdb=" O ASP g 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'g' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET g 35 " --> pdb=" O VAL g 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL g 51 " --> pdb=" O MET g 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP g 37 " --> pdb=" O VAL g 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN g 59 " --> pdb=" O VAL g 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET h 35 " --> pdb=" O VAL h 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL h 51 " --> pdb=" O MET h 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP h 37 " --> pdb=" O VAL h 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN h 59 " --> pdb=" O VAL h 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'i' and resid 6 through 8 removed outlier: 3.702A pdb=" N THR i 78 " --> pdb=" O ASP i 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'i' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET i 35 " --> pdb=" O VAL i 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL i 51 " --> pdb=" O MET i 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP i 37 " --> pdb=" O VAL i 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN i 59 " --> pdb=" O VAL i 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR j 78 " --> pdb=" O ASP j 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'j' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET j 35 " --> pdb=" O VAL j 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL j 51 " --> pdb=" O MET j 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP j 37 " --> pdb=" O VAL j 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN j 59 " --> pdb=" O VAL j 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'k' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR k 78 " --> pdb=" O ASP k 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'k' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET k 35 " --> pdb=" O VAL k 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL k 51 " --> pdb=" O MET k 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP k 37 " --> pdb=" O VAL k 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN k 59 " --> pdb=" O VAL k 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'l' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR l 78 " --> pdb=" O ASP l 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'l' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET l 35 " --> pdb=" O VAL l 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL l 51 " --> pdb=" O MET l 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP l 37 " --> pdb=" O VAL l 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN l 59 " --> pdb=" O VAL l 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'm' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR m 78 " --> pdb=" O ASP m 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'm' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET m 35 " --> pdb=" O VAL m 51 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL m 51 " --> pdb=" O MET m 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP m 37 " --> pdb=" O VAL m 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN m 59 " --> pdb=" O VAL m 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'n' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR n 78 " --> pdb=" O ASP n 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 11 through 13 removed outlier: 6.736A pdb=" N MET n 35 " --> pdb=" O VAL n 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL n 51 " --> pdb=" O MET n 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP n 37 " --> pdb=" O VAL n 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN n 59 " --> pdb=" O VAL n 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'o' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR o 78 " --> pdb=" O ASP o 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o' and resid 11 through 13 removed outlier: 6.737A pdb=" N MET o 35 " --> pdb=" O VAL o 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL o 51 " --> pdb=" O MET o 35 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP o 37 " --> pdb=" O VAL o 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN o 59 " --> pdb=" O VAL o 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'p' and resid 6 through 8 removed outlier: 3.701A pdb=" N THR p 78 " --> pdb=" O ASP p 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'p' and resid 11 through 13 removed outlier: 6.738A pdb=" N MET p 35 " --> pdb=" O VAL p 51 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL p 51 " --> pdb=" O MET p 35 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP p 37 " --> pdb=" O VAL p 49 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN p 59 " --> pdb=" O VAL p 51 " (cutoff:3.500A) 1921 hydrogen bonds defined for protein. 5190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.83 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13685 1.34 - 1.45: 7253 1.45 - 1.57: 22102 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 43328 Sorted by residual: bond pdb=" CB THR C 502 " pdb=" CG2 THR C 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.77e+00 bond pdb=" CB THR D 502 " pdb=" CG2 THR D 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB THR I 502 " pdb=" CG2 THR I 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB THR P 502 " pdb=" CG2 THR P 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.74e+00 bond pdb=" CB THR K 502 " pdb=" CG2 THR K 502 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.73e+00 ... (remaining 43323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 56549 2.49 - 4.98: 1601 4.98 - 7.47: 282 7.47 - 9.97: 112 9.97 - 12.46: 32 Bond angle restraints: 58576 Sorted by residual: angle pdb=" CA LEU N 333 " pdb=" CB LEU N 333 " pdb=" CG LEU N 333 " ideal model delta sigma weight residual 116.30 128.76 -12.46 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU E 333 " pdb=" CB LEU E 333 " pdb=" CG LEU E 333 " ideal model delta sigma weight residual 116.30 128.76 -12.46 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU P 333 " pdb=" CB LEU P 333 " pdb=" CG LEU P 333 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA LEU M 333 " pdb=" CB LEU M 333 " pdb=" CG LEU M 333 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU H 333 " pdb=" CB LEU H 333 " pdb=" CG LEU H 333 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.26e+01 ... (remaining 58571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 23213 16.06 - 32.13: 2487 32.13 - 48.19: 476 48.19 - 64.26: 128 64.26 - 80.32: 64 Dihedral angle restraints: 26368 sinusoidal: 10688 harmonic: 15680 Sorted by residual: dihedral pdb=" CA ASN d 99 " pdb=" C ASN d 99 " pdb=" N VAL d 100 " pdb=" CA VAL d 100 " ideal model delta harmonic sigma weight residual 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN f 99 " pdb=" C ASN f 99 " pdb=" N VAL f 100 " pdb=" CA VAL f 100 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ASN j 99 " pdb=" C ASN j 99 " pdb=" N VAL j 100 " pdb=" CA VAL j 100 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 26365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4201 0.049 - 0.097: 1583 0.097 - 0.146: 539 0.146 - 0.194: 237 0.194 - 0.243: 48 Chirality restraints: 6608 Sorted by residual: chirality pdb=" CG LEU L 397 " pdb=" CB LEU L 397 " pdb=" CD1 LEU L 397 " pdb=" CD2 LEU L 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU K 397 " pdb=" CB LEU K 397 " pdb=" CD1 LEU K 397 " pdb=" CD2 LEU K 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU C 397 " pdb=" CB LEU C 397 " pdb=" CD1 LEU C 397 " pdb=" CD2 LEU C 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 6605 not shown) Planarity restraints: 7536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 361 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C LYS N 361 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS N 361 " 0.018 2.00e-02 2.50e+03 pdb=" N THR N 362 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 361 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C LYS A 361 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS A 361 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 362 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 361 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.73e+00 pdb=" C LYS F 361 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS F 361 " 0.017 2.00e-02 2.50e+03 pdb=" N THR F 362 " 0.015 2.00e-02 2.50e+03 ... (remaining 7533 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2359 2.71 - 3.26: 41837 3.26 - 3.81: 64755 3.81 - 4.35: 79292 4.35 - 4.90: 139564 Nonbonded interactions: 327807 Sorted by model distance: nonbonded pdb=" NE1 TRP D 412 " pdb=" OE2 GLU d 101 " model vdw 2.166 3.120 nonbonded pdb=" OH TYR J 380 " pdb=" O ARG j 31 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASP K 441 " pdb=" OH TYR K 503 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP C 441 " pdb=" OH TYR C 503 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP P 441 " pdb=" OH TYR P 503 " model vdw 2.252 3.040 ... (remaining 327802 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 34.770 Find NCS groups from input model: 0.280 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:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.010 0.089 43344 Z= 0.407 Angle : 1.104 12.458 58608 Z= 0.566 Chirality : 0.064 0.243 6608 Planarity : 0.007 0.051 7536 Dihedral : 14.182 80.319 16240 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 aren not related in a simple way. whole: -3.24 (0.10), residues: 5360 helix: -1.71 (0.09), residues: 2304 sheet: -2.11 (0.15), residues: 976 loop : -2.48 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG e 72 TYR 0.019 0.003 TYR A 348 PHE 0.019 0.002 PHE M 467 TRP 0.017 0.003 TRP N 490 HIS 0.003 0.001 HIS G 547 Details of bonding type rmsd covalent geometry : bond 0.00959 (43328) covalent geometry : angle 1.10317 (58576) SS BOND : bond 0.00603 ( 16) SS BOND : angle 1.77903 ( 32) hydrogen bonds : bond 0.18284 ( 1921) hydrogen bonds : angle 6.07398 ( 5190) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1116 time to evaluate : 1.164 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 486 ASN cc_start: 0.8848 (t0) cc_final: 0.7885 (t0) REVERT: a 77 ASN cc_start: 0.8923 (m-40) cc_final: 0.8498 (m-40) REVERT: a 86 LEU cc_start: 0.9052 (mt) cc_final: 0.8820 (mp) REVERT: a 87 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8183 (mppt) REVERT: a 105 GLN cc_start: 0.7911 (pm20) cc_final: 0.7669 (pm20) REVERT: B 439 ASP cc_start: 0.8367 (p0) cc_final: 0.8119 (p0) REVERT: B 486 ASN cc_start: 0.8924 (t0) cc_final: 0.8210 (t0) REVERT: B 489 ASP cc_start: 0.8192 (m-30) cc_final: 0.7930 (m-30) REVERT: b 73 ASP cc_start: 0.8216 (t70) cc_final: 0.7992 (t0) REVERT: b 86 LEU cc_start: 0.9076 (mt) cc_final: 0.8842 (mm) REVERT: b 87 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8113 (mppt) REVERT: b 105 GLN cc_start: 0.8170 (pm20) cc_final: 0.7830 (pm20) REVERT: C 439 ASP cc_start: 0.8223 (p0) cc_final: 0.7966 (p0) REVERT: C 486 ASN cc_start: 0.8904 (t0) cc_final: 0.8023 (t0) REVERT: c 77 ASN cc_start: 0.8913 (m-40) cc_final: 0.8606 (m-40) REVERT: c 86 LEU cc_start: 0.9041 (mt) cc_final: 0.8785 (mp) REVERT: c 87 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8192 (mppt) REVERT: D 439 ASP cc_start: 0.8459 (p0) cc_final: 0.8135 (p0) REVERT: D 486 ASN cc_start: 0.8963 (t0) cc_final: 0.8261 (t0) REVERT: d 4 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8444 (mp10) REVERT: d 73 ASP cc_start: 0.8104 (t70) cc_final: 0.7847 (t0) REVERT: d 86 LEU cc_start: 0.9130 (mt) cc_final: 0.8842 (mm) REVERT: d 87 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8123 (mppt) REVERT: d 105 GLN cc_start: 0.8274 (pm20) cc_final: 0.8046 (pm20) REVERT: E 486 ASN cc_start: 0.8918 (t0) cc_final: 0.7979 (t0) REVERT: e 4 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8581 (mm-40) REVERT: e 14 GLN cc_start: 0.8702 (pm20) cc_final: 0.8324 (mp10) REVERT: e 77 ASN cc_start: 0.8907 (m-40) cc_final: 0.8613 (m-40) REVERT: e 87 LYS cc_start: 0.8502 (mmtt) cc_final: 0.8086 (mppt) REVERT: e 105 GLN cc_start: 0.7986 (pm20) cc_final: 0.7765 (pm20) REVERT: F 486 ASN cc_start: 0.8986 (t0) cc_final: 0.8311 (t0) REVERT: f 86 LEU cc_start: 0.9136 (mt) cc_final: 0.8930 (mm) REVERT: f 87 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8204 (mppt) REVERT: f 105 GLN cc_start: 0.8190 (pm20) cc_final: 0.7897 (pm20) REVERT: G 439 ASP cc_start: 0.8186 (p0) cc_final: 0.7971 (p0) REVERT: G 486 ASN cc_start: 0.8895 (t0) cc_final: 0.7978 (t0) REVERT: g 4 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8517 (mm-40) REVERT: g 14 GLN cc_start: 0.8739 (pm20) cc_final: 0.8441 (mp10) REVERT: g 73 ASP cc_start: 0.8386 (t70) cc_final: 0.8115 (t0) REVERT: g 77 ASN cc_start: 0.8794 (m-40) cc_final: 0.8451 (m110) REVERT: g 86 LEU cc_start: 0.9249 (mt) cc_final: 0.9030 (mm) REVERT: g 87 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8257 (mppt) REVERT: H 486 ASN cc_start: 0.8960 (t0) cc_final: 0.8457 (t0) REVERT: h 86 LEU cc_start: 0.9100 (mt) cc_final: 0.8899 (mm) REVERT: h 87 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8185 (mppt) REVERT: I 486 ASN cc_start: 0.8979 (t0) cc_final: 0.8310 (t0) REVERT: I 489 ASP cc_start: 0.8211 (m-30) cc_final: 0.7988 (m-30) REVERT: I 516 HIS cc_start: 0.8304 (p90) cc_final: 0.7055 (p90) REVERT: i 4 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8473 (mm-40) REVERT: i 86 LEU cc_start: 0.9042 (mt) cc_final: 0.8784 (mp) REVERT: i 87 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7781 (mppt) REVERT: i 105 GLN cc_start: 0.8100 (pm20) cc_final: 0.7755 (pm20) REVERT: J 486 ASN cc_start: 0.8869 (t0) cc_final: 0.8072 (t0) REVERT: j 4 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8496 (mm-40) REVERT: j 86 LEU cc_start: 0.9205 (mt) cc_final: 0.8767 (mm) REVERT: j 87 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8005 (mppt) REVERT: j 105 GLN cc_start: 0.7994 (pm20) cc_final: 0.7542 (pm20) REVERT: K 486 ASN cc_start: 0.8898 (t0) cc_final: 0.7913 (t0) REVERT: k 14 GLN cc_start: 0.8587 (pm20) cc_final: 0.8294 (mp10) REVERT: k 86 LEU cc_start: 0.9191 (mt) cc_final: 0.8915 (mm) REVERT: k 87 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8110 (mppt) REVERT: k 105 GLN cc_start: 0.8014 (pm20) cc_final: 0.7727 (pm20) REVERT: L 486 ASN cc_start: 0.8831 (t0) cc_final: 0.7913 (t0) REVERT: l 4 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8551 (mm-40) REVERT: l 7 GLU cc_start: 0.8437 (mp0) cc_final: 0.7981 (mp0) REVERT: l 86 LEU cc_start: 0.9285 (mt) cc_final: 0.8975 (mm) REVERT: l 87 LYS cc_start: 0.8494 (mmtt) cc_final: 0.7977 (mppt) REVERT: l 105 GLN cc_start: 0.7951 (pm20) cc_final: 0.7361 (pm20) REVERT: M 486 ASN cc_start: 0.8851 (t0) cc_final: 0.7980 (t0) REVERT: M 516 HIS cc_start: 0.8216 (p90) cc_final: 0.7905 (p90) REVERT: m 4 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8565 (mm-40) REVERT: m 14 GLN cc_start: 0.8551 (pm20) cc_final: 0.8350 (mp10) REVERT: m 86 LEU cc_start: 0.9159 (mt) cc_final: 0.8896 (mm) REVERT: m 87 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8141 (mppt) REVERT: m 105 GLN cc_start: 0.8002 (pm20) cc_final: 0.7801 (pm20) REVERT: N 486 ASN cc_start: 0.8834 (t0) cc_final: 0.7940 (t0) REVERT: N 516 HIS cc_start: 0.8361 (p90) cc_final: 0.8143 (p90) REVERT: n 4 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8497 (mm-40) REVERT: n 7 GLU cc_start: 0.8485 (mp0) cc_final: 0.7923 (mp0) REVERT: n 46 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8257 (mtt90) REVERT: n 86 LEU cc_start: 0.9197 (mt) cc_final: 0.8978 (mm) REVERT: n 87 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7821 (mppt) REVERT: n 105 GLN cc_start: 0.8005 (pm20) cc_final: 0.7443 (pm20) REVERT: O 486 ASN cc_start: 0.8943 (t0) cc_final: 0.8248 (t0) REVERT: O 489 ASP cc_start: 0.8217 (m-30) cc_final: 0.7998 (m-30) REVERT: O 516 HIS cc_start: 0.8292 (p90) cc_final: 0.7188 (p90) REVERT: o 4 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8570 (mm-40) REVERT: o 14 GLN cc_start: 0.8642 (pm20) cc_final: 0.8418 (mp10) REVERT: o 87 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8000 (mppt) REVERT: P 486 ASN cc_start: 0.8864 (t0) cc_final: 0.7984 (t0) REVERT: p 4 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8550 (mm-40) REVERT: p 86 LEU cc_start: 0.9167 (mt) cc_final: 0.8875 (mm) REVERT: p 87 LYS cc_start: 0.8517 (mmtt) cc_final: 0.7961 (mppt) REVERT: p 105 GLN cc_start: 0.8089 (pm20) cc_final: 0.7602 (pm20) outliers start: 0 outliers final: 5 residues processed: 1116 average time/residue: 0.6821 time to fit residues: 915.4726 Evaluate side-chains 881 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 876 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 73 ASP Chi-restraints excluded: chain j residue 73 ASP Chi-restraints excluded: chain l residue 73 ASP Chi-restraints excluded: chain N residue 483 ASP Chi-restraints excluded: chain n residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 0.0470 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 436 GLN a 97 ASN B 328 GLN B 436 GLN b 97 ASN C 328 GLN C 436 GLN c 97 ASN D 328 GLN D 436 GLN d 97 ASN E 328 GLN E 436 GLN e 97 ASN F 328 GLN F 436 GLN f 97 ASN G 328 GLN G 436 GLN g 97 ASN H 328 GLN H 418 GLN H 436 GLN h 97 ASN I 328 GLN I 436 GLN I 516 HIS i 97 ASN J 328 GLN J 436 GLN j 97 ASN K 328 GLN K 436 GLN ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 97 ASN L 328 GLN L 436 GLN l 14 GLN l 97 ASN M 328 GLN M 436 GLN m 97 ASN N 328 GLN N 436 GLN n 14 GLN n 97 ASN O 328 GLN O 436 GLN O 516 HIS o 97 ASN P 328 GLN P 418 GLN P 436 GLN p 14 GLN p 97 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.149435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094631 restraints weight = 65031.323| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.74 r_work: 0.3202 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 43344 Z= 0.126 Angle : 0.631 6.038 58608 Z= 0.319 Chirality : 0.041 0.133 6608 Planarity : 0.005 0.041 7536 Dihedral : 4.931 22.917 6026 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.46 % Allowed : 12.20 % Favored : 86.34 % 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 aren not related in a simple way. whole: -1.60 (0.11), residues: 5360 helix: -0.43 (0.10), residues: 2304 sheet: -1.42 (0.16), residues: 960 loop : -1.42 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 403 TYR 0.013 0.001 TYR h 54 PHE 0.008 0.001 PHE H 466 TRP 0.013 0.002 TRP a 103 HIS 0.004 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00284 (43328) covalent geometry : angle 0.63065 (58576) SS BOND : bond 0.00164 ( 16) SS BOND : angle 0.84294 ( 32) hydrogen bonds : bond 0.03672 ( 1921) hydrogen bonds : angle 4.58405 ( 5190) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1058 time to evaluate : 1.756 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: symmetry clash revert: symmetry clash REVERT: A 441 ASP cc_start: 0.8658 (t0) cc_final: 0.8427 (t0) REVERT: A 450 GLU cc_start: 0.8760 (mp0) cc_final: 0.8338 (mt-10) REVERT: A 486 ASN cc_start: 0.9051 (t0) cc_final: 0.8646 (t0) REVERT: A 516 HIS cc_start: 0.8690 (p90) cc_final: 0.8431 (p90) REVERT: A 517 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8855 (pmm-80) REVERT: a 4 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8551 (mm-40) REVERT: a 7 GLU cc_start: 0.7877 (mp0) cc_final: 0.7339 (mp0) REVERT: a 44 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8407 (mtmm) REVERT: a 73 ASP cc_start: 0.8144 (t0) cc_final: 0.7364 (t0) REVERT: a 76 LYS cc_start: 0.9141 (pmtt) cc_final: 0.8750 (pmtt) REVERT: a 77 ASN cc_start: 0.8866 (m-40) cc_final: 0.8375 (m-40) REVERT: a 86 LEU cc_start: 0.9072 (mt) cc_final: 0.8568 (mp) REVERT: a 87 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7311 (mppt) REVERT: a 90 ASP cc_start: 0.8095 (m-30) cc_final: 0.7835 (m-30) REVERT: a 105 GLN cc_start: 0.7846 (pm20) cc_final: 0.7578 (pm20) REVERT: B 439 ASP cc_start: 0.8396 (p0) cc_final: 0.8104 (p0) REVERT: B 484 ARG cc_start: 0.8967 (tpp-160) cc_final: 0.8539 (mmp80) REVERT: B 486 ASN cc_start: 0.8989 (t0) cc_final: 0.8537 (t0) REVERT: B 489 ASP cc_start: 0.9033 (m-30) cc_final: 0.8682 (m-30) REVERT: B 516 HIS cc_start: 0.8448 (p90) cc_final: 0.7621 (p-80) REVERT: B 517 ARG cc_start: 0.9229 (ptm160) cc_final: 0.8554 (ptp-110) REVERT: b 4 GLN cc_start: 0.8801 (mp10) cc_final: 0.8471 (mp10) REVERT: b 7 GLU cc_start: 0.7820 (mp0) cc_final: 0.6960 (mp0) REVERT: b 32 ILE cc_start: 0.8805 (mt) cc_final: 0.8549 (mp) REVERT: b 73 ASP cc_start: 0.7889 (t70) cc_final: 0.7568 (t0) REVERT: b 86 LEU cc_start: 0.9074 (mt) cc_final: 0.8644 (mm) REVERT: b 87 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7212 (mppt) REVERT: b 89 GLU cc_start: 0.8989 (pm20) cc_final: 0.8786 (pm20) REVERT: b 90 ASP cc_start: 0.8081 (m-30) cc_final: 0.7876 (m-30) REVERT: b 105 GLN cc_start: 0.8203 (pm20) cc_final: 0.7726 (pm20) REVERT: C 439 ASP cc_start: 0.8236 (p0) cc_final: 0.7954 (p0) REVERT: C 486 ASN cc_start: 0.9141 (t0) cc_final: 0.8776 (t0) REVERT: C 489 ASP cc_start: 0.8969 (m-30) cc_final: 0.8768 (m-30) REVERT: c 4 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8667 (mp10) REVERT: c 44 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8475 (mtmm) REVERT: c 77 ASN cc_start: 0.8917 (m-40) cc_final: 0.8428 (m-40) REVERT: c 86 LEU cc_start: 0.9027 (mt) cc_final: 0.8662 (mp) REVERT: c 90 ASP cc_start: 0.7984 (m-30) cc_final: 0.7668 (m-30) REVERT: D 439 ASP cc_start: 0.8532 (p0) cc_final: 0.8180 (p0) REVERT: D 458 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8649 (mmpt) REVERT: D 486 ASN cc_start: 0.9040 (t0) cc_final: 0.8753 (t0) REVERT: d 4 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8320 (mp10) REVERT: d 7 GLU cc_start: 0.7871 (mp0) cc_final: 0.7199 (mp0) REVERT: d 32 ILE cc_start: 0.8892 (mt) cc_final: 0.8651 (mp) REVERT: d 44 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8637 (mtmm) REVERT: d 73 ASP cc_start: 0.7633 (t70) cc_final: 0.7331 (t0) REVERT: d 86 LEU cc_start: 0.9068 (mt) cc_final: 0.8474 (mm) REVERT: d 87 LYS cc_start: 0.7593 (mmtt) cc_final: 0.6948 (mppt) REVERT: d 90 ASP cc_start: 0.8010 (m-30) cc_final: 0.7620 (m-30) REVERT: d 105 GLN cc_start: 0.8264 (pm20) cc_final: 0.7917 (pm20) REVERT: E 439 ASP cc_start: 0.8153 (p0) cc_final: 0.7925 (p0) REVERT: E 450 GLU cc_start: 0.8751 (mp0) cc_final: 0.8334 (mt-10) REVERT: E 486 ASN cc_start: 0.9126 (t0) cc_final: 0.8742 (t0) REVERT: E 517 ARG cc_start: 0.9102 (ptt180) cc_final: 0.8714 (ptp-110) REVERT: E 544 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8601 (pp20) REVERT: e 4 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8690 (mm-40) REVERT: e 7 GLU cc_start: 0.7803 (mp0) cc_final: 0.7091 (mp0) REVERT: e 14 GLN cc_start: 0.8821 (pm20) cc_final: 0.8186 (mp10) REVERT: e 77 ASN cc_start: 0.8933 (m-40) cc_final: 0.8433 (m-40) REVERT: e 86 LEU cc_start: 0.8717 (mp) cc_final: 0.8387 (mm) REVERT: e 87 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7251 (mppt) REVERT: e 105 GLN cc_start: 0.7839 (pm20) cc_final: 0.7510 (pm20) REVERT: F 486 ASN cc_start: 0.9034 (t0) cc_final: 0.8736 (t0) REVERT: f 4 GLN cc_start: 0.8847 (mp10) cc_final: 0.8505 (mp10) REVERT: f 7 GLU cc_start: 0.7824 (mp0) cc_final: 0.7587 (mp0) REVERT: f 32 ILE cc_start: 0.8880 (mt) cc_final: 0.8631 (mp) REVERT: f 44 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8314 (mtmm) REVERT: f 73 ASP cc_start: 0.8023 (t0) cc_final: 0.7549 (t0) REVERT: f 86 LEU cc_start: 0.9167 (mt) cc_final: 0.8794 (mm) REVERT: f 87 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7322 (mppt) REVERT: f 90 ASP cc_start: 0.8073 (m-30) cc_final: 0.7825 (m-30) REVERT: G 439 ASP cc_start: 0.8176 (p0) cc_final: 0.7893 (p0) REVERT: G 486 ASN cc_start: 0.9144 (t0) cc_final: 0.8710 (t0) REVERT: G 517 ARG cc_start: 0.9139 (ptt180) cc_final: 0.8833 (ptm160) REVERT: g 4 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8575 (mm-40) REVERT: g 7 GLU cc_start: 0.7934 (mp0) cc_final: 0.7567 (mp0) REVERT: g 14 GLN cc_start: 0.8790 (pm20) cc_final: 0.8343 (mp10) REVERT: g 73 ASP cc_start: 0.7849 (t70) cc_final: 0.7411 (t0) REVERT: g 76 LYS cc_start: 0.9081 (pmtt) cc_final: 0.8860 (pmtt) REVERT: g 77 ASN cc_start: 0.8981 (m-40) cc_final: 0.8429 (m110) REVERT: g 86 LEU cc_start: 0.9286 (mt) cc_final: 0.8896 (mm) REVERT: g 87 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7303 (mppt) REVERT: g 90 ASP cc_start: 0.8032 (m-30) cc_final: 0.7795 (m-30) REVERT: g 105 GLN cc_start: 0.7897 (pm20) cc_final: 0.7596 (pm20) REVERT: H 486 ASN cc_start: 0.9175 (t0) cc_final: 0.8882 (t0) REVERT: h 4 GLN cc_start: 0.8840 (mp10) cc_final: 0.8495 (mp10) REVERT: h 44 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8317 (mtmm) REVERT: h 73 ASP cc_start: 0.8043 (t0) cc_final: 0.7615 (t0) REVERT: h 86 LEU cc_start: 0.9117 (mt) cc_final: 0.8659 (mm) REVERT: h 87 LYS cc_start: 0.7666 (mmtt) cc_final: 0.7237 (mppt) REVERT: h 89 GLU cc_start: 0.8929 (pm20) cc_final: 0.8709 (pm20) REVERT: h 90 ASP cc_start: 0.8013 (m-30) cc_final: 0.7753 (m-30) REVERT: I 439 ASP cc_start: 0.8246 (p0) cc_final: 0.7991 (p0) REVERT: I 483 ASP cc_start: 0.8246 (t0) cc_final: 0.8019 (t0) REVERT: I 486 ASN cc_start: 0.8983 (t0) cc_final: 0.8490 (t0) REVERT: I 489 ASP cc_start: 0.8936 (m-30) cc_final: 0.8622 (m-30) REVERT: I 516 HIS cc_start: 0.8494 (p-80) cc_final: 0.7937 (p90) REVERT: I 517 ARG cc_start: 0.8921 (ptp-170) cc_final: 0.8409 (ptp-170) REVERT: i 4 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8541 (mm-40) REVERT: i 7 GLU cc_start: 0.7877 (mp0) cc_final: 0.7553 (mp0) REVERT: i 73 ASP cc_start: 0.8211 (t0) cc_final: 0.7738 (t0) REVERT: i 76 LYS cc_start: 0.9262 (pmtt) cc_final: 0.9020 (pmmt) REVERT: i 86 LEU cc_start: 0.9087 (mt) cc_final: 0.8549 (mm) REVERT: i 87 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6947 (mppt) REVERT: i 90 ASP cc_start: 0.7929 (m-30) cc_final: 0.7529 (m-30) REVERT: J 486 ASN cc_start: 0.9011 (t0) cc_final: 0.8728 (t0) REVERT: j 4 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8507 (mm-40) REVERT: j 7 GLU cc_start: 0.7855 (mp0) cc_final: 0.7548 (mp0) REVERT: j 44 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8596 (mtmm) REVERT: j 73 ASP cc_start: 0.7689 (t0) cc_final: 0.6939 (t0) REVERT: j 76 LYS cc_start: 0.9181 (pmtt) cc_final: 0.8856 (pmtt) REVERT: j 86 LEU cc_start: 0.9165 (mt) cc_final: 0.8700 (mm) REVERT: j 87 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7390 (mppt) REVERT: j 89 GLU cc_start: 0.8934 (pm20) cc_final: 0.8725 (pm20) REVERT: j 105 GLN cc_start: 0.8030 (pm20) cc_final: 0.7745 (pm20) REVERT: K 450 GLU cc_start: 0.8883 (mp0) cc_final: 0.8509 (mt-10) REVERT: K 483 ASP cc_start: 0.8087 (t0) cc_final: 0.7846 (t0) REVERT: K 486 ASN cc_start: 0.9010 (t0) cc_final: 0.8663 (t0) REVERT: K 516 HIS cc_start: 0.8634 (p-80) cc_final: 0.7553 (p90) REVERT: K 517 ARG cc_start: 0.9061 (ptt180) cc_final: 0.8701 (ptp-110) REVERT: k 7 GLU cc_start: 0.7948 (mp0) cc_final: 0.7538 (mp0) REVERT: k 14 GLN cc_start: 0.8691 (pm20) cc_final: 0.8158 (mp10) REVERT: k 73 ASP cc_start: 0.8236 (t0) cc_final: 0.7924 (t0) REVERT: k 76 LYS cc_start: 0.9261 (pmtt) cc_final: 0.9016 (pmmt) REVERT: k 86 LEU cc_start: 0.9254 (mt) cc_final: 0.8822 (mm) REVERT: k 87 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7196 (mppt) REVERT: k 90 ASP cc_start: 0.7902 (m-30) cc_final: 0.7436 (m-30) REVERT: k 105 GLN cc_start: 0.8207 (pm20) cc_final: 0.7891 (pm20) REVERT: L 486 ASN cc_start: 0.9050 (t0) cc_final: 0.8704 (t0) REVERT: l 4 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8511 (mm-40) REVERT: l 86 LEU cc_start: 0.9215 (mt) cc_final: 0.8717 (mm) REVERT: l 87 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7126 (mppt) REVERT: l 90 ASP cc_start: 0.7984 (m-30) cc_final: 0.7615 (m-30) REVERT: l 105 GLN cc_start: 0.7920 (pm20) cc_final: 0.7377 (mp10) REVERT: M 486 ASN cc_start: 0.8960 (t0) cc_final: 0.8559 (t0) REVERT: M 516 HIS cc_start: 0.8564 (p90) cc_final: 0.8306 (p90) REVERT: m 4 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8682 (mm-40) REVERT: m 7 GLU cc_start: 0.8056 (mp0) cc_final: 0.7665 (mp0) REVERT: m 14 GLN cc_start: 0.8732 (pm20) cc_final: 0.8281 (mp10) REVERT: m 73 ASP cc_start: 0.8199 (t0) cc_final: 0.7879 (t0) REVERT: m 76 LYS cc_start: 0.9230 (pmtt) cc_final: 0.8959 (pmmt) REVERT: m 86 LEU cc_start: 0.9214 (mt) cc_final: 0.8718 (mm) REVERT: m 87 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7317 (mppt) REVERT: m 90 ASP cc_start: 0.7847 (m-30) cc_final: 0.7420 (m-30) REVERT: m 105 GLN cc_start: 0.8115 (pm20) cc_final: 0.7857 (pm20) REVERT: N 483 ASP cc_start: 0.8338 (t0) cc_final: 0.8036 (t0) REVERT: N 486 ASN cc_start: 0.9048 (t0) cc_final: 0.8690 (t0) REVERT: N 516 HIS cc_start: 0.8551 (p90) cc_final: 0.8344 (p90) REVERT: n 4 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8537 (mm-40) REVERT: n 7 GLU cc_start: 0.7933 (mp0) cc_final: 0.7304 (mp0) REVERT: n 73 ASP cc_start: 0.7725 (t0) cc_final: 0.6981 (t0) REVERT: n 76 LYS cc_start: 0.9213 (pmtt) cc_final: 0.8929 (pmtt) REVERT: n 86 LEU cc_start: 0.9255 (mt) cc_final: 0.8859 (mm) REVERT: n 87 LYS cc_start: 0.7395 (mmtt) cc_final: 0.6760 (mppt) REVERT: n 90 ASP cc_start: 0.8243 (m-30) cc_final: 0.7779 (m-30) REVERT: n 105 GLN cc_start: 0.8021 (pm20) cc_final: 0.7156 (pm20) REVERT: O 439 ASP cc_start: 0.8287 (p0) cc_final: 0.8010 (p0) REVERT: O 486 ASN cc_start: 0.9000 (t0) cc_final: 0.8497 (t0) REVERT: O 489 ASP cc_start: 0.8960 (m-30) cc_final: 0.8606 (m-30) REVERT: O 516 HIS cc_start: 0.8545 (p-80) cc_final: 0.7948 (p-80) REVERT: O 517 ARG cc_start: 0.8901 (ptp-170) cc_final: 0.8415 (ptp-110) REVERT: o 4 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8656 (mm-40) REVERT: o 14 GLN cc_start: 0.8785 (pm20) cc_final: 0.8345 (mp10) REVERT: o 73 ASP cc_start: 0.8159 (t0) cc_final: 0.7779 (t0) REVERT: o 86 LEU cc_start: 0.9152 (mt) cc_final: 0.8612 (mm) REVERT: o 87 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7397 (mppt) REVERT: o 90 ASP cc_start: 0.7842 (m-30) cc_final: 0.7390 (m-30) REVERT: o 105 GLN cc_start: 0.7962 (pm20) cc_final: 0.7756 (pm20) REVERT: P 439 ASP cc_start: 0.8283 (p0) cc_final: 0.8049 (p0) REVERT: P 457 MET cc_start: 0.8656 (mtt) cc_final: 0.8446 (mtt) REVERT: P 486 ASN cc_start: 0.9075 (t0) cc_final: 0.8796 (t0) REVERT: P 517 ARG cc_start: 0.9088 (ptt180) cc_final: 0.8645 (ptp-110) REVERT: p 4 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8566 (mm-40) REVERT: p 7 GLU cc_start: 0.7941 (mp0) cc_final: 0.7372 (mp0) REVERT: p 73 ASP cc_start: 0.8073 (t0) cc_final: 0.7596 (t0) REVERT: p 76 LYS cc_start: 0.9138 (pmmt) cc_final: 0.8791 (pmtt) REVERT: p 86 LEU cc_start: 0.9232 (mt) cc_final: 0.8755 (mm) REVERT: p 87 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7195 (mppt) REVERT: p 90 ASP cc_start: 0.8168 (m-30) cc_final: 0.7729 (m-30) outliers start: 68 outliers final: 25 residues processed: 1075 average time/residue: 0.6752 time to fit residues: 884.5480 Evaluate side-chains 966 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 939 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 508 CYS Chi-restraints excluded: chain m residue 5 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain o residue 5 LEU Chi-restraints excluded: chain p residue 5 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 50 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 88 optimal weight: 0.0010 chunk 134 optimal weight: 20.0000 chunk 280 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN D 418 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 418 GLN ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 4 GLN ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 418 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.144392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089126 restraints weight = 64927.344| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.64 r_work: 0.3093 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 43344 Z= 0.263 Angle : 0.646 7.598 58608 Z= 0.331 Chirality : 0.044 0.146 6608 Planarity : 0.004 0.056 7536 Dihedral : 5.036 25.930 6016 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.99 % Allowed : 13.68 % Favored : 82.32 % 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 aren not related in a simple way. whole: -1.10 (0.11), residues: 5360 helix: 0.04 (0.11), residues: 2272 sheet: -1.34 (0.17), residues: 960 loop : -1.13 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG i 53 TYR 0.017 0.002 TYR M 479 PHE 0.009 0.001 PHE P 466 TRP 0.012 0.002 TRP a 103 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00625 (43328) covalent geometry : angle 0.64539 (58576) SS BOND : bond 0.00229 ( 16) SS BOND : angle 1.03096 ( 32) hydrogen bonds : bond 0.04357 ( 1921) hydrogen bonds : angle 4.46242 ( 5190) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 899 time to evaluate : 1.447 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: 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 486 ASN cc_start: 0.9130 (t0) cc_final: 0.8868 (t0) REVERT: a 4 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8642 (mm-40) REVERT: a 7 GLU cc_start: 0.7852 (mp0) cc_final: 0.7260 (mp0) REVERT: a 73 ASP cc_start: 0.8019 (t0) cc_final: 0.7285 (t0) REVERT: a 76 LYS cc_start: 0.8990 (pmtt) cc_final: 0.8765 (pmtt) REVERT: a 77 ASN cc_start: 0.8916 (m-40) cc_final: 0.8398 (m-40) REVERT: a 86 LEU cc_start: 0.9099 (mt) cc_final: 0.8674 (mp) REVERT: a 90 ASP cc_start: 0.8520 (m-30) cc_final: 0.8256 (m-30) REVERT: a 105 GLN cc_start: 0.7947 (pm20) cc_final: 0.7548 (pm20) REVERT: B 486 ASN cc_start: 0.9004 (t0) cc_final: 0.8789 (t0) REVERT: B 517 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8952 (ptp-110) REVERT: b 73 ASP cc_start: 0.8120 (t70) cc_final: 0.7665 (t0) REVERT: b 76 LYS cc_start: 0.9050 (pmmt) cc_final: 0.8787 (pmtt) REVERT: b 86 LEU cc_start: 0.9134 (mt) cc_final: 0.8689 (mm) REVERT: b 87 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7459 (mppt) REVERT: b 89 GLU cc_start: 0.8980 (pm20) cc_final: 0.8704 (pm20) REVERT: b 90 ASP cc_start: 0.8491 (m-30) cc_final: 0.8110 (m-30) REVERT: C 486 ASN cc_start: 0.9112 (t0) cc_final: 0.8628 (t0) REVERT: C 489 ASP cc_start: 0.8942 (m-30) cc_final: 0.8701 (m-30) REVERT: c 4 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8655 (mp10) REVERT: c 7 GLU cc_start: 0.7946 (mp0) cc_final: 0.7338 (mp0) REVERT: c 76 LYS cc_start: 0.9013 (pmtt) cc_final: 0.8738 (pmtt) REVERT: c 77 ASN cc_start: 0.8893 (m-40) cc_final: 0.8483 (m-40) REVERT: c 86 LEU cc_start: 0.9104 (mt) cc_final: 0.8687 (mm) REVERT: c 90 ASP cc_start: 0.8490 (m-30) cc_final: 0.8228 (m-30) REVERT: c 105 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: D 439 ASP cc_start: 0.8473 (p0) cc_final: 0.8255 (p0) REVERT: D 458 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8736 (mmpt) REVERT: D 486 ASN cc_start: 0.9136 (t0) cc_final: 0.8903 (t0) REVERT: D 517 ARG cc_start: 0.9165 (ptm160) cc_final: 0.8882 (ptp-110) REVERT: d 4 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8332 (mp10) REVERT: d 7 GLU cc_start: 0.7774 (mp0) cc_final: 0.7157 (mp0) REVERT: d 73 ASP cc_start: 0.7902 (t70) cc_final: 0.7480 (t0) REVERT: d 76 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8861 (pmtt) REVERT: d 86 LEU cc_start: 0.9138 (mt) cc_final: 0.8808 (mm) REVERT: d 90 ASP cc_start: 0.8433 (m-30) cc_final: 0.8063 (m-30) REVERT: d 105 GLN cc_start: 0.8294 (pm20) cc_final: 0.7842 (pm20) REVERT: E 486 ASN cc_start: 0.9116 (t0) cc_final: 0.8832 (t0) REVERT: e 4 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8664 (mm-40) REVERT: e 7 GLU cc_start: 0.7849 (mp0) cc_final: 0.7158 (mp0) REVERT: e 14 GLN cc_start: 0.8684 (pm20) cc_final: 0.8197 (mp10) REVERT: e 76 LYS cc_start: 0.9099 (pmtt) cc_final: 0.8821 (pmtt) REVERT: e 77 ASN cc_start: 0.8917 (m-40) cc_final: 0.8515 (m-40) REVERT: e 86 LEU cc_start: 0.8780 (mp) cc_final: 0.8456 (mm) REVERT: e 87 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7361 (mppt) REVERT: e 105 GLN cc_start: 0.7769 (pm20) cc_final: 0.7350 (pm20) REVERT: f 4 GLN cc_start: 0.8829 (mp10) cc_final: 0.8486 (mp10) REVERT: f 73 ASP cc_start: 0.8150 (t0) cc_final: 0.7420 (t0) REVERT: f 76 LYS cc_start: 0.9142 (pmmt) cc_final: 0.8823 (pmtt) REVERT: f 86 LEU cc_start: 0.9186 (mt) cc_final: 0.8869 (mm) REVERT: f 90 ASP cc_start: 0.8370 (m-30) cc_final: 0.8004 (m-30) REVERT: G 486 ASN cc_start: 0.9129 (t0) cc_final: 0.8853 (t0) REVERT: g 4 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8630 (mm-40) REVERT: g 7 GLU cc_start: 0.8028 (mp0) cc_final: 0.7480 (mp0) REVERT: g 14 GLN cc_start: 0.8722 (pm20) cc_final: 0.8335 (mp10) REVERT: g 73 ASP cc_start: 0.7964 (t70) cc_final: 0.7511 (t0) REVERT: g 77 ASN cc_start: 0.8973 (m-40) cc_final: 0.8425 (m110) REVERT: g 86 LEU cc_start: 0.9280 (mt) cc_final: 0.8954 (mm) REVERT: g 105 GLN cc_start: 0.7886 (pm20) cc_final: 0.7410 (pm20) REVERT: H 486 ASN cc_start: 0.9178 (t0) cc_final: 0.8952 (t0) REVERT: h 73 ASP cc_start: 0.8243 (t0) cc_final: 0.7721 (t0) REVERT: h 76 LYS cc_start: 0.9167 (pmmt) cc_final: 0.8919 (pmtt) REVERT: h 86 LEU cc_start: 0.9159 (mt) cc_final: 0.8739 (mm) REVERT: h 87 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7487 (mppt) REVERT: h 89 GLU cc_start: 0.8942 (pm20) cc_final: 0.8672 (pm20) REVERT: h 90 ASP cc_start: 0.8459 (m-30) cc_final: 0.8093 (m-30) REVERT: h 105 GLN cc_start: 0.8092 (mp10) cc_final: 0.7816 (pm20) REVERT: I 439 ASP cc_start: 0.8370 (p0) cc_final: 0.8096 (p0) REVERT: I 450 GLU cc_start: 0.8773 (mp0) cc_final: 0.8368 (mt-10) REVERT: I 483 ASP cc_start: 0.8220 (t0) cc_final: 0.7976 (t0) REVERT: I 486 ASN cc_start: 0.8835 (t0) cc_final: 0.8489 (t0) REVERT: I 495 ASP cc_start: 0.8557 (t0) cc_final: 0.8244 (t0) REVERT: I 516 HIS cc_start: 0.8581 (p-80) cc_final: 0.7976 (p90) REVERT: I 517 ARG cc_start: 0.8835 (ptp-110) cc_final: 0.8279 (ptp-170) REVERT: i 4 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8564 (mm-40) REVERT: i 73 ASP cc_start: 0.8146 (t0) cc_final: 0.7552 (t0) REVERT: i 76 LYS cc_start: 0.9187 (pmtt) cc_final: 0.8940 (pmmt) REVERT: i 86 LEU cc_start: 0.9176 (mt) cc_final: 0.8746 (mm) REVERT: i 87 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7683 (mppt) REVERT: i 90 ASP cc_start: 0.8584 (m-30) cc_final: 0.8321 (m-30) REVERT: J 486 ASN cc_start: 0.9020 (t0) cc_final: 0.8768 (t0) REVERT: J 521 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8102 (tp40) REVERT: j 4 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8633 (mm-40) REVERT: j 7 GLU cc_start: 0.7862 (mp0) cc_final: 0.7575 (mp0) REVERT: j 44 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8490 (mtmm) REVERT: j 86 LEU cc_start: 0.9178 (mt) cc_final: 0.8615 (mm) REVERT: j 87 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7228 (mppt) REVERT: j 89 GLU cc_start: 0.8965 (pm20) cc_final: 0.8699 (pm20) REVERT: j 90 ASP cc_start: 0.8403 (m-30) cc_final: 0.7819 (m-30) REVERT: j 105 GLN cc_start: 0.7962 (pm20) cc_final: 0.7535 (pm20) REVERT: K 450 GLU cc_start: 0.8787 (mp0) cc_final: 0.8325 (mt-10) REVERT: K 483 ASP cc_start: 0.8243 (t0) cc_final: 0.7974 (t0) REVERT: K 486 ASN cc_start: 0.9047 (t0) cc_final: 0.8661 (t0) REVERT: K 516 HIS cc_start: 0.8674 (p-80) cc_final: 0.7539 (p90) REVERT: K 517 ARG cc_start: 0.9126 (ptt180) cc_final: 0.8778 (ptp-110) REVERT: k 4 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8434 (mm-40) REVERT: k 7 GLU cc_start: 0.8006 (mp0) cc_final: 0.7485 (mp0) REVERT: k 14 GLN cc_start: 0.8681 (pm20) cc_final: 0.8165 (mp10) REVERT: k 83 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8682 (mtp) REVERT: k 86 LEU cc_start: 0.9293 (mt) cc_final: 0.8875 (mm) REVERT: k 87 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7307 (mppt) REVERT: k 90 ASP cc_start: 0.8504 (m-30) cc_final: 0.8118 (m-30) REVERT: k 105 GLN cc_start: 0.8087 (pm20) cc_final: 0.7650 (pm20) REVERT: L 486 ASN cc_start: 0.9061 (t0) cc_final: 0.8764 (t0) REVERT: l 4 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8616 (mm-40) REVERT: l 7 GLU cc_start: 0.7717 (mp0) cc_final: 0.7357 (mp0) REVERT: l 44 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8399 (mtmm) REVERT: l 73 ASP cc_start: 0.8268 (t0) cc_final: 0.7714 (t0) REVERT: l 76 LYS cc_start: 0.9142 (pmmt) cc_final: 0.8860 (pmmt) REVERT: l 86 LEU cc_start: 0.9205 (mt) cc_final: 0.8728 (mm) REVERT: l 87 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7167 (mppt) REVERT: l 90 ASP cc_start: 0.8394 (m-30) cc_final: 0.7842 (m-30) REVERT: M 486 ASN cc_start: 0.8952 (t0) cc_final: 0.8545 (t0) REVERT: M 516 HIS cc_start: 0.8537 (p90) cc_final: 0.8220 (p90) REVERT: m 4 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8558 (mm-40) REVERT: m 7 GLU cc_start: 0.8097 (mp0) cc_final: 0.7871 (mp0) REVERT: m 14 GLN cc_start: 0.8705 (pm20) cc_final: 0.8254 (mp10) REVERT: m 83 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8735 (mtp) REVERT: m 86 LEU cc_start: 0.9278 (mt) cc_final: 0.8854 (mm) REVERT: m 87 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7309 (mppt) REVERT: m 90 ASP cc_start: 0.8403 (m-30) cc_final: 0.7993 (m-30) REVERT: m 105 GLN cc_start: 0.8047 (pm20) cc_final: 0.7718 (pm20) REVERT: N 423 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8882 (tt0) REVERT: N 439 ASP cc_start: 0.8387 (p0) cc_final: 0.8143 (p0) REVERT: N 486 ASN cc_start: 0.9160 (t0) cc_final: 0.8804 (t0) REVERT: n 4 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8538 (mm-40) REVERT: n 7 GLU cc_start: 0.7882 (mp0) cc_final: 0.7208 (mp0) REVERT: n 86 LEU cc_start: 0.9221 (mt) cc_final: 0.8773 (mm) REVERT: n 87 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7164 (mppt) REVERT: n 90 ASP cc_start: 0.8502 (m-30) cc_final: 0.8028 (m-30) REVERT: n 105 GLN cc_start: 0.7861 (pm20) cc_final: 0.6934 (pm20) REVERT: O 439 ASP cc_start: 0.8390 (p0) cc_final: 0.8125 (p0) REVERT: O 486 ASN cc_start: 0.8878 (t0) cc_final: 0.8642 (t0) REVERT: O 495 ASP cc_start: 0.8556 (t0) cc_final: 0.8292 (t0) REVERT: O 516 HIS cc_start: 0.8604 (p-80) cc_final: 0.7972 (p90) REVERT: O 517 ARG cc_start: 0.8860 (ptp-170) cc_final: 0.8311 (ptp-170) REVERT: o 4 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8576 (mm-40) REVERT: o 7 GLU cc_start: 0.8237 (mp0) cc_final: 0.7974 (mp0) REVERT: o 14 GLN cc_start: 0.8773 (pm20) cc_final: 0.8405 (mp10) REVERT: o 73 ASP cc_start: 0.8287 (t0) cc_final: 0.7849 (t0) REVERT: o 83 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (mtp) REVERT: o 86 LEU cc_start: 0.9221 (mt) cc_final: 0.8967 (mm) REVERT: o 90 ASP cc_start: 0.8350 (m-30) cc_final: 0.7964 (m-30) REVERT: o 102 THR cc_start: 0.8622 (p) cc_final: 0.8324 (t) REVERT: o 105 GLN cc_start: 0.8068 (pm20) cc_final: 0.7743 (pm20) REVERT: P 439 ASP cc_start: 0.8349 (p0) cc_final: 0.8134 (p0) REVERT: P 486 ASN cc_start: 0.9045 (t0) cc_final: 0.8804 (t0) REVERT: P 517 ARG cc_start: 0.9176 (ptt180) cc_final: 0.8720 (ptp-110) REVERT: p 4 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8642 (mm-40) REVERT: p 73 ASP cc_start: 0.8147 (t0) cc_final: 0.7537 (t0) REVERT: p 76 LYS cc_start: 0.9150 (pmmt) cc_final: 0.8814 (pmtt) REVERT: p 86 LEU cc_start: 0.9267 (mt) cc_final: 0.8818 (mm) REVERT: p 87 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7268 (mppt) REVERT: p 90 ASP cc_start: 0.8518 (m-30) cc_final: 0.8078 (m-30) outliers start: 186 outliers final: 81 residues processed: 980 average time/residue: 0.7441 time to fit residues: 883.6522 Evaluate side-chains 936 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 847 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain D residue 508 CYS Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 76 LYS Chi-restraints excluded: chain d residue 83 MET Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 69 THR Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 69 THR Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 35 MET Chi-restraints excluded: chain g residue 69 THR Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 508 CYS Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain I residue 502 THR Chi-restraints excluded: chain I residue 508 CYS Chi-restraints excluded: chain i residue 83 MET Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 505 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 508 CYS Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 83 MET Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 378 VAL Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 502 THR Chi-restraints excluded: chain M residue 508 CYS Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 69 THR Chi-restraints excluded: chain m residue 83 MET Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 423 GLN Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 502 THR Chi-restraints excluded: chain O residue 508 CYS Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 83 MET Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 0.9990 chunk 376 optimal weight: 0.9990 chunk 151 optimal weight: 0.0060 chunk 477 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 421 optimal weight: 4.9990 chunk 473 optimal weight: 2.9990 chunk 409 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 433 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** 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 = 0.4137 r_free = 0.4137 target = 0.147876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093484 restraints weight = 64772.994| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.58 r_work: 0.3187 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 43344 Z= 0.106 Angle : 0.578 9.526 58608 Z= 0.290 Chirality : 0.039 0.141 6608 Planarity : 0.004 0.038 7536 Dihedral : 4.658 23.059 6016 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.13 % Allowed : 16.88 % Favored : 80.99 % 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 aren not related in a simple way. whole: -0.72 (0.12), residues: 5360 helix: 0.38 (0.11), residues: 2304 sheet: -1.13 (0.17), residues: 960 loop : -0.98 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 484 TYR 0.011 0.001 TYR a 80 PHE 0.007 0.001 PHE I 467 TRP 0.011 0.001 TRP a 103 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00244 (43328) covalent geometry : angle 0.57800 (58576) SS BOND : bond 0.00115 ( 16) SS BOND : angle 0.73236 ( 32) hydrogen bonds : bond 0.03146 ( 1921) hydrogen bonds : angle 4.10729 ( 5190) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 946 time to evaluate : 1.678 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8442 (ptmt) cc_final: 0.7916 (ptpp) REVERT: A 450 GLU cc_start: 0.8657 (mp0) cc_final: 0.8270 (mt-10) REVERT: A 486 ASN cc_start: 0.9120 (t0) cc_final: 0.8858 (t0) REVERT: a 4 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8755 (mm-40) REVERT: a 7 GLU cc_start: 0.7706 (mp0) cc_final: 0.7301 (mp0) REVERT: a 44 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8372 (mtmm) REVERT: a 73 ASP cc_start: 0.8060 (t0) cc_final: 0.7194 (t0) REVERT: a 76 LYS cc_start: 0.9100 (pmtt) cc_final: 0.8688 (pmtt) REVERT: a 77 ASN cc_start: 0.8847 (m-40) cc_final: 0.8405 (m-40) REVERT: a 86 LEU cc_start: 0.9131 (mt) cc_final: 0.8497 (mm) REVERT: a 87 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7058 (mppt) REVERT: a 90 ASP cc_start: 0.8186 (m-30) cc_final: 0.7871 (m-30) REVERT: a 105 GLN cc_start: 0.7847 (pm20) cc_final: 0.7450 (pm20) REVERT: B 486 ASN cc_start: 0.8980 (t0) cc_final: 0.8762 (t0) REVERT: B 517 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.9019 (ptp-110) REVERT: b 4 GLN cc_start: 0.8773 (mp10) cc_final: 0.7955 (mp10) REVERT: b 73 ASP cc_start: 0.8130 (t70) cc_final: 0.7666 (t0) REVERT: b 76 LYS cc_start: 0.9091 (pmmt) cc_final: 0.8821 (pmtt) REVERT: b 87 LYS cc_start: 0.7603 (mmtt) cc_final: 0.6854 (mppt) REVERT: b 89 GLU cc_start: 0.8945 (pm20) cc_final: 0.8655 (pm20) REVERT: b 90 ASP cc_start: 0.8180 (m-30) cc_final: 0.7614 (m-30) REVERT: b 105 GLN cc_start: 0.8297 (mp10) cc_final: 0.8041 (pm20) REVERT: C 486 ASN cc_start: 0.9098 (t0) cc_final: 0.8570 (t0) REVERT: C 489 ASP cc_start: 0.8909 (m-30) cc_final: 0.8658 (m-30) REVERT: c 4 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8676 (mp10) REVERT: c 7 GLU cc_start: 0.7935 (mp0) cc_final: 0.7264 (mp0) REVERT: c 44 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8407 (mtmm) REVERT: c 77 ASN cc_start: 0.8910 (m-40) cc_final: 0.8417 (m-40) REVERT: c 86 LEU cc_start: 0.9113 (mt) cc_final: 0.8501 (mm) REVERT: c 87 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7109 (mppt) REVERT: c 90 ASP cc_start: 0.8179 (m-30) cc_final: 0.7886 (m-30) REVERT: c 105 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: D 439 ASP cc_start: 0.8361 (p0) cc_final: 0.8142 (p0) REVERT: D 458 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8748 (mmpt) REVERT: D 472 GLU cc_start: 0.8930 (tt0) cc_final: 0.8415 (tp30) REVERT: D 486 ASN cc_start: 0.9042 (t0) cc_final: 0.8802 (t0) REVERT: D 517 ARG cc_start: 0.9192 (ptm160) cc_final: 0.8950 (ptp-110) REVERT: d 4 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8296 (mp10) REVERT: d 73 ASP cc_start: 0.7965 (t70) cc_final: 0.7667 (t0) REVERT: d 86 LEU cc_start: 0.9155 (mt) cc_final: 0.8565 (mm) REVERT: d 87 LYS cc_start: 0.7690 (mmtt) cc_final: 0.6955 (mppt) REVERT: d 90 ASP cc_start: 0.8186 (m-30) cc_final: 0.7818 (m-30) REVERT: d 105 GLN cc_start: 0.8219 (pm20) cc_final: 0.7922 (pm20) REVERT: E 450 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8318 (mt-10) REVERT: E 486 ASN cc_start: 0.9104 (t0) cc_final: 0.8823 (t0) REVERT: E 544 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8413 (pp20) REVERT: e 4 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8644 (mm-40) REVERT: e 7 GLU cc_start: 0.7729 (mp0) cc_final: 0.7061 (mp0) REVERT: e 14 GLN cc_start: 0.8757 (pm20) cc_final: 0.8198 (mp10) REVERT: e 77 ASN cc_start: 0.8917 (m-40) cc_final: 0.8425 (m-40) REVERT: e 86 LEU cc_start: 0.8877 (mp) cc_final: 0.8651 (mm) REVERT: e 105 GLN cc_start: 0.7973 (pm20) cc_final: 0.7375 (pm20) REVERT: F 403 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8439 (mmm-85) REVERT: F 472 GLU cc_start: 0.8919 (tt0) cc_final: 0.8404 (tp30) REVERT: F 486 ASN cc_start: 0.9000 (t0) cc_final: 0.8685 (t0) REVERT: F 517 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8772 (ptp-110) REVERT: f 4 GLN cc_start: 0.8938 (mp10) cc_final: 0.8593 (mp10) REVERT: f 44 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8418 (mtmm) REVERT: f 73 ASP cc_start: 0.8172 (t0) cc_final: 0.7375 (t0) REVERT: f 76 LYS cc_start: 0.9232 (pmmt) cc_final: 0.8854 (pmtt) REVERT: f 86 LEU cc_start: 0.9170 (mt) cc_final: 0.8698 (mm) REVERT: f 87 LYS cc_start: 0.7564 (mmtt) cc_final: 0.6832 (mppt) REVERT: f 90 ASP cc_start: 0.8182 (m-30) cc_final: 0.7795 (m-30) REVERT: f 105 GLN cc_start: 0.8246 (mp10) cc_final: 0.7975 (pm20) REVERT: G 486 ASN cc_start: 0.9121 (t0) cc_final: 0.8862 (t0) REVERT: g 4 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8674 (mm-40) REVERT: g 7 GLU cc_start: 0.7831 (mp0) cc_final: 0.7049 (mp0) REVERT: g 14 GLN cc_start: 0.8812 (pm20) cc_final: 0.8335 (mp10) REVERT: g 73 ASP cc_start: 0.7939 (t70) cc_final: 0.7471 (t0) REVERT: g 77 ASN cc_start: 0.8966 (m-40) cc_final: 0.8382 (m110) REVERT: g 86 LEU cc_start: 0.9284 (mt) cc_final: 0.9005 (mm) REVERT: g 105 GLN cc_start: 0.7884 (pm20) cc_final: 0.7228 (pm20) REVERT: H 472 GLU cc_start: 0.8885 (tt0) cc_final: 0.8412 (tp30) REVERT: H 486 ASN cc_start: 0.9106 (t0) cc_final: 0.8770 (t0) REVERT: H 517 ARG cc_start: 0.9134 (ptm160) cc_final: 0.8852 (ptp-110) REVERT: h 4 GLN cc_start: 0.8795 (mp10) cc_final: 0.7940 (mp10) REVERT: h 73 ASP cc_start: 0.8163 (t0) cc_final: 0.7574 (t0) REVERT: h 76 LYS cc_start: 0.9234 (pmmt) cc_final: 0.8824 (pmtt) REVERT: h 86 LEU cc_start: 0.9127 (mt) cc_final: 0.8574 (mm) REVERT: h 87 LYS cc_start: 0.7604 (mmtt) cc_final: 0.6852 (mppt) REVERT: h 89 GLU cc_start: 0.8906 (pm20) cc_final: 0.8633 (pm20) REVERT: h 90 ASP cc_start: 0.8224 (m-30) cc_final: 0.7750 (m-30) REVERT: h 105 GLN cc_start: 0.8142 (mp10) cc_final: 0.7914 (pm20) REVERT: I 439 ASP cc_start: 0.8229 (p0) cc_final: 0.7972 (p0) REVERT: I 450 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8355 (mt-10) REVERT: I 483 ASP cc_start: 0.8238 (t0) cc_final: 0.8028 (t0) REVERT: I 486 ASN cc_start: 0.8864 (t0) cc_final: 0.8505 (t0) REVERT: I 516 HIS cc_start: 0.8602 (p-80) cc_final: 0.7918 (p90) REVERT: I 517 ARG cc_start: 0.8867 (ptp-110) cc_final: 0.8337 (ptp-110) REVERT: i 4 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8567 (mm-40) REVERT: i 7 GLU cc_start: 0.7828 (mp0) cc_final: 0.7502 (mp0) REVERT: i 73 ASP cc_start: 0.8093 (t0) cc_final: 0.7435 (t0) REVERT: i 76 LYS cc_start: 0.9256 (pmtt) cc_final: 0.8985 (pmmt) REVERT: i 86 LEU cc_start: 0.9214 (mt) cc_final: 0.8671 (mm) REVERT: i 87 LYS cc_start: 0.7620 (mmtt) cc_final: 0.6973 (mppt) REVERT: i 90 ASP cc_start: 0.8207 (m-30) cc_final: 0.7781 (m-30) REVERT: J 486 ASN cc_start: 0.9008 (t0) cc_final: 0.8661 (t0) REVERT: j 4 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8581 (mm-40) REVERT: j 7 GLU cc_start: 0.7835 (mp0) cc_final: 0.7573 (mp0) REVERT: j 44 LYS cc_start: 0.8890 (mtmm) cc_final: 0.8563 (mtmm) REVERT: j 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7380 (t0) REVERT: j 76 LYS cc_start: 0.9204 (pmtt) cc_final: 0.8997 (pmmt) REVERT: j 86 LEU cc_start: 0.9200 (mt) cc_final: 0.8678 (mm) REVERT: j 87 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7131 (mppt) REVERT: j 89 GLU cc_start: 0.8875 (pm20) cc_final: 0.8551 (pm20) REVERT: j 90 ASP cc_start: 0.8046 (m-30) cc_final: 0.7447 (m-30) REVERT: j 105 GLN cc_start: 0.7945 (pm20) cc_final: 0.7507 (pm20) REVERT: K 450 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8501 (mt-10) REVERT: K 483 ASP cc_start: 0.8260 (t0) cc_final: 0.8044 (t0) REVERT: K 486 ASN cc_start: 0.9071 (t0) cc_final: 0.8635 (t0) REVERT: K 516 HIS cc_start: 0.8661 (p-80) cc_final: 0.7541 (p90) REVERT: K 517 ARG cc_start: 0.9113 (ptt180) cc_final: 0.8826 (ptp-110) REVERT: k 4 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8443 (mm-40) REVERT: k 7 GLU cc_start: 0.7820 (mp0) cc_final: 0.7489 (mp0) REVERT: k 14 GLN cc_start: 0.8724 (pm20) cc_final: 0.8216 (mp10) REVERT: k 38 TYR cc_start: 0.9112 (m-80) cc_final: 0.8906 (m-80) REVERT: k 86 LEU cc_start: 0.9324 (mt) cc_final: 0.8883 (mm) REVERT: k 87 LYS cc_start: 0.7651 (mmtt) cc_final: 0.6969 (mppt) REVERT: k 90 ASP cc_start: 0.8135 (m-30) cc_final: 0.7680 (m-30) REVERT: k 105 GLN cc_start: 0.8042 (pm20) cc_final: 0.7658 (pm20) REVERT: L 472 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8601 (tp30) REVERT: L 486 ASN cc_start: 0.9065 (t0) cc_final: 0.8707 (t0) REVERT: L 543 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8107 (mtt-85) REVERT: l 4 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8592 (mm-40) REVERT: l 44 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8381 (mtmm) REVERT: l 73 ASP cc_start: 0.8274 (t0) cc_final: 0.7696 (t0) REVERT: l 76 LYS cc_start: 0.9157 (pmmt) cc_final: 0.8892 (pmmt) REVERT: l 86 LEU cc_start: 0.9225 (mt) cc_final: 0.8754 (mm) REVERT: l 87 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7206 (mppt) REVERT: l 90 ASP cc_start: 0.8158 (m-30) cc_final: 0.7599 (m-30) REVERT: l 105 GLN cc_start: 0.7911 (mp10) cc_final: 0.7570 (pm20) REVERT: M 450 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8287 (mt-10) REVERT: M 486 ASN cc_start: 0.8934 (t0) cc_final: 0.8463 (t0) REVERT: M 516 HIS cc_start: 0.8600 (p90) cc_final: 0.8284 (p90) REVERT: m 4 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8580 (mm-40) REVERT: m 14 GLN cc_start: 0.8717 (pm20) cc_final: 0.8270 (mp10) REVERT: m 44 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8460 (mtmm) REVERT: m 86 LEU cc_start: 0.9320 (mt) cc_final: 0.8880 (mm) REVERT: m 87 LYS cc_start: 0.7673 (mmtt) cc_final: 0.6973 (mppt) REVERT: m 90 ASP cc_start: 0.8127 (m-30) cc_final: 0.7678 (m-30) REVERT: m 105 GLN cc_start: 0.7936 (pm20) cc_final: 0.7639 (pm20) REVERT: N 472 GLU cc_start: 0.8891 (tt0) cc_final: 0.8419 (tp30) REVERT: N 486 ASN cc_start: 0.9047 (t0) cc_final: 0.8529 (t0) REVERT: n 4 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8634 (mm-40) REVERT: n 73 ASP cc_start: 0.8080 (t0) cc_final: 0.7370 (t0) REVERT: n 76 LYS cc_start: 0.9253 (pmtt) cc_final: 0.8979 (pmtt) REVERT: n 86 LEU cc_start: 0.9236 (mt) cc_final: 0.8808 (mm) REVERT: n 87 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7193 (mppt) REVERT: n 90 ASP cc_start: 0.8259 (m-30) cc_final: 0.7759 (m-30) REVERT: n 105 GLN cc_start: 0.7817 (pm20) cc_final: 0.7162 (mp10) REVERT: O 439 ASP cc_start: 0.8243 (p0) cc_final: 0.8000 (p0) REVERT: O 486 ASN cc_start: 0.8856 (t0) cc_final: 0.8299 (t0) REVERT: O 489 ASP cc_start: 0.8930 (m-30) cc_final: 0.8609 (m-30) REVERT: O 516 HIS cc_start: 0.8619 (p-80) cc_final: 0.7933 (p90) REVERT: O 517 ARG cc_start: 0.8884 (ptp-170) cc_final: 0.8354 (ptp-110) REVERT: o 4 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8624 (mm-40) REVERT: o 14 GLN cc_start: 0.8831 (pm20) cc_final: 0.8443 (mp10) REVERT: o 73 ASP cc_start: 0.8352 (t0) cc_final: 0.7829 (t0) REVERT: o 86 LEU cc_start: 0.9214 (mt) cc_final: 0.8707 (mm) REVERT: o 87 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7027 (mppt) REVERT: o 90 ASP cc_start: 0.8178 (m-30) cc_final: 0.7717 (m-30) REVERT: o 102 THR cc_start: 0.8726 (p) cc_final: 0.8474 (t) REVERT: P 439 ASP cc_start: 0.8134 (p0) cc_final: 0.7933 (p0) REVERT: P 486 ASN cc_start: 0.9019 (t0) cc_final: 0.8532 (t0) REVERT: P 517 ARG cc_start: 0.9153 (ptt180) cc_final: 0.8713 (ptp-110) REVERT: p 4 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8573 (mm-40) REVERT: p 73 ASP cc_start: 0.8152 (t0) cc_final: 0.7531 (t0) REVERT: p 76 LYS cc_start: 0.9186 (pmmt) cc_final: 0.8844 (pmtt) REVERT: p 86 LEU cc_start: 0.9248 (mt) cc_final: 0.8789 (mm) REVERT: p 87 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7239 (mppt) REVERT: p 90 ASP cc_start: 0.8198 (m-30) cc_final: 0.7773 (m-30) outliers start: 99 outliers final: 45 residues processed: 983 average time/residue: 0.6896 time to fit residues: 821.0556 Evaluate side-chains 953 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 904 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain I residue 523 LEU Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 505 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 523 LEU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain O residue 483 ASP Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 59 optimal weight: 4.9990 chunk 352 optimal weight: 6.9990 chunk 296 optimal weight: 5.9990 chunk 338 optimal weight: 1.9990 chunk 406 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 414 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 chunk 394 optimal weight: 0.9980 chunk 165 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** 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 = 0.4103 r_free = 0.4103 target = 0.145153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090837 restraints weight = 64461.475| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.57 r_work: 0.3119 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 43344 Z= 0.207 Angle : 0.606 8.811 58608 Z= 0.308 Chirality : 0.042 0.139 6608 Planarity : 0.004 0.043 7536 Dihedral : 4.770 24.113 6016 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.11 % Allowed : 17.55 % Favored : 79.34 % 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 aren not related in a simple way. whole: -0.57 (0.12), residues: 5360 helix: 0.52 (0.11), residues: 2320 sheet: -1.08 (0.17), residues: 960 loop : -0.91 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 403 TYR 0.013 0.001 TYR h 54 PHE 0.008 0.001 PHE L 466 TRP 0.009 0.001 TRP c 103 HIS 0.005 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00496 (43328) covalent geometry : angle 0.60628 (58576) SS BOND : bond 0.00171 ( 16) SS BOND : angle 0.87226 ( 32) hydrogen bonds : bond 0.03722 ( 1921) hydrogen bonds : angle 4.10671 ( 5190) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 901 time to evaluate : 1.294 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: 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 386 LYS cc_start: 0.8483 (ptmt) cc_final: 0.7917 (ptpp) REVERT: A 450 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 486 ASN cc_start: 0.9117 (t0) cc_final: 0.8830 (t0) REVERT: a 4 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8773 (mm-40) REVERT: a 7 GLU cc_start: 0.7724 (mp0) cc_final: 0.7310 (mp0) REVERT: a 44 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8319 (mtmm) REVERT: a 73 ASP cc_start: 0.7962 (t0) cc_final: 0.7191 (t0) REVERT: a 76 LYS cc_start: 0.9005 (pmtt) cc_final: 0.8788 (pmtt) REVERT: a 77 ASN cc_start: 0.8909 (m-40) cc_final: 0.8395 (m-40) REVERT: a 86 LEU cc_start: 0.9176 (mt) cc_final: 0.8844 (mm) REVERT: a 87 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7635 (ttmm) REVERT: a 89 GLU cc_start: 0.8984 (pm20) cc_final: 0.8542 (pm20) REVERT: a 105 GLN cc_start: 0.7880 (pm20) cc_final: 0.7447 (pm20) REVERT: b 4 GLN cc_start: 0.8799 (mp10) cc_final: 0.8509 (mp10) REVERT: b 73 ASP cc_start: 0.8121 (t70) cc_final: 0.7606 (t0) REVERT: b 76 LYS cc_start: 0.9083 (pmmt) cc_final: 0.8766 (pmtt) REVERT: b 89 GLU cc_start: 0.8981 (pm20) cc_final: 0.8661 (pm20) REVERT: b 90 ASP cc_start: 0.8419 (m-30) cc_final: 0.8002 (m-30) REVERT: C 439 ASP cc_start: 0.8275 (p0) cc_final: 0.8045 (p0) REVERT: C 486 ASN cc_start: 0.9064 (t0) cc_final: 0.8487 (t0) REVERT: C 489 ASP cc_start: 0.8900 (m-30) cc_final: 0.8603 (m-30) REVERT: c 4 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: c 7 GLU cc_start: 0.7961 (mp0) cc_final: 0.7404 (mp0) REVERT: c 44 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8348 (mtmm) REVERT: c 76 LYS cc_start: 0.9070 (pmtt) cc_final: 0.8782 (pmtt) REVERT: c 77 ASN cc_start: 0.8886 (m-40) cc_final: 0.8464 (m-40) REVERT: c 86 LEU cc_start: 0.9161 (mt) cc_final: 0.8826 (mm) REVERT: c 87 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7619 (ttmm) REVERT: c 89 GLU cc_start: 0.8995 (pm20) cc_final: 0.8568 (pm20) REVERT: c 105 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: D 439 ASP cc_start: 0.8412 (p0) cc_final: 0.8194 (p0) REVERT: D 458 LYS cc_start: 0.9056 (mtpp) cc_final: 0.8773 (mmpt) REVERT: D 486 ASN cc_start: 0.9083 (t0) cc_final: 0.8651 (t0) REVERT: D 517 ARG cc_start: 0.9177 (ptm160) cc_final: 0.8938 (ptp-110) REVERT: d 4 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8249 (mp10) REVERT: d 7 GLU cc_start: 0.7624 (mp0) cc_final: 0.7227 (mp0) REVERT: d 73 ASP cc_start: 0.8077 (t70) cc_final: 0.7608 (t0) REVERT: d 86 LEU cc_start: 0.9189 (mt) cc_final: 0.8836 (mm) REVERT: d 87 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7325 (mttm) REVERT: d 89 GLU cc_start: 0.8925 (pm20) cc_final: 0.8687 (pm20) REVERT: d 90 ASP cc_start: 0.8335 (m-30) cc_final: 0.7995 (m-30) REVERT: d 105 GLN cc_start: 0.8407 (pm20) cc_final: 0.8146 (pm20) REVERT: E 450 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8257 (mt-10) REVERT: E 486 ASN cc_start: 0.9106 (t0) cc_final: 0.8813 (t0) REVERT: e 4 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8654 (mm-40) REVERT: e 7 GLU cc_start: 0.7785 (mp0) cc_final: 0.7150 (mp0) REVERT: e 14 GLN cc_start: 0.8678 (pm20) cc_final: 0.8182 (mp10) REVERT: e 44 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8290 (mppt) REVERT: e 76 LYS cc_start: 0.9153 (pmtt) cc_final: 0.8844 (pmtt) REVERT: e 77 ASN cc_start: 0.8892 (m-40) cc_final: 0.8476 (m-40) REVERT: e 105 GLN cc_start: 0.7959 (pm20) cc_final: 0.7413 (pm20) REVERT: F 403 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8441 (mmm-85) REVERT: F 486 ASN cc_start: 0.9091 (t0) cc_final: 0.8796 (t0) REVERT: F 517 ARG cc_start: 0.9101 (ptm160) cc_final: 0.8592 (ptp-110) REVERT: f 4 GLN cc_start: 0.8952 (mp10) cc_final: 0.8664 (mp10) REVERT: f 73 ASP cc_start: 0.8156 (t0) cc_final: 0.7267 (t0) REVERT: f 76 LYS cc_start: 0.9215 (pmmt) cc_final: 0.8724 (pmtt) REVERT: f 86 LEU cc_start: 0.9244 (mt) cc_final: 0.8876 (mm) REVERT: f 87 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7290 (mttm) REVERT: f 89 GLU cc_start: 0.8903 (pm20) cc_final: 0.8682 (pm20) REVERT: f 90 ASP cc_start: 0.8298 (m-30) cc_final: 0.7998 (m-30) REVERT: G 457 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8928 (mtm) REVERT: G 486 ASN cc_start: 0.9144 (t0) cc_final: 0.8863 (t0) REVERT: g 4 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8682 (mm-40) REVERT: g 7 GLU cc_start: 0.7867 (mp0) cc_final: 0.7082 (mp0) REVERT: g 14 GLN cc_start: 0.8725 (pm20) cc_final: 0.8313 (mp10) REVERT: g 73 ASP cc_start: 0.8036 (t70) cc_final: 0.7513 (t0) REVERT: g 77 ASN cc_start: 0.8971 (m-40) cc_final: 0.8390 (m110) REVERT: g 86 LEU cc_start: 0.9273 (mt) cc_final: 0.8978 (mm) REVERT: g 87 LYS cc_start: 0.7784 (mmtt) cc_final: 0.7532 (ttmm) REVERT: g 89 GLU cc_start: 0.8959 (pm20) cc_final: 0.8480 (pm20) REVERT: g 105 GLN cc_start: 0.7922 (pm20) cc_final: 0.7220 (pm20) REVERT: H 472 GLU cc_start: 0.8912 (tt0) cc_final: 0.8431 (tp30) REVERT: H 486 ASN cc_start: 0.9116 (t0) cc_final: 0.8800 (t0) REVERT: H 516 HIS cc_start: 0.8564 (p90) cc_final: 0.7892 (p90) REVERT: H 517 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8522 (ptp-170) REVERT: h 4 GLN cc_start: 0.8818 (mp10) cc_final: 0.8539 (mp10) REVERT: h 73 ASP cc_start: 0.8133 (t0) cc_final: 0.7573 (t0) REVERT: h 76 LYS cc_start: 0.9144 (pmmt) cc_final: 0.8874 (pmtt) REVERT: h 86 LEU cc_start: 0.9145 (mt) cc_final: 0.8856 (mm) REVERT: h 89 GLU cc_start: 0.8940 (pm20) cc_final: 0.8633 (pm20) REVERT: h 90 ASP cc_start: 0.8382 (m-30) cc_final: 0.8000 (m-30) REVERT: I 439 ASP cc_start: 0.8331 (p0) cc_final: 0.8069 (p0) REVERT: I 450 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8398 (mt-10) REVERT: I 483 ASP cc_start: 0.8272 (t0) cc_final: 0.8051 (t0) REVERT: I 486 ASN cc_start: 0.8802 (t0) cc_final: 0.8452 (t0) REVERT: I 516 HIS cc_start: 0.8613 (p-80) cc_final: 0.8329 (p90) REVERT: i 4 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8519 (mm-40) REVERT: i 44 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8251 (mppt) REVERT: i 73 ASP cc_start: 0.8135 (t0) cc_final: 0.7424 (t0) REVERT: i 76 LYS cc_start: 0.9219 (pmtt) cc_final: 0.8937 (pmmt) REVERT: i 86 LEU cc_start: 0.9288 (mt) cc_final: 0.8985 (mm) REVERT: i 87 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7274 (ttmm) REVERT: i 89 GLU cc_start: 0.8980 (pm20) cc_final: 0.8515 (pm20) REVERT: i 90 ASP cc_start: 0.8531 (m-30) cc_final: 0.8249 (m-30) REVERT: J 403 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8197 (mmm-85) REVERT: J 486 ASN cc_start: 0.9007 (t0) cc_final: 0.8478 (t0) REVERT: j 4 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8578 (mm-40) REVERT: j 7 GLU cc_start: 0.7868 (mp0) cc_final: 0.7665 (mp0) REVERT: j 44 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8547 (mtmm) REVERT: j 73 ASP cc_start: 0.8074 (t0) cc_final: 0.7285 (t0) REVERT: j 76 LYS cc_start: 0.9204 (pmtt) cc_final: 0.8843 (pmtt) REVERT: j 86 LEU cc_start: 0.9200 (mt) cc_final: 0.8906 (mm) REVERT: j 87 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7379 (ttmm) REVERT: j 89 GLU cc_start: 0.8910 (pm20) cc_final: 0.8228 (pm20) REVERT: j 90 ASP cc_start: 0.8316 (m-30) cc_final: 0.7910 (m-30) REVERT: j 105 GLN cc_start: 0.7946 (pm20) cc_final: 0.7468 (pm20) REVERT: K 450 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8331 (mt-10) REVERT: K 483 ASP cc_start: 0.8270 (t0) cc_final: 0.8003 (t0) REVERT: K 484 ARG cc_start: 0.8977 (tpp-160) cc_final: 0.8769 (tpp-160) REVERT: K 486 ASN cc_start: 0.9056 (t0) cc_final: 0.8623 (t0) REVERT: k 4 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8525 (mm-40) REVERT: k 7 GLU cc_start: 0.7855 (mp0) cc_final: 0.7637 (mp0) REVERT: k 14 GLN cc_start: 0.8691 (pm20) cc_final: 0.8193 (mp10) REVERT: k 73 ASP cc_start: 0.8364 (t0) cc_final: 0.7807 (t0) REVERT: k 86 LEU cc_start: 0.9319 (mt) cc_final: 0.9061 (mm) REVERT: k 87 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7407 (ttmm) REVERT: k 89 GLU cc_start: 0.8999 (pm20) cc_final: 0.8541 (pm20) REVERT: k 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.8050 (m-30) REVERT: k 105 GLN cc_start: 0.8005 (pm20) cc_final: 0.7582 (pm20) REVERT: L 472 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8619 (tp30) REVERT: L 486 ASN cc_start: 0.9031 (t0) cc_final: 0.8459 (t0) REVERT: L 543 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8112 (mtt-85) REVERT: l 4 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8598 (mm-40) REVERT: l 44 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8366 (mtmm) REVERT: l 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7700 (t0) REVERT: l 76 LYS cc_start: 0.9179 (pmmt) cc_final: 0.8897 (pmmt) REVERT: l 86 LEU cc_start: 0.9235 (mt) cc_final: 0.8875 (mm) REVERT: l 87 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7522 (ttmm) REVERT: l 89 GLU cc_start: 0.8878 (pm20) cc_final: 0.8311 (pm20) REVERT: l 90 ASP cc_start: 0.8333 (m-30) cc_final: 0.8020 (m-30) REVERT: M 450 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8314 (mt-10) REVERT: M 458 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8637 (mmpt) REVERT: M 486 ASN cc_start: 0.8938 (t0) cc_final: 0.8523 (t0) REVERT: M 516 HIS cc_start: 0.8596 (p90) cc_final: 0.8237 (p90) REVERT: m 4 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8492 (mm-40) REVERT: m 7 GLU cc_start: 0.7850 (mp0) cc_final: 0.7543 (mp0) REVERT: m 14 GLN cc_start: 0.8701 (pm20) cc_final: 0.8255 (mp10) REVERT: m 73 ASP cc_start: 0.8382 (t0) cc_final: 0.7828 (t0) REVERT: m 86 LEU cc_start: 0.9314 (mt) cc_final: 0.9058 (mm) REVERT: m 87 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7444 (ttmm) REVERT: m 89 GLU cc_start: 0.8999 (pm20) cc_final: 0.8583 (pm20) REVERT: m 90 ASP cc_start: 0.8340 (m-30) cc_final: 0.8002 (m-30) REVERT: m 105 GLN cc_start: 0.8170 (pm20) cc_final: 0.7864 (pm20) REVERT: N 486 ASN cc_start: 0.8997 (t0) cc_final: 0.8610 (t0) REVERT: n 4 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8640 (mm-40) REVERT: n 73 ASP cc_start: 0.8062 (t0) cc_final: 0.7278 (t0) REVERT: n 76 LYS cc_start: 0.9256 (pmtt) cc_final: 0.8949 (pmtt) REVERT: n 86 LEU cc_start: 0.9223 (mt) cc_final: 0.8856 (mm) REVERT: n 87 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7391 (ttmm) REVERT: n 89 GLU cc_start: 0.8942 (pm20) cc_final: 0.8487 (pm20) REVERT: n 90 ASP cc_start: 0.8401 (m-30) cc_final: 0.8022 (m-30) REVERT: O 439 ASP cc_start: 0.8353 (p0) cc_final: 0.8086 (p0) REVERT: O 450 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8259 (mt-10) REVERT: O 458 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8692 (mmpt) REVERT: O 486 ASN cc_start: 0.8747 (t0) cc_final: 0.8487 (t0) REVERT: O 516 HIS cc_start: 0.8645 (p-80) cc_final: 0.8364 (p90) REVERT: o 4 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8579 (mm-40) REVERT: o 7 GLU cc_start: 0.8111 (mp0) cc_final: 0.7808 (mp0) REVERT: o 14 GLN cc_start: 0.8773 (pm20) cc_final: 0.8288 (mp10) REVERT: o 73 ASP cc_start: 0.8323 (t0) cc_final: 0.7753 (t0) REVERT: o 86 LEU cc_start: 0.9268 (mt) cc_final: 0.9025 (mm) REVERT: o 87 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7613 (ttmm) REVERT: o 89 GLU cc_start: 0.9052 (pm20) cc_final: 0.8633 (pm20) REVERT: o 90 ASP cc_start: 0.8298 (m-30) cc_final: 0.7926 (m-30) REVERT: o 105 GLN cc_start: 0.8248 (mp10) cc_final: 0.7761 (pm20) REVERT: P 439 ASP cc_start: 0.8246 (p0) cc_final: 0.8044 (p0) REVERT: P 458 LYS cc_start: 0.9082 (mtmm) cc_final: 0.8777 (mmpt) REVERT: P 486 ASN cc_start: 0.9027 (t0) cc_final: 0.8506 (t0) REVERT: P 517 ARG cc_start: 0.9173 (ptt180) cc_final: 0.8764 (ptp-110) REVERT: p 4 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8568 (mm-40) REVERT: p 7 GLU cc_start: 0.8074 (mp0) cc_final: 0.7763 (mp0) REVERT: p 73 ASP cc_start: 0.8141 (t0) cc_final: 0.7488 (t0) REVERT: p 76 LYS cc_start: 0.9194 (pmmt) cc_final: 0.8839 (pmtt) REVERT: p 86 LEU cc_start: 0.9176 (mt) cc_final: 0.8842 (mm) REVERT: p 87 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7440 (ttmm) REVERT: p 89 GLU cc_start: 0.9041 (pm20) cc_final: 0.8633 (pm20) REVERT: p 90 ASP cc_start: 0.8407 (m-30) cc_final: 0.7981 (m-30) REVERT: p 105 GLN cc_start: 0.8175 (pm20) cc_final: 0.7754 (mp10) outliers start: 145 outliers final: 74 residues processed: 973 average time/residue: 0.7340 time to fit residues: 863.3800 Evaluate side-chains 941 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 861 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 502 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 502 THR Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain I residue 502 THR Chi-restraints excluded: chain I residue 544 GLU Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 505 LEU Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain L residue 481 THR Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 458 LYS Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 419 THR Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain O residue 502 THR Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 153 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 526 optimal weight: 3.9990 chunk 358 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 502 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 304 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 GLN ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.146590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.091994 restraints weight = 65032.563| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.60 r_work: 0.3159 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43344 Z= 0.130 Angle : 0.587 9.548 58608 Z= 0.295 Chirality : 0.040 0.154 6608 Planarity : 0.004 0.040 7536 Dihedral : 4.637 23.790 6016 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.36 % Allowed : 19.46 % Favored : 78.18 % 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 aren not related in a simple way. whole: -0.33 (0.12), residues: 5360 helix: 0.73 (0.11), residues: 2336 sheet: -0.97 (0.17), residues: 960 loop : -0.80 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 403 TYR 0.010 0.001 TYR m 80 PHE 0.008 0.001 PHE p 68 TRP 0.010 0.001 TRP a 103 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00310 (43328) covalent geometry : angle 0.58669 (58576) SS BOND : bond 0.00103 ( 16) SS BOND : angle 0.68894 ( 32) hydrogen bonds : bond 0.03282 ( 1921) hydrogen bonds : angle 3.96453 ( 5190) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 920 time to evaluate : 1.686 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8441 (ptmt) cc_final: 0.7875 (ptpp) REVERT: A 450 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 486 ASN cc_start: 0.9071 (t0) cc_final: 0.8827 (t0) REVERT: a 4 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8752 (mm-40) REVERT: a 7 GLU cc_start: 0.7681 (mp0) cc_final: 0.7309 (mp0) REVERT: a 44 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8320 (mtmm) REVERT: a 73 ASP cc_start: 0.7952 (t0) cc_final: 0.7145 (t0) REVERT: a 76 LYS cc_start: 0.9095 (pmtt) cc_final: 0.8761 (pmtt) REVERT: a 77 ASN cc_start: 0.8844 (m-40) cc_final: 0.8425 (m-40) REVERT: a 86 LEU cc_start: 0.9191 (mt) cc_final: 0.8873 (mm) REVERT: a 87 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7393 (ttmm) REVERT: a 89 GLU cc_start: 0.8960 (pm20) cc_final: 0.8495 (pm20) REVERT: a 105 GLN cc_start: 0.7839 (pm20) cc_final: 0.7379 (pm20) REVERT: B 472 GLU cc_start: 0.8931 (tt0) cc_final: 0.8334 (tp30) REVERT: B 489 ASP cc_start: 0.8889 (m-30) cc_final: 0.8652 (m-30) REVERT: b 4 GLN cc_start: 0.8882 (mp10) cc_final: 0.8515 (mp10) REVERT: b 73 ASP cc_start: 0.8142 (t70) cc_final: 0.7667 (t0) REVERT: b 76 LYS cc_start: 0.9121 (pmmt) cc_final: 0.8895 (pmtt) REVERT: b 87 LYS cc_start: 0.7649 (mmtt) cc_final: 0.6857 (mppt) REVERT: b 89 GLU cc_start: 0.8979 (pm20) cc_final: 0.8637 (pm20) REVERT: b 90 ASP cc_start: 0.8284 (m-30) cc_final: 0.7796 (m-30) REVERT: C 439 ASP cc_start: 0.8189 (p0) cc_final: 0.7954 (p0) REVERT: C 486 ASN cc_start: 0.9058 (t0) cc_final: 0.8461 (t0) REVERT: C 489 ASP cc_start: 0.8869 (m-30) cc_final: 0.8566 (m-30) REVERT: c 4 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8663 (mp10) REVERT: c 7 GLU cc_start: 0.7868 (mp0) cc_final: 0.7126 (mp0) REVERT: c 44 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8325 (mtmm) REVERT: c 77 ASN cc_start: 0.8904 (m-40) cc_final: 0.8421 (m-40) REVERT: c 86 LEU cc_start: 0.9192 (mt) cc_final: 0.8866 (mm) REVERT: c 87 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7377 (ttmm) REVERT: c 89 GLU cc_start: 0.8954 (pm20) cc_final: 0.8528 (pm20) REVERT: c 105 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: D 439 ASP cc_start: 0.8365 (p0) cc_final: 0.8161 (p0) REVERT: D 458 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8824 (mmpt) REVERT: D 472 GLU cc_start: 0.8924 (tt0) cc_final: 0.8403 (tp30) REVERT: D 486 ASN cc_start: 0.9039 (t0) cc_final: 0.8720 (t0) REVERT: D 517 ARG cc_start: 0.9184 (ptm160) cc_final: 0.8977 (ptp-110) REVERT: D 543 ARG cc_start: 0.8730 (ttm170) cc_final: 0.8119 (mtt-85) REVERT: d 4 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8275 (mp10) REVERT: d 7 GLU cc_start: 0.7594 (mp0) cc_final: 0.7333 (mp0) REVERT: d 73 ASP cc_start: 0.8068 (t70) cc_final: 0.7561 (t0) REVERT: d 86 LEU cc_start: 0.9185 (mt) cc_final: 0.8806 (mm) REVERT: d 87 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7193 (mttm) REVERT: d 89 GLU cc_start: 0.8916 (pm20) cc_final: 0.8610 (pm20) REVERT: d 90 ASP cc_start: 0.8220 (m-30) cc_final: 0.7879 (m-30) REVERT: d 105 GLN cc_start: 0.8330 (pm20) cc_final: 0.8109 (pm20) REVERT: E 450 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 486 ASN cc_start: 0.9089 (t0) cc_final: 0.8815 (t0) REVERT: E 544 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8365 (pp20) REVERT: e 4 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8813 (mm-40) REVERT: e 7 GLU cc_start: 0.7744 (mp0) cc_final: 0.6947 (mp0) REVERT: e 14 GLN cc_start: 0.8705 (pm20) cc_final: 0.8226 (mp10) REVERT: e 44 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8296 (mppt) REVERT: e 77 ASN cc_start: 0.8910 (m-40) cc_final: 0.8435 (m-40) REVERT: e 87 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7528 (ttmm) REVERT: e 89 GLU cc_start: 0.9029 (pm20) cc_final: 0.8681 (pm20) REVERT: e 105 GLN cc_start: 0.7962 (pm20) cc_final: 0.7284 (pm20) REVERT: F 403 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8431 (mmm-85) REVERT: F 517 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8909 (ptp-110) REVERT: F 543 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8219 (mtt-85) REVERT: f 4 GLN cc_start: 0.8966 (mp10) cc_final: 0.8666 (mp10) REVERT: f 73 ASP cc_start: 0.8122 (t0) cc_final: 0.7553 (t0) REVERT: f 76 LYS cc_start: 0.9150 (pmmt) cc_final: 0.8853 (pmtt) REVERT: f 86 LEU cc_start: 0.9233 (mt) cc_final: 0.8858 (mm) REVERT: f 87 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7164 (mttm) REVERT: f 89 GLU cc_start: 0.8915 (pm20) cc_final: 0.8625 (pm20) REVERT: f 90 ASP cc_start: 0.8193 (m-30) cc_final: 0.7823 (m-30) REVERT: G 439 ASP cc_start: 0.8251 (p0) cc_final: 0.8012 (p0) REVERT: G 457 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8906 (mtm) REVERT: G 486 ASN cc_start: 0.9120 (t0) cc_final: 0.8875 (t0) REVERT: g 4 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8878 (mm-40) REVERT: g 7 GLU cc_start: 0.7851 (mp0) cc_final: 0.7062 (mp0) REVERT: g 14 GLN cc_start: 0.8749 (pm20) cc_final: 0.8349 (mp10) REVERT: g 73 ASP cc_start: 0.8001 (t70) cc_final: 0.7442 (t0) REVERT: g 76 LYS cc_start: 0.9225 (pmtt) cc_final: 0.8974 (pmtt) REVERT: g 77 ASN cc_start: 0.8923 (m-40) cc_final: 0.8382 (m110) REVERT: g 86 LEU cc_start: 0.9297 (mt) cc_final: 0.8995 (mm) REVERT: g 87 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7432 (ttmm) REVERT: g 89 GLU cc_start: 0.8968 (pm20) cc_final: 0.8565 (pm20) REVERT: g 105 GLN cc_start: 0.7942 (pm20) cc_final: 0.7252 (pm20) REVERT: H 472 GLU cc_start: 0.8915 (tt0) cc_final: 0.8428 (tp30) REVERT: H 486 ASN cc_start: 0.9060 (t0) cc_final: 0.8810 (t0) REVERT: H 517 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8432 (ptp-110) REVERT: h 4 GLN cc_start: 0.8891 (mp10) cc_final: 0.8585 (mp10) REVERT: h 73 ASP cc_start: 0.8149 (t0) cc_final: 0.7600 (t0) REVERT: h 76 LYS cc_start: 0.9145 (pmmt) cc_final: 0.8874 (pmtt) REVERT: h 86 LEU cc_start: 0.9144 (mt) cc_final: 0.8856 (mm) REVERT: h 89 GLU cc_start: 0.8931 (pm20) cc_final: 0.8597 (pm20) REVERT: h 90 ASP cc_start: 0.8242 (m-30) cc_final: 0.7852 (m-30) REVERT: I 439 ASP cc_start: 0.8254 (p0) cc_final: 0.8008 (p0) REVERT: I 450 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8359 (mt-10) REVERT: I 483 ASP cc_start: 0.8244 (t0) cc_final: 0.8011 (t0) REVERT: I 486 ASN cc_start: 0.8795 (t0) cc_final: 0.8402 (t0) REVERT: I 516 HIS cc_start: 0.8627 (p-80) cc_final: 0.8308 (p90) REVERT: i 4 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8569 (mm-40) REVERT: i 7 GLU cc_start: 0.7601 (mp0) cc_final: 0.7395 (mp0) REVERT: i 44 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8268 (mppt) REVERT: i 73 ASP cc_start: 0.8028 (t0) cc_final: 0.7281 (t0) REVERT: i 76 LYS cc_start: 0.9233 (pmtt) cc_final: 0.8905 (pmtt) REVERT: i 86 LEU cc_start: 0.9287 (mt) cc_final: 0.8982 (mm) REVERT: i 87 LYS cc_start: 0.7672 (mmtt) cc_final: 0.7247 (ttmm) REVERT: i 89 GLU cc_start: 0.9040 (pm20) cc_final: 0.8632 (pm20) REVERT: i 90 ASP cc_start: 0.8303 (m-30) cc_final: 0.8008 (m-30) REVERT: J 403 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8253 (mmm-85) REVERT: J 439 ASP cc_start: 0.8226 (p0) cc_final: 0.8002 (p0) REVERT: J 486 ASN cc_start: 0.8990 (t0) cc_final: 0.8559 (t0) REVERT: J 517 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8603 (ptp-110) REVERT: j 4 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8591 (mm-40) REVERT: j 7 GLU cc_start: 0.7852 (mp0) cc_final: 0.7602 (mp0) REVERT: j 44 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8556 (mtmm) REVERT: j 73 ASP cc_start: 0.8005 (t0) cc_final: 0.7249 (t0) REVERT: j 76 LYS cc_start: 0.9233 (pmtt) cc_final: 0.8924 (pmtt) REVERT: j 86 LEU cc_start: 0.9207 (mt) cc_final: 0.8913 (mm) REVERT: j 87 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7206 (ttmm) REVERT: j 89 GLU cc_start: 0.8932 (pm20) cc_final: 0.8272 (pm20) REVERT: j 90 ASP cc_start: 0.8293 (m-30) cc_final: 0.7797 (m-30) REVERT: j 105 GLN cc_start: 0.7927 (pm20) cc_final: 0.7429 (pm20) REVERT: K 450 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8368 (mt-10) REVERT: K 483 ASP cc_start: 0.8286 (t0) cc_final: 0.8042 (t0) REVERT: K 486 ASN cc_start: 0.9060 (t0) cc_final: 0.8617 (t0) REVERT: k 4 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8502 (mm-40) REVERT: k 7 GLU cc_start: 0.7834 (mp0) cc_final: 0.7608 (mp0) REVERT: k 14 GLN cc_start: 0.8693 (pm20) cc_final: 0.8188 (mp10) REVERT: k 73 ASP cc_start: 0.8396 (t0) cc_final: 0.7823 (t0) REVERT: k 86 LEU cc_start: 0.9325 (mt) cc_final: 0.9092 (mm) REVERT: k 87 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7060 (ttmm) REVERT: k 89 GLU cc_start: 0.9021 (pm20) cc_final: 0.8698 (pm20) REVERT: k 90 ASP cc_start: 0.8268 (m-30) cc_final: 0.7633 (m-30) REVERT: k 105 GLN cc_start: 0.7962 (pm20) cc_final: 0.7517 (pm20) REVERT: L 450 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8444 (mt-10) REVERT: L 472 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8616 (tp30) REVERT: L 486 ASN cc_start: 0.9002 (t0) cc_final: 0.8494 (t0) REVERT: L 543 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8111 (mtt-85) REVERT: l 4 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8651 (mm-40) REVERT: l 44 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8372 (mtmm) REVERT: l 73 ASP cc_start: 0.8291 (t0) cc_final: 0.7675 (t0) REVERT: l 76 LYS cc_start: 0.9210 (pmmt) cc_final: 0.8932 (pmmt) REVERT: l 86 LEU cc_start: 0.9230 (mt) cc_final: 0.8874 (mm) REVERT: l 87 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7337 (ttmm) REVERT: l 89 GLU cc_start: 0.8861 (pm20) cc_final: 0.8232 (pm20) REVERT: l 90 ASP cc_start: 0.8286 (m-30) cc_final: 0.7932 (m-30) REVERT: M 450 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8310 (mt-10) REVERT: M 458 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8646 (mmpt) REVERT: M 486 ASN cc_start: 0.8943 (t0) cc_final: 0.8522 (t0) REVERT: M 516 HIS cc_start: 0.8590 (p90) cc_final: 0.8304 (p90) REVERT: m 4 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8569 (mm-40) REVERT: m 7 GLU cc_start: 0.7783 (mp0) cc_final: 0.7472 (mp0) REVERT: m 14 GLN cc_start: 0.8698 (pm20) cc_final: 0.8258 (mp10) REVERT: m 73 ASP cc_start: 0.8432 (t0) cc_final: 0.7809 (t0) REVERT: m 86 LEU cc_start: 0.9313 (mt) cc_final: 0.9080 (mm) REVERT: m 87 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7095 (ttmm) REVERT: m 89 GLU cc_start: 0.9010 (pm20) cc_final: 0.8685 (pm20) REVERT: m 90 ASP cc_start: 0.8237 (m-30) cc_final: 0.7606 (m-30) REVERT: m 105 GLN cc_start: 0.8103 (pm20) cc_final: 0.7743 (pm20) REVERT: N 486 ASN cc_start: 0.8975 (t0) cc_final: 0.8487 (t0) REVERT: N 517 ARG cc_start: 0.9021 (pmm-80) cc_final: 0.8738 (pmm-80) REVERT: N 545 MET cc_start: 0.7570 (ttp) cc_final: 0.7143 (ttp) REVERT: n 4 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8639 (mm-40) REVERT: n 73 ASP cc_start: 0.8071 (t0) cc_final: 0.7273 (t0) REVERT: n 76 LYS cc_start: 0.9246 (pmtt) cc_final: 0.8935 (pmtt) REVERT: n 86 LEU cc_start: 0.9227 (mt) cc_final: 0.8873 (mm) REVERT: n 87 LYS cc_start: 0.7705 (mmtt) cc_final: 0.7373 (ttmm) REVERT: n 89 GLU cc_start: 0.8912 (pm20) cc_final: 0.8434 (pm20) REVERT: n 90 ASP cc_start: 0.8316 (m-30) cc_final: 0.7984 (m-30) REVERT: n 105 GLN cc_start: 0.8037 (pm20) cc_final: 0.7688 (pm20) REVERT: O 439 ASP cc_start: 0.8273 (p0) cc_final: 0.8018 (p0) REVERT: O 450 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8313 (mt-10) REVERT: O 458 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8692 (mmpt) REVERT: O 484 ARG cc_start: 0.8800 (tpp-160) cc_final: 0.8567 (tpp-160) REVERT: O 486 ASN cc_start: 0.8746 (t0) cc_final: 0.8510 (t0) REVERT: O 516 HIS cc_start: 0.8654 (p-80) cc_final: 0.8302 (p90) REVERT: o 4 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8589 (mm-40) REVERT: o 7 GLU cc_start: 0.8041 (mp0) cc_final: 0.7748 (mp0) REVERT: o 14 GLN cc_start: 0.8764 (pm20) cc_final: 0.8333 (mp10) REVERT: o 73 ASP cc_start: 0.8416 (t0) cc_final: 0.7828 (t0) REVERT: o 86 LEU cc_start: 0.9301 (mt) cc_final: 0.9054 (mm) REVERT: o 87 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7297 (ttmm) REVERT: o 89 GLU cc_start: 0.9098 (pm20) cc_final: 0.8722 (pm20) REVERT: o 90 ASP cc_start: 0.8265 (m-30) cc_final: 0.7952 (m-30) REVERT: o 102 THR cc_start: 0.8733 (p) cc_final: 0.8486 (t) REVERT: o 105 GLN cc_start: 0.8266 (mp10) cc_final: 0.7679 (pm20) REVERT: P 439 ASP cc_start: 0.8173 (p0) cc_final: 0.7960 (p0) REVERT: P 458 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8768 (mmpt) REVERT: P 486 ASN cc_start: 0.8990 (t0) cc_final: 0.8530 (t0) REVERT: P 517 ARG cc_start: 0.9164 (ptt180) cc_final: 0.8750 (ptp-110) REVERT: p 4 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8586 (mm-40) REVERT: p 7 GLU cc_start: 0.8124 (mp0) cc_final: 0.7876 (mp0) REVERT: p 73 ASP cc_start: 0.8152 (t0) cc_final: 0.7471 (t0) REVERT: p 76 LYS cc_start: 0.9193 (pmmt) cc_final: 0.8843 (pmtt) REVERT: p 86 LEU cc_start: 0.9207 (mt) cc_final: 0.8857 (mm) REVERT: p 87 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7425 (ttmm) REVERT: p 89 GLU cc_start: 0.9012 (pm20) cc_final: 0.8554 (pm20) REVERT: p 90 ASP cc_start: 0.8285 (m-30) cc_final: 0.7885 (m-30) outliers start: 110 outliers final: 67 residues processed: 974 average time/residue: 0.7799 time to fit residues: 917.5659 Evaluate side-chains 962 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 889 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain e residue 21 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 378 VAL Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain O residue 544 GLU Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 6.9990 chunk 512 optimal weight: 2.9990 chunk 304 optimal weight: 0.0770 chunk 212 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 445 optimal weight: 5.9990 chunk 510 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 473 optimal weight: 6.9990 chunk 272 optimal weight: 0.0170 chunk 237 optimal weight: 6.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.147144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092144 restraints weight = 64094.467| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.70 r_work: 0.3146 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43344 Z= 0.144 Angle : 0.589 10.173 58608 Z= 0.295 Chirality : 0.040 0.152 6608 Planarity : 0.004 0.040 7536 Dihedral : 4.601 22.516 6016 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.51 % Allowed : 19.89 % Favored : 77.60 % 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 aren not related in a simple way. whole: -0.23 (0.12), residues: 5360 helix: 0.81 (0.11), residues: 2336 sheet: -0.92 (0.17), residues: 960 loop : -0.75 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 403 TYR 0.015 0.001 TYR c 80 PHE 0.008 0.001 PHE j 68 TRP 0.009 0.001 TRP c 103 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00346 (43328) covalent geometry : angle 0.58909 (58576) SS BOND : bond 0.00106 ( 16) SS BOND : angle 0.66971 ( 32) hydrogen bonds : bond 0.03332 ( 1921) hydrogen bonds : angle 3.93442 ( 5190) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 913 time to evaluate : 1.758 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8398 (ptmt) cc_final: 0.7837 (ptpp) REVERT: A 450 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 486 ASN cc_start: 0.9065 (t0) cc_final: 0.8818 (t0) REVERT: a 4 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8534 (mm-40) REVERT: a 7 GLU cc_start: 0.7646 (mp0) cc_final: 0.7235 (mp0) REVERT: a 44 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8295 (mtmm) REVERT: a 73 ASP cc_start: 0.7852 (t0) cc_final: 0.7028 (t0) REVERT: a 76 LYS cc_start: 0.9024 (pmtt) cc_final: 0.8760 (pmtt) REVERT: a 77 ASN cc_start: 0.8893 (m-40) cc_final: 0.8428 (m-40) REVERT: a 86 LEU cc_start: 0.9202 (mt) cc_final: 0.8892 (mm) REVERT: a 87 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7132 (ttmm) REVERT: a 89 GLU cc_start: 0.8949 (pm20) cc_final: 0.8549 (pm20) REVERT: a 90 ASP cc_start: 0.8196 (m-30) cc_final: 0.7875 (m-30) REVERT: a 105 GLN cc_start: 0.7826 (pm20) cc_final: 0.7353 (pm20) REVERT: B 472 GLU cc_start: 0.8924 (tt0) cc_final: 0.8294 (tp30) REVERT: B 489 ASP cc_start: 0.8892 (m-30) cc_final: 0.8656 (m-30) REVERT: b 73 ASP cc_start: 0.8121 (t70) cc_final: 0.7632 (t0) REVERT: b 76 LYS cc_start: 0.9114 (pmmt) cc_final: 0.8882 (pmtt) REVERT: b 89 GLU cc_start: 0.8976 (pm20) cc_final: 0.8651 (pm20) REVERT: b 90 ASP cc_start: 0.8293 (m-30) cc_final: 0.7940 (m-30) REVERT: C 439 ASP cc_start: 0.8251 (p0) cc_final: 0.8011 (p0) REVERT: C 450 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 486 ASN cc_start: 0.9050 (t0) cc_final: 0.8441 (t0) REVERT: C 489 ASP cc_start: 0.8868 (m-30) cc_final: 0.8555 (m-30) REVERT: C 543 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8255 (mtt-85) REVERT: c 4 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: c 7 GLU cc_start: 0.7815 (mp0) cc_final: 0.7068 (mp0) REVERT: c 44 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8301 (mtmm) REVERT: c 76 LYS cc_start: 0.9177 (pmtt) cc_final: 0.8920 (pmtt) REVERT: c 77 ASN cc_start: 0.8843 (m-40) cc_final: 0.8455 (m-40) REVERT: c 86 LEU cc_start: 0.9201 (mt) cc_final: 0.8888 (mm) REVERT: c 87 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7121 (ttmm) REVERT: c 89 GLU cc_start: 0.8945 (pm20) cc_final: 0.8569 (pm20) REVERT: c 90 ASP cc_start: 0.8189 (m-30) cc_final: 0.7844 (m-30) REVERT: c 105 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: D 458 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8824 (mmpt) REVERT: D 472 GLU cc_start: 0.8925 (tt0) cc_final: 0.8412 (tp30) REVERT: D 486 ASN cc_start: 0.9041 (t0) cc_final: 0.8734 (t0) REVERT: D 517 ARG cc_start: 0.9187 (ptm160) cc_final: 0.8978 (ptp-110) REVERT: D 543 ARG cc_start: 0.8721 (ttm170) cc_final: 0.8141 (mtt-85) REVERT: D 544 GLU cc_start: 0.8221 (pp20) cc_final: 0.8011 (OUTLIER) REVERT: d 4 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8251 (mp10) REVERT: d 73 ASP cc_start: 0.8035 (t70) cc_final: 0.7535 (t0) REVERT: d 86 LEU cc_start: 0.9168 (mt) cc_final: 0.8822 (mm) REVERT: d 87 LYS cc_start: 0.7616 (mmtt) cc_final: 0.6957 (ttmm) REVERT: d 89 GLU cc_start: 0.8948 (pm20) cc_final: 0.8440 (pm20) REVERT: d 90 ASP cc_start: 0.8223 (m-30) cc_final: 0.7661 (m-30) REVERT: E 450 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8216 (mt-10) REVERT: E 486 ASN cc_start: 0.9085 (t0) cc_final: 0.8816 (t0) REVERT: E 544 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8430 (pp20) REVERT: e 4 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8831 (mm-40) REVERT: e 7 GLU cc_start: 0.7721 (mp0) cc_final: 0.6904 (mp0) REVERT: e 14 GLN cc_start: 0.8727 (pm20) cc_final: 0.8272 (mp10) REVERT: e 44 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8336 (mppt) REVERT: e 76 LYS cc_start: 0.9242 (pmtt) cc_final: 0.8938 (pmtt) REVERT: e 77 ASN cc_start: 0.8846 (m-40) cc_final: 0.8470 (m-40) REVERT: e 87 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7430 (ttmm) REVERT: e 89 GLU cc_start: 0.9017 (pm20) cc_final: 0.8650 (pm20) REVERT: e 105 GLN cc_start: 0.7920 (pm20) cc_final: 0.7208 (pm20) REVERT: F 403 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8452 (mmm-85) REVERT: F 489 ASP cc_start: 0.8862 (m-30) cc_final: 0.8533 (p0) REVERT: F 517 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8870 (ptp-110) REVERT: f 4 GLN cc_start: 0.8957 (mp10) cc_final: 0.8653 (mp10) REVERT: f 73 ASP cc_start: 0.8130 (t0) cc_final: 0.7577 (t0) REVERT: f 76 LYS cc_start: 0.9148 (pmmt) cc_final: 0.8844 (pmmt) REVERT: f 86 LEU cc_start: 0.9222 (mt) cc_final: 0.8860 (mm) REVERT: f 87 LYS cc_start: 0.7578 (mmtt) cc_final: 0.7117 (mttm) REVERT: f 89 GLU cc_start: 0.8938 (pm20) cc_final: 0.8635 (pm20) REVERT: f 90 ASP cc_start: 0.8218 (m-30) cc_final: 0.7864 (m-30) REVERT: G 439 ASP cc_start: 0.8249 (p0) cc_final: 0.8001 (p0) REVERT: G 457 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8888 (mtm) REVERT: G 486 ASN cc_start: 0.9113 (t0) cc_final: 0.8862 (t0) REVERT: G 543 ARG cc_start: 0.8741 (ttm170) cc_final: 0.8291 (mtt-85) REVERT: g 4 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8670 (mm-40) REVERT: g 7 GLU cc_start: 0.7890 (mp0) cc_final: 0.7252 (mp0) REVERT: g 14 GLN cc_start: 0.8756 (pm20) cc_final: 0.8365 (mp10) REVERT: g 73 ASP cc_start: 0.7971 (t70) cc_final: 0.7366 (t0) REVERT: g 76 LYS cc_start: 0.9216 (pmtt) cc_final: 0.8900 (pmtt) REVERT: g 77 ASN cc_start: 0.8908 (m-40) cc_final: 0.8368 (m110) REVERT: g 86 LEU cc_start: 0.9287 (mt) cc_final: 0.8993 (mm) REVERT: g 87 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7190 (ttmm) REVERT: g 89 GLU cc_start: 0.8957 (pm20) cc_final: 0.8524 (pm20) REVERT: g 90 ASP cc_start: 0.8126 (m-30) cc_final: 0.7863 (m-30) REVERT: g 105 GLN cc_start: 0.7942 (pm20) cc_final: 0.7234 (pm20) REVERT: H 472 GLU cc_start: 0.8916 (tt0) cc_final: 0.8427 (tp30) REVERT: H 486 ASN cc_start: 0.9052 (t0) cc_final: 0.8783 (t0) REVERT: H 517 ARG cc_start: 0.9124 (ptm160) cc_final: 0.8551 (ptp-110) REVERT: h 4 GLN cc_start: 0.8893 (mp10) cc_final: 0.8574 (mp10) REVERT: h 73 ASP cc_start: 0.8159 (t0) cc_final: 0.7587 (t0) REVERT: h 76 LYS cc_start: 0.9144 (pmmt) cc_final: 0.8844 (pmtt) REVERT: h 86 LEU cc_start: 0.9135 (mt) cc_final: 0.8851 (mm) REVERT: h 89 GLU cc_start: 0.8971 (pm20) cc_final: 0.8651 (pm20) REVERT: h 90 ASP cc_start: 0.8268 (m-30) cc_final: 0.7911 (m-30) REVERT: I 439 ASP cc_start: 0.8243 (p0) cc_final: 0.8004 (p0) REVERT: I 450 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8369 (mt-10) REVERT: I 483 ASP cc_start: 0.8216 (t0) cc_final: 0.8013 (t0) REVERT: I 486 ASN cc_start: 0.8770 (t0) cc_final: 0.8378 (t0) REVERT: I 516 HIS cc_start: 0.8641 (p-80) cc_final: 0.8320 (p90) REVERT: i 4 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8575 (mm-40) REVERT: i 44 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8256 (mppt) REVERT: i 86 LEU cc_start: 0.9275 (mt) cc_final: 0.9059 (mm) REVERT: i 87 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7219 (ttmm) REVERT: i 89 GLU cc_start: 0.9014 (pm20) cc_final: 0.8559 (pm20) REVERT: i 90 ASP cc_start: 0.8281 (m-30) cc_final: 0.7965 (m-30) REVERT: J 439 ASP cc_start: 0.8206 (p0) cc_final: 0.8000 (p0) REVERT: J 486 ASN cc_start: 0.8984 (t0) cc_final: 0.8551 (t0) REVERT: J 516 HIS cc_start: 0.8735 (p-80) cc_final: 0.8413 (p90) REVERT: J 517 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8708 (ptp-170) REVERT: j 4 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8580 (mm-40) REVERT: j 7 GLU cc_start: 0.7813 (mp0) cc_final: 0.7560 (mp0) REVERT: j 44 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8551 (mtmm) REVERT: j 73 ASP cc_start: 0.8040 (t0) cc_final: 0.7289 (t0) REVERT: j 76 LYS cc_start: 0.9219 (pmtt) cc_final: 0.8947 (pmtt) REVERT: j 86 LEU cc_start: 0.9180 (mt) cc_final: 0.8887 (mm) REVERT: j 87 LYS cc_start: 0.7698 (mmtt) cc_final: 0.7217 (ttmm) REVERT: j 89 GLU cc_start: 0.8924 (pm20) cc_final: 0.8262 (pm20) REVERT: j 90 ASP cc_start: 0.8281 (m-30) cc_final: 0.7801 (m-30) REVERT: j 105 GLN cc_start: 0.7894 (pm20) cc_final: 0.7392 (pm20) REVERT: K 450 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8327 (mt-10) REVERT: K 483 ASP cc_start: 0.8261 (t0) cc_final: 0.8041 (t0) REVERT: K 484 ARG cc_start: 0.9036 (tpp-160) cc_final: 0.8819 (tpp-160) REVERT: K 486 ASN cc_start: 0.9048 (t0) cc_final: 0.8591 (t0) REVERT: k 4 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8520 (mm-40) REVERT: k 7 GLU cc_start: 0.7805 (mp0) cc_final: 0.7571 (mp0) REVERT: k 14 GLN cc_start: 0.8678 (pm20) cc_final: 0.8185 (mp10) REVERT: k 73 ASP cc_start: 0.8400 (t0) cc_final: 0.7875 (OUTLIER) REVERT: k 86 LEU cc_start: 0.9318 (mt) cc_final: 0.9056 (mm) REVERT: k 87 LYS cc_start: 0.7644 (mmtt) cc_final: 0.6987 (ttmm) REVERT: k 89 GLU cc_start: 0.9016 (pm20) cc_final: 0.8695 (pm20) REVERT: k 90 ASP cc_start: 0.8253 (m-30) cc_final: 0.7507 (m-30) REVERT: k 105 GLN cc_start: 0.7932 (pm20) cc_final: 0.7471 (pm20) REVERT: L 450 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8422 (mt-10) REVERT: L 457 MET cc_start: 0.9143 (mtm) cc_final: 0.8914 (mtp) REVERT: L 472 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: L 486 ASN cc_start: 0.8990 (t0) cc_final: 0.8479 (t0) REVERT: L 517 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8708 (ptp-110) REVERT: L 543 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8183 (mtt-85) REVERT: l 4 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8646 (mm-40) REVERT: l 44 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8434 (mtmm) REVERT: l 73 ASP cc_start: 0.8287 (t0) cc_final: 0.7683 (t0) REVERT: l 76 LYS cc_start: 0.9202 (pmmt) cc_final: 0.8919 (pmmt) REVERT: l 86 LEU cc_start: 0.9225 (mt) cc_final: 0.8874 (mm) REVERT: l 87 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7262 (ttmm) REVERT: l 89 GLU cc_start: 0.8847 (pm20) cc_final: 0.8174 (pm20) REVERT: l 90 ASP cc_start: 0.8242 (m-30) cc_final: 0.7834 (m-30) REVERT: M 450 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8337 (mt-10) REVERT: M 458 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8647 (mmpt) REVERT: M 486 ASN cc_start: 0.8932 (t0) cc_final: 0.8518 (t0) REVERT: M 516 HIS cc_start: 0.8596 (p90) cc_final: 0.8318 (p90) REVERT: m 4 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8583 (mm-40) REVERT: m 7 GLU cc_start: 0.7779 (mp0) cc_final: 0.7466 (mp0) REVERT: m 14 GLN cc_start: 0.8708 (pm20) cc_final: 0.8285 (mp10) REVERT: m 73 ASP cc_start: 0.8397 (t0) cc_final: 0.7874 (OUTLIER) REVERT: m 86 LEU cc_start: 0.9314 (mt) cc_final: 0.9081 (mm) REVERT: m 87 LYS cc_start: 0.7665 (mmtt) cc_final: 0.6995 (ttmm) REVERT: m 89 GLU cc_start: 0.9015 (pm20) cc_final: 0.8705 (pm20) REVERT: m 90 ASP cc_start: 0.8236 (m-30) cc_final: 0.7493 (m-30) REVERT: m 105 GLN cc_start: 0.8085 (pm20) cc_final: 0.7759 (pm20) REVERT: N 486 ASN cc_start: 0.8974 (t0) cc_final: 0.8483 (t0) REVERT: N 517 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8688 (ptp-110) REVERT: N 545 MET cc_start: 0.7638 (ttp) cc_final: 0.7205 (ttp) REVERT: n 4 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8642 (mm-40) REVERT: n 73 ASP cc_start: 0.8042 (t0) cc_final: 0.7247 (t0) REVERT: n 76 LYS cc_start: 0.9235 (pmtt) cc_final: 0.8917 (pmtt) REVERT: n 86 LEU cc_start: 0.9200 (mt) cc_final: 0.8841 (mm) REVERT: n 87 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7354 (ttmm) REVERT: n 89 GLU cc_start: 0.8899 (pm20) cc_final: 0.8376 (pm20) REVERT: n 90 ASP cc_start: 0.8304 (m-30) cc_final: 0.7935 (m-30) REVERT: O 439 ASP cc_start: 0.8274 (p0) cc_final: 0.8023 (p0) REVERT: O 450 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8326 (mt-10) REVERT: O 458 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8688 (mmpt) REVERT: O 484 ARG cc_start: 0.8816 (tpp-160) cc_final: 0.8578 (tpp-160) REVERT: O 486 ASN cc_start: 0.8726 (t0) cc_final: 0.8487 (t0) REVERT: O 516 HIS cc_start: 0.8647 (p-80) cc_final: 0.8372 (p90) REVERT: o 4 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8605 (mm-40) REVERT: o 7 GLU cc_start: 0.8060 (mp0) cc_final: 0.7792 (mp0) REVERT: o 14 GLN cc_start: 0.8742 (pm20) cc_final: 0.8303 (mp10) REVERT: o 73 ASP cc_start: 0.8434 (t0) cc_final: 0.7885 (OUTLIER) REVERT: o 86 LEU cc_start: 0.9270 (mt) cc_final: 0.9032 (mm) REVERT: o 87 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7265 (ttmm) REVERT: o 89 GLU cc_start: 0.9079 (pm20) cc_final: 0.8669 (pm20) REVERT: o 90 ASP cc_start: 0.8259 (m-30) cc_final: 0.7909 (m-30) REVERT: o 105 GLN cc_start: 0.8318 (mp10) cc_final: 0.7726 (pm20) REVERT: P 439 ASP cc_start: 0.8161 (p0) cc_final: 0.7952 (p0) REVERT: P 450 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8402 (mt-10) REVERT: P 458 LYS cc_start: 0.9087 (mtmm) cc_final: 0.8738 (mmpt) REVERT: P 486 ASN cc_start: 0.8986 (t0) cc_final: 0.8538 (t0) REVERT: P 517 ARG cc_start: 0.9170 (ptt180) cc_final: 0.8755 (ptp-110) REVERT: p 4 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8573 (mm-40) REVERT: p 7 GLU cc_start: 0.7974 (mp0) cc_final: 0.7623 (mp0) REVERT: p 73 ASP cc_start: 0.8138 (t0) cc_final: 0.7450 (t0) REVERT: p 76 LYS cc_start: 0.9199 (pmmt) cc_final: 0.8851 (pmtt) REVERT: p 86 LEU cc_start: 0.9185 (mt) cc_final: 0.8836 (mm) REVERT: p 87 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7390 (ttmm) REVERT: p 89 GLU cc_start: 0.8968 (pm20) cc_final: 0.8475 (pm20) REVERT: p 90 ASP cc_start: 0.8344 (m-30) cc_final: 0.7968 (m-30) REVERT: p 105 GLN cc_start: 0.8095 (pm20) cc_final: 0.7650 (mp10) outliers start: 117 outliers final: 84 residues processed: 974 average time/residue: 0.7865 time to fit residues: 925.0915 Evaluate side-chains 968 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 879 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 35 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 83 MET Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 378 VAL Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain I residue 523 LEU Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 481 THR Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 183 optimal weight: 5.9990 chunk 399 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 327 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 441 optimal weight: 0.8980 chunk 466 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 445 optimal weight: 4.9990 chunk 468 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.146927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092211 restraints weight = 64397.054| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.65 r_work: 0.3144 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43344 Z= 0.151 Angle : 0.603 10.920 58608 Z= 0.300 Chirality : 0.041 0.172 6608 Planarity : 0.004 0.040 7536 Dihedral : 4.604 23.015 6016 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.38 % Allowed : 20.30 % Favored : 77.32 % 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 aren not related in a simple way. whole: -0.17 (0.12), residues: 5360 helix: 0.87 (0.11), residues: 2336 sheet: -0.88 (0.17), residues: 960 loop : -0.74 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 484 TYR 0.012 0.001 TYR K 479 PHE 0.010 0.001 PHE l 68 TRP 0.009 0.001 TRP c 103 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00363 (43328) covalent geometry : angle 0.60322 (58576) SS BOND : bond 0.00108 ( 16) SS BOND : angle 0.66644 ( 32) hydrogen bonds : bond 0.03348 ( 1921) hydrogen bonds : angle 3.91086 ( 5190) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 914 time to evaluate : 1.774 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8417 (ptmt) cc_final: 0.7852 (ptpp) REVERT: A 450 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 486 ASN cc_start: 0.9052 (t0) cc_final: 0.8845 (t0) REVERT: a 4 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8530 (mm-40) REVERT: a 7 GLU cc_start: 0.7638 (mp0) cc_final: 0.7205 (mp0) REVERT: a 44 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8289 (mtmm) REVERT: a 73 ASP cc_start: 0.7860 (t0) cc_final: 0.7091 (t0) REVERT: a 77 ASN cc_start: 0.8891 (m-40) cc_final: 0.8371 (m-40) REVERT: a 86 LEU cc_start: 0.9211 (mt) cc_final: 0.8930 (mm) REVERT: a 87 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7124 (ttmm) REVERT: a 89 GLU cc_start: 0.8945 (pm20) cc_final: 0.8544 (pm20) REVERT: a 90 ASP cc_start: 0.8176 (m-30) cc_final: 0.7805 (m-30) REVERT: a 105 GLN cc_start: 0.7830 (pm20) cc_final: 0.7257 (pm20) REVERT: B 472 GLU cc_start: 0.8912 (tt0) cc_final: 0.8331 (tp30) REVERT: B 489 ASP cc_start: 0.8931 (m-30) cc_final: 0.8708 (m-30) REVERT: b 4 GLN cc_start: 0.8800 (mp10) cc_final: 0.8541 (mp10) REVERT: b 73 ASP cc_start: 0.8098 (t70) cc_final: 0.7608 (t0) REVERT: b 76 LYS cc_start: 0.9125 (pmmt) cc_final: 0.8899 (pmtt) REVERT: b 89 GLU cc_start: 0.8969 (pm20) cc_final: 0.8646 (pm20) REVERT: b 90 ASP cc_start: 0.8248 (m-30) cc_final: 0.7910 (m-30) REVERT: C 439 ASP cc_start: 0.8243 (p0) cc_final: 0.7994 (p0) REVERT: C 450 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 486 ASN cc_start: 0.9043 (t0) cc_final: 0.8400 (t0) REVERT: C 489 ASP cc_start: 0.8858 (m-30) cc_final: 0.8521 (m-30) REVERT: C 543 ARG cc_start: 0.8740 (ttm170) cc_final: 0.8215 (mtt-85) REVERT: c 4 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8652 (mp10) REVERT: c 7 GLU cc_start: 0.7801 (mp0) cc_final: 0.7091 (mp0) REVERT: c 44 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8292 (mtmm) REVERT: c 77 ASN cc_start: 0.8888 (m-40) cc_final: 0.8414 (m-40) REVERT: c 86 LEU cc_start: 0.9209 (mt) cc_final: 0.8927 (mm) REVERT: c 87 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7115 (ttmm) REVERT: c 89 GLU cc_start: 0.8943 (pm20) cc_final: 0.8562 (pm20) REVERT: c 90 ASP cc_start: 0.8194 (m-30) cc_final: 0.7811 (m-30) REVERT: c 105 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: D 458 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8822 (mmpt) REVERT: D 472 GLU cc_start: 0.8918 (tt0) cc_final: 0.8408 (tp30) REVERT: D 486 ASN cc_start: 0.9035 (t0) cc_final: 0.8729 (t0) REVERT: D 517 ARG cc_start: 0.9190 (ptm160) cc_final: 0.8852 (ptp-110) REVERT: D 543 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8149 (mtt-85) REVERT: d 4 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8219 (mp10) REVERT: d 73 ASP cc_start: 0.8029 (t70) cc_final: 0.7488 (t0) REVERT: d 86 LEU cc_start: 0.9174 (mt) cc_final: 0.8828 (mm) REVERT: d 87 LYS cc_start: 0.7610 (mmtt) cc_final: 0.6941 (ttmm) REVERT: d 89 GLU cc_start: 0.8931 (pm20) cc_final: 0.8407 (pm20) REVERT: d 90 ASP cc_start: 0.8207 (m-30) cc_final: 0.7691 (m-30) REVERT: E 450 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8252 (mt-10) REVERT: E 486 ASN cc_start: 0.9062 (t0) cc_final: 0.8810 (t0) REVERT: e 4 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8825 (mm-40) REVERT: e 7 GLU cc_start: 0.7699 (mp0) cc_final: 0.7108 (mp0) REVERT: e 14 GLN cc_start: 0.8710 (pm20) cc_final: 0.8264 (mp10) REVERT: e 44 LYS cc_start: 0.8772 (mtmm) cc_final: 0.8346 (mppt) REVERT: e 77 ASN cc_start: 0.8876 (m-40) cc_final: 0.8432 (m-40) REVERT: e 87 LYS cc_start: 0.7652 (mmtt) cc_final: 0.7354 (ttmm) REVERT: e 89 GLU cc_start: 0.8978 (pm20) cc_final: 0.8457 (pm20) REVERT: e 105 GLN cc_start: 0.7925 (pm20) cc_final: 0.7364 (pm20) REVERT: F 403 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8484 (mmm-85) REVERT: F 517 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8871 (ptp-110) REVERT: f 4 GLN cc_start: 0.8969 (mp10) cc_final: 0.8666 (mp10) REVERT: f 73 ASP cc_start: 0.8145 (t0) cc_final: 0.7575 (t0) REVERT: f 76 LYS cc_start: 0.9146 (pmmt) cc_final: 0.8842 (pmmt) REVERT: f 86 LEU cc_start: 0.9224 (mt) cc_final: 0.8872 (mm) REVERT: f 87 LYS cc_start: 0.7572 (mmtt) cc_final: 0.6928 (ttmm) REVERT: f 89 GLU cc_start: 0.8952 (pm20) cc_final: 0.8472 (pm20) REVERT: f 90 ASP cc_start: 0.8188 (m-30) cc_final: 0.7694 (m-30) REVERT: G 439 ASP cc_start: 0.8233 (p0) cc_final: 0.7980 (p0) REVERT: G 450 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8211 (mt-10) REVERT: G 457 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8868 (mtm) REVERT: G 486 ASN cc_start: 0.9063 (t0) cc_final: 0.8850 (t0) REVERT: G 543 ARG cc_start: 0.8748 (ttm170) cc_final: 0.8283 (mtt-85) REVERT: g 4 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8663 (mm-40) REVERT: g 7 GLU cc_start: 0.7894 (mp0) cc_final: 0.7294 (mp0) REVERT: g 14 GLN cc_start: 0.8761 (pm20) cc_final: 0.8375 (mp10) REVERT: g 73 ASP cc_start: 0.7955 (t70) cc_final: 0.7393 (t0) REVERT: g 77 ASN cc_start: 0.8898 (m-40) cc_final: 0.8412 (m-40) REVERT: g 86 LEU cc_start: 0.9286 (mt) cc_final: 0.8992 (mm) REVERT: g 87 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7170 (ttmm) REVERT: g 89 GLU cc_start: 0.8910 (pm20) cc_final: 0.8406 (pm20) REVERT: g 90 ASP cc_start: 0.8117 (m-30) cc_final: 0.7883 (m-30) REVERT: g 105 GLN cc_start: 0.7949 (pm20) cc_final: 0.7236 (pm20) REVERT: H 472 GLU cc_start: 0.8918 (tt0) cc_final: 0.8427 (tp30) REVERT: H 486 ASN cc_start: 0.9040 (t0) cc_final: 0.8760 (t0) REVERT: H 517 ARG cc_start: 0.9125 (ptm160) cc_final: 0.8841 (ptp-110) REVERT: h 4 GLN cc_start: 0.8865 (mp10) cc_final: 0.8627 (mp10) REVERT: h 73 ASP cc_start: 0.8186 (t0) cc_final: 0.7612 (t0) REVERT: h 76 LYS cc_start: 0.9182 (pmmt) cc_final: 0.8926 (pmtt) REVERT: h 86 LEU cc_start: 0.9138 (mt) cc_final: 0.8855 (mm) REVERT: h 89 GLU cc_start: 0.8991 (pm20) cc_final: 0.8685 (pm20) REVERT: h 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7887 (m-30) REVERT: I 439 ASP cc_start: 0.8241 (p0) cc_final: 0.8001 (p0) REVERT: I 450 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8353 (mt-10) REVERT: I 483 ASP cc_start: 0.8255 (t0) cc_final: 0.8001 (t0) REVERT: I 486 ASN cc_start: 0.8755 (t0) cc_final: 0.8365 (t0) REVERT: I 516 HIS cc_start: 0.8623 (p-80) cc_final: 0.8343 (p90) REVERT: i 4 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8566 (mm-40) REVERT: i 44 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8260 (mppt) REVERT: i 73 ASP cc_start: 0.8319 (t0) cc_final: 0.7759 (OUTLIER) REVERT: i 76 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8870 (pmmt) REVERT: i 86 LEU cc_start: 0.9282 (mt) cc_final: 0.9009 (mm) REVERT: i 87 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7247 (ttmm) REVERT: i 89 GLU cc_start: 0.8995 (pm20) cc_final: 0.8525 (pm20) REVERT: i 90 ASP cc_start: 0.8278 (m-30) cc_final: 0.7981 (m-30) REVERT: i 105 GLN cc_start: 0.8402 (mp10) cc_final: 0.7652 (pm20) REVERT: J 439 ASP cc_start: 0.8201 (p0) cc_final: 0.7996 (p0) REVERT: J 486 ASN cc_start: 0.8959 (t0) cc_final: 0.8504 (t0) REVERT: J 516 HIS cc_start: 0.8741 (p-80) cc_final: 0.8402 (p90) REVERT: J 517 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8708 (ptp-170) REVERT: j 4 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8583 (mm-40) REVERT: j 7 GLU cc_start: 0.7763 (mp0) cc_final: 0.7550 (mp0) REVERT: j 44 LYS cc_start: 0.8908 (mtmm) cc_final: 0.8557 (mtmm) REVERT: j 73 ASP cc_start: 0.8047 (t0) cc_final: 0.7282 (t0) REVERT: j 76 LYS cc_start: 0.9229 (pmtt) cc_final: 0.8940 (pmtt) REVERT: j 86 LEU cc_start: 0.9179 (mt) cc_final: 0.8911 (mm) REVERT: j 87 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7219 (ttmm) REVERT: j 89 GLU cc_start: 0.8933 (pm20) cc_final: 0.8274 (pm20) REVERT: j 90 ASP cc_start: 0.8257 (m-30) cc_final: 0.7775 (m-30) REVERT: j 105 GLN cc_start: 0.7869 (pm20) cc_final: 0.7366 (pm20) REVERT: K 450 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8311 (mt-10) REVERT: K 483 ASP cc_start: 0.8311 (t0) cc_final: 0.8053 (t0) REVERT: K 484 ARG cc_start: 0.8997 (tpp-160) cc_final: 0.8776 (tpp-160) REVERT: K 486 ASN cc_start: 0.9034 (t0) cc_final: 0.8585 (t0) REVERT: K 517 ARG cc_start: 0.9148 (ptt180) cc_final: 0.8943 (ptp-110) REVERT: k 4 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8513 (mm-40) REVERT: k 7 GLU cc_start: 0.7789 (mp0) cc_final: 0.7565 (mp0) REVERT: k 14 GLN cc_start: 0.8670 (pm20) cc_final: 0.8182 (mp10) REVERT: k 73 ASP cc_start: 0.8416 (t0) cc_final: 0.7900 (t0) REVERT: k 86 LEU cc_start: 0.9311 (mt) cc_final: 0.9076 (mm) REVERT: k 87 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7262 (ttmm) REVERT: k 89 GLU cc_start: 0.9021 (pm20) cc_final: 0.8557 (pm20) REVERT: k 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7918 (m-30) REVERT: k 105 GLN cc_start: 0.7910 (pm20) cc_final: 0.7444 (pm20) REVERT: L 450 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8298 (mt-10) REVERT: L 472 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: L 486 ASN cc_start: 0.8986 (t0) cc_final: 0.8475 (t0) REVERT: L 517 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8654 (ptp-110) REVERT: L 543 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8189 (mtt-85) REVERT: l 4 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8696 (mm-40) REVERT: l 44 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8443 (mtmm) REVERT: l 73 ASP cc_start: 0.8279 (t0) cc_final: 0.7698 (t0) REVERT: l 76 LYS cc_start: 0.9198 (pmmt) cc_final: 0.8989 (pmmt) REVERT: l 86 LEU cc_start: 0.9228 (mt) cc_final: 0.8865 (mm) REVERT: l 87 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7196 (ttmm) REVERT: l 89 GLU cc_start: 0.8844 (pm20) cc_final: 0.8166 (pm20) REVERT: l 90 ASP cc_start: 0.8237 (m-30) cc_final: 0.7801 (m-30) REVERT: M 450 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8322 (mt-10) REVERT: M 458 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8666 (mmpt) REVERT: M 486 ASN cc_start: 0.8937 (t0) cc_final: 0.8557 (t0) REVERT: M 516 HIS cc_start: 0.8596 (p90) cc_final: 0.8312 (p90) REVERT: m 4 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8532 (mm-40) REVERT: m 7 GLU cc_start: 0.7792 (mp0) cc_final: 0.7479 (mp0) REVERT: m 14 GLN cc_start: 0.8705 (pm20) cc_final: 0.8286 (mp10) REVERT: m 73 ASP cc_start: 0.8409 (t0) cc_final: 0.7895 (t0) REVERT: m 83 MET cc_start: 0.8630 (mtm) cc_final: 0.8426 (mpp) REVERT: m 86 LEU cc_start: 0.9306 (mt) cc_final: 0.9075 (mm) REVERT: m 87 LYS cc_start: 0.7671 (mmtt) cc_final: 0.6977 (ttmm) REVERT: m 89 GLU cc_start: 0.9004 (pm20) cc_final: 0.8666 (pm20) REVERT: m 90 ASP cc_start: 0.8212 (m-30) cc_final: 0.7423 (m-30) REVERT: m 105 GLN cc_start: 0.8064 (pm20) cc_final: 0.7720 (pm20) REVERT: N 486 ASN cc_start: 0.8974 (t0) cc_final: 0.8495 (t0) REVERT: N 517 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8665 (ptp-110) REVERT: N 545 MET cc_start: 0.7669 (ttp) cc_final: 0.7237 (ttp) REVERT: n 4 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8639 (mm-40) REVERT: n 73 ASP cc_start: 0.8035 (t0) cc_final: 0.7269 (t0) REVERT: n 76 LYS cc_start: 0.9235 (pmtt) cc_final: 0.8948 (pmtt) REVERT: n 86 LEU cc_start: 0.9198 (mt) cc_final: 0.8839 (mm) REVERT: n 87 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7394 (ttmm) REVERT: n 89 GLU cc_start: 0.8889 (pm20) cc_final: 0.8341 (pm20) REVERT: n 90 ASP cc_start: 0.8297 (m-30) cc_final: 0.7947 (m-30) REVERT: n 105 GLN cc_start: 0.8073 (pm20) cc_final: 0.7738 (pm20) REVERT: O 439 ASP cc_start: 0.8260 (p0) cc_final: 0.7994 (p0) REVERT: O 450 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8314 (mt-10) REVERT: O 458 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8691 (mmpt) REVERT: O 484 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8536 (tpp-160) REVERT: O 486 ASN cc_start: 0.8710 (t0) cc_final: 0.8431 (t0) REVERT: O 516 HIS cc_start: 0.8639 (p-80) cc_final: 0.8340 (p90) REVERT: o 4 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8599 (mm-40) REVERT: o 7 GLU cc_start: 0.8051 (mp0) cc_final: 0.7782 (mp0) REVERT: o 14 GLN cc_start: 0.8738 (pm20) cc_final: 0.8303 (mp10) REVERT: o 73 ASP cc_start: 0.8451 (t0) cc_final: 0.7894 (t0) REVERT: o 86 LEU cc_start: 0.9264 (mt) cc_final: 0.9052 (mm) REVERT: o 87 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7283 (ttmm) REVERT: o 89 GLU cc_start: 0.9076 (pm20) cc_final: 0.8661 (pm20) REVERT: o 90 ASP cc_start: 0.8247 (m-30) cc_final: 0.7940 (m-30) REVERT: o 102 THR cc_start: 0.8721 (p) cc_final: 0.8457 (t) REVERT: o 105 GLN cc_start: 0.8317 (mp10) cc_final: 0.7712 (pm20) REVERT: P 439 ASP cc_start: 0.8134 (p0) cc_final: 0.7930 (p0) REVERT: P 450 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8387 (mt-10) REVERT: P 486 ASN cc_start: 0.8988 (t0) cc_final: 0.8538 (t0) REVERT: P 517 ARG cc_start: 0.9194 (ptt180) cc_final: 0.8768 (ptp-170) REVERT: p 4 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8576 (mm-40) REVERT: p 7 GLU cc_start: 0.7966 (mp0) cc_final: 0.7693 (mp0) REVERT: p 73 ASP cc_start: 0.8108 (t0) cc_final: 0.7513 (t0) REVERT: p 76 LYS cc_start: 0.9215 (pmmt) cc_final: 0.8927 (pmmt) REVERT: p 86 LEU cc_start: 0.9190 (mt) cc_final: 0.8849 (mm) REVERT: p 87 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7451 (ttmm) REVERT: p 89 GLU cc_start: 0.8944 (pm20) cc_final: 0.8401 (pm20) REVERT: p 90 ASP cc_start: 0.8257 (m-30) cc_final: 0.7924 (m-30) REVERT: p 105 GLN cc_start: 0.8175 (pm20) cc_final: 0.7697 (mp10) outliers start: 111 outliers final: 84 residues processed: 972 average time/residue: 0.7940 time to fit residues: 935.8446 Evaluate side-chains 991 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 897 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 35 MET Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 83 MET Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain I residue 517 ARG Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 76 LYS Chi-restraints excluded: chain i residue 83 MET Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 502 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 458 LYS Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 502 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 21 LEU Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 544 GLU Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 378 VAL Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain P residue 502 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 21 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 215 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 451 optimal weight: 7.9990 chunk 477 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 512 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 493 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 494 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.147655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092742 restraints weight = 64987.479| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.63 r_work: 0.3174 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43344 Z= 0.110 Angle : 0.596 11.403 58608 Z= 0.294 Chirality : 0.039 0.188 6608 Planarity : 0.004 0.040 7536 Dihedral : 4.485 21.172 6016 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.02 % Allowed : 20.75 % Favored : 77.23 % 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 aren not related in a simple way. whole: -0.04 (0.12), residues: 5360 helix: 1.00 (0.11), residues: 2320 sheet: -0.81 (0.17), residues: 960 loop : -0.70 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 403 TYR 0.012 0.001 TYR o 80 PHE 0.011 0.001 PHE l 68 TRP 0.010 0.001 TRP c 103 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00255 (43328) covalent geometry : angle 0.59620 (58576) SS BOND : bond 0.00084 ( 16) SS BOND : angle 0.56453 ( 32) hydrogen bonds : bond 0.03064 ( 1921) hydrogen bonds : angle 3.82270 ( 5190) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 945 time to evaluate : 1.689 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: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8463 (ptmt) cc_final: 0.7901 (ptpp) REVERT: A 450 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8218 (mt-10) REVERT: a 4 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8548 (mm-40) REVERT: a 7 GLU cc_start: 0.7618 (mp0) cc_final: 0.7155 (mp0) REVERT: a 44 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8282 (mtmm) REVERT: a 59 ASN cc_start: 0.8101 (m-40) cc_final: 0.7860 (m-40) REVERT: a 73 ASP cc_start: 0.8013 (t0) cc_final: 0.7091 (t0) REVERT: a 76 LYS cc_start: 0.9143 (pmtt) cc_final: 0.8754 (pmtt) REVERT: a 77 ASN cc_start: 0.8817 (m-40) cc_final: 0.8406 (m-40) REVERT: a 86 LEU cc_start: 0.9207 (mt) cc_final: 0.8935 (mm) REVERT: a 87 LYS cc_start: 0.7403 (mmtt) cc_final: 0.6968 (ttmm) REVERT: a 89 GLU cc_start: 0.8928 (pm20) cc_final: 0.8413 (pm20) REVERT: a 90 ASP cc_start: 0.7988 (m-30) cc_final: 0.7701 (m-30) REVERT: a 105 GLN cc_start: 0.7828 (pm20) cc_final: 0.7350 (pm20) REVERT: B 472 GLU cc_start: 0.8899 (tt0) cc_final: 0.8392 (tp30) REVERT: B 489 ASP cc_start: 0.8921 (m-30) cc_final: 0.8700 (m-30) REVERT: b 4 GLN cc_start: 0.8897 (mp10) cc_final: 0.8637 (mp10) REVERT: b 73 ASP cc_start: 0.8124 (t70) cc_final: 0.7626 (t0) REVERT: b 76 LYS cc_start: 0.9124 (pmmt) cc_final: 0.8900 (pmtt) REVERT: b 87 LYS cc_start: 0.7470 (mmtt) cc_final: 0.6881 (ttmm) REVERT: b 89 GLU cc_start: 0.8974 (pm20) cc_final: 0.8224 (pm20) REVERT: b 90 ASP cc_start: 0.8093 (m-30) cc_final: 0.7631 (m-30) REVERT: C 450 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8196 (mt-10) REVERT: C 486 ASN cc_start: 0.9024 (t0) cc_final: 0.8317 (t0) REVERT: C 489 ASP cc_start: 0.8853 (m-30) cc_final: 0.8523 (m-30) REVERT: C 543 ARG cc_start: 0.8715 (ttm170) cc_final: 0.8179 (mtt-85) REVERT: c 4 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: c 7 GLU cc_start: 0.7830 (mp0) cc_final: 0.7162 (mp0) REVERT: c 44 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8339 (mtmm) REVERT: c 59 ASN cc_start: 0.8110 (m-40) cc_final: 0.7870 (m-40) REVERT: c 76 LYS cc_start: 0.9244 (pmtt) cc_final: 0.8972 (pmtt) REVERT: c 77 ASN cc_start: 0.8810 (m-40) cc_final: 0.8446 (m-40) REVERT: c 86 LEU cc_start: 0.9206 (mt) cc_final: 0.8927 (mm) REVERT: c 87 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6904 (ttmm) REVERT: c 89 GLU cc_start: 0.8914 (pm20) cc_final: 0.8352 (pm20) REVERT: c 90 ASP cc_start: 0.7980 (m-30) cc_final: 0.7690 (m-30) REVERT: c 105 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: D 458 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8817 (mmpt) REVERT: D 472 GLU cc_start: 0.8915 (tt0) cc_final: 0.8395 (tp30) REVERT: D 486 ASN cc_start: 0.8998 (t0) cc_final: 0.8690 (t0) REVERT: D 517 ARG cc_start: 0.9189 (ptm160) cc_final: 0.8867 (ptp-110) REVERT: D 543 ARG cc_start: 0.8714 (ttm170) cc_final: 0.8135 (mtt-85) REVERT: d 4 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8751 (mp10) REVERT: d 73 ASP cc_start: 0.8085 (t70) cc_final: 0.7523 (t0) REVERT: d 86 LEU cc_start: 0.9165 (mt) cc_final: 0.8802 (mm) REVERT: d 87 LYS cc_start: 0.7458 (mmtt) cc_final: 0.6848 (ttmm) REVERT: d 89 GLU cc_start: 0.8900 (pm20) cc_final: 0.8325 (pm20) REVERT: d 90 ASP cc_start: 0.8059 (m-30) cc_final: 0.7609 (m-30) REVERT: E 450 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8221 (mt-10) REVERT: E 472 GLU cc_start: 0.8882 (tt0) cc_final: 0.8389 (tp30) REVERT: E 486 ASN cc_start: 0.9048 (t0) cc_final: 0.8821 (t0) REVERT: E 544 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8484 (pp20) REVERT: e 4 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8823 (mm-40) REVERT: e 7 GLU cc_start: 0.7629 (mp0) cc_final: 0.6964 (mp0) REVERT: e 14 GLN cc_start: 0.8710 (pm20) cc_final: 0.8481 (mp-120) REVERT: e 44 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8346 (mppt) REVERT: e 76 LYS cc_start: 0.9320 (pmtt) cc_final: 0.9057 (pmtt) REVERT: e 77 ASN cc_start: 0.8868 (m-40) cc_final: 0.8537 (m-40) REVERT: e 87 LYS cc_start: 0.7437 (mmtt) cc_final: 0.7169 (ttmm) REVERT: e 89 GLU cc_start: 0.8945 (pm20) cc_final: 0.8488 (pm20) REVERT: e 105 GLN cc_start: 0.7953 (pm20) cc_final: 0.7297 (pm20) REVERT: F 403 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8511 (mmm-85) REVERT: F 472 GLU cc_start: 0.8881 (tt0) cc_final: 0.8409 (tp30) REVERT: F 489 ASP cc_start: 0.8817 (m-30) cc_final: 0.8546 (p0) REVERT: F 517 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8892 (ptp-110) REVERT: f 4 GLN cc_start: 0.8968 (mp10) cc_final: 0.8659 (mp10) REVERT: f 73 ASP cc_start: 0.8119 (t0) cc_final: 0.7513 (t0) REVERT: f 76 LYS cc_start: 0.9172 (pmmt) cc_final: 0.8894 (pmmt) REVERT: f 87 LYS cc_start: 0.7436 (mmtt) cc_final: 0.6879 (ttmm) REVERT: f 89 GLU cc_start: 0.8924 (pm20) cc_final: 0.8390 (pm20) REVERT: f 90 ASP cc_start: 0.8032 (m-30) cc_final: 0.7575 (m-30) REVERT: G 450 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8134 (mt-10) REVERT: G 457 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8854 (mtm) REVERT: G 486 ASN cc_start: 0.9053 (t0) cc_final: 0.8838 (t0) REVERT: g 4 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8663 (mm-40) REVERT: g 14 GLN cc_start: 0.8756 (pm20) cc_final: 0.8381 (mp10) REVERT: g 73 ASP cc_start: 0.8001 (t70) cc_final: 0.7422 (t0) REVERT: g 76 LYS cc_start: 0.9222 (pmtt) cc_final: 0.8975 (pmtt) REVERT: g 77 ASN cc_start: 0.8877 (m-40) cc_final: 0.8387 (m-40) REVERT: g 86 LEU cc_start: 0.9266 (mt) cc_final: 0.8985 (mm) REVERT: g 87 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6976 (ttmm) REVERT: g 89 GLU cc_start: 0.8861 (pm20) cc_final: 0.8285 (pm20) REVERT: g 90 ASP cc_start: 0.8035 (m-30) cc_final: 0.7771 (m-30) REVERT: H 472 GLU cc_start: 0.8906 (tt0) cc_final: 0.8408 (tp30) REVERT: H 486 ASN cc_start: 0.9013 (t0) cc_final: 0.8707 (t0) REVERT: H 517 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8822 (ptp-110) REVERT: h 4 GLN cc_start: 0.8852 (mp10) cc_final: 0.8608 (mp10) REVERT: h 73 ASP cc_start: 0.8179 (t0) cc_final: 0.7598 (t0) REVERT: h 76 LYS cc_start: 0.9183 (pmmt) cc_final: 0.8932 (pmtt) REVERT: h 86 LEU cc_start: 0.9121 (mt) cc_final: 0.8820 (mm) REVERT: h 87 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6774 (ttmm) REVERT: h 89 GLU cc_start: 0.8970 (pm20) cc_final: 0.8213 (pm20) REVERT: h 90 ASP cc_start: 0.8034 (m-30) cc_final: 0.7522 (m-30) REVERT: I 450 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8395 (mt-10) REVERT: I 483 ASP cc_start: 0.8242 (t0) cc_final: 0.7995 (t0) REVERT: I 486 ASN cc_start: 0.8759 (t0) cc_final: 0.8366 (t0) REVERT: I 516 HIS cc_start: 0.8586 (p-80) cc_final: 0.8317 (p90) REVERT: i 4 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8552 (mm-40) REVERT: i 73 ASP cc_start: 0.8368 (t0) cc_final: 0.7810 (OUTLIER) REVERT: i 76 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8884 (pmmt) REVERT: i 86 LEU cc_start: 0.9235 (mt) cc_final: 0.8975 (mm) REVERT: i 87 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7375 (ttmm) REVERT: J 486 ASN cc_start: 0.8938 (t0) cc_final: 0.8539 (t0) REVERT: J 516 HIS cc_start: 0.8760 (p-80) cc_final: 0.8479 (p90) REVERT: J 517 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8754 (ptp-170) REVERT: j 4 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8578 (mm-40) REVERT: j 7 GLU cc_start: 0.7712 (mp0) cc_final: 0.7492 (mp0) REVERT: j 44 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8554 (mtmm) REVERT: j 73 ASP cc_start: 0.8031 (t0) cc_final: 0.7319 (t0) REVERT: j 86 LEU cc_start: 0.9181 (mt) cc_final: 0.8898 (mm) REVERT: j 87 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7202 (ttmm) REVERT: j 89 GLU cc_start: 0.8909 (pm20) cc_final: 0.8254 (pm20) REVERT: j 90 ASP cc_start: 0.8088 (m-30) cc_final: 0.7584 (m-30) REVERT: j 105 GLN cc_start: 0.7865 (pm20) cc_final: 0.7373 (pm20) REVERT: K 450 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8377 (mt-10) REVERT: K 483 ASP cc_start: 0.8285 (t0) cc_final: 0.8032 (t0) REVERT: K 484 ARG cc_start: 0.8986 (tpp-160) cc_final: 0.8765 (tpp-160) REVERT: K 486 ASN cc_start: 0.9036 (t0) cc_final: 0.8569 (t0) REVERT: K 517 ARG cc_start: 0.9200 (ptt180) cc_final: 0.8960 (ptp-110) REVERT: k 4 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8574 (mm-40) REVERT: k 7 GLU cc_start: 0.7748 (mp0) cc_final: 0.7508 (mp0) REVERT: k 14 GLN cc_start: 0.8682 (pm20) cc_final: 0.8213 (mp10) REVERT: k 73 ASP cc_start: 0.8421 (t0) cc_final: 0.7913 (t0) REVERT: k 86 LEU cc_start: 0.9279 (mt) cc_final: 0.9056 (mm) REVERT: k 87 LYS cc_start: 0.7567 (mmtt) cc_final: 0.6899 (ttmm) REVERT: k 89 GLU cc_start: 0.9018 (pm20) cc_final: 0.8663 (pm20) REVERT: k 90 ASP cc_start: 0.8116 (m-30) cc_final: 0.7340 (m-30) REVERT: k 105 GLN cc_start: 0.7871 (pm20) cc_final: 0.7394 (pm20) REVERT: L 423 GLN cc_start: 0.9069 (tt0) cc_final: 0.8844 (tt0) REVERT: L 450 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8366 (mt-10) REVERT: L 472 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (tp30) REVERT: L 486 ASN cc_start: 0.8968 (t0) cc_final: 0.8475 (t0) REVERT: L 517 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8579 (ptp-110) REVERT: L 543 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8211 (mtt-85) REVERT: l 4 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8623 (mm-40) REVERT: l 44 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8442 (mtmm) REVERT: l 73 ASP cc_start: 0.8279 (t0) cc_final: 0.7646 (t0) REVERT: l 76 LYS cc_start: 0.9257 (pmmt) cc_final: 0.9003 (pmmt) REVERT: l 86 LEU cc_start: 0.9200 (mt) cc_final: 0.8895 (mm) REVERT: l 87 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7192 (ttmm) REVERT: l 89 GLU cc_start: 0.8826 (pm20) cc_final: 0.8146 (pm20) REVERT: l 90 ASP cc_start: 0.8091 (m-30) cc_final: 0.7657 (m-30) REVERT: M 450 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8329 (mt-10) REVERT: M 458 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8665 (mmpt) REVERT: M 486 ASN cc_start: 0.8843 (t0) cc_final: 0.8484 (t0) REVERT: M 516 HIS cc_start: 0.8612 (p90) cc_final: 0.8191 (p90) REVERT: M 543 ARG cc_start: 0.8845 (ttm-80) cc_final: 0.8209 (mtt-85) REVERT: m 4 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8616 (mm-40) REVERT: m 7 GLU cc_start: 0.7721 (mp0) cc_final: 0.7412 (mp0) REVERT: m 14 GLN cc_start: 0.8699 (pm20) cc_final: 0.8238 (mp10) REVERT: m 73 ASP cc_start: 0.8418 (t0) cc_final: 0.7888 (t0) REVERT: m 87 LYS cc_start: 0.7563 (mmtt) cc_final: 0.6840 (ttmm) REVERT: m 89 GLU cc_start: 0.9005 (pm20) cc_final: 0.8655 (pm20) REVERT: m 90 ASP cc_start: 0.8070 (m-30) cc_final: 0.7278 (m-30) REVERT: m 105 GLN cc_start: 0.8097 (pm20) cc_final: 0.7749 (pm20) REVERT: N 450 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8317 (mt-10) REVERT: N 486 ASN cc_start: 0.8929 (t0) cc_final: 0.8550 (t0) REVERT: N 517 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8681 (ptp-110) REVERT: N 545 MET cc_start: 0.7506 (ttp) cc_final: 0.7118 (ttp) REVERT: n 4 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8594 (mm-40) REVERT: n 73 ASP cc_start: 0.8022 (t0) cc_final: 0.7256 (t0) REVERT: n 76 LYS cc_start: 0.9230 (pmtt) cc_final: 0.8938 (pmtt) REVERT: n 86 LEU cc_start: 0.9194 (mt) cc_final: 0.8855 (mm) REVERT: n 87 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7382 (ttmm) REVERT: n 89 GLU cc_start: 0.8862 (pm20) cc_final: 0.8307 (pm20) REVERT: n 90 ASP cc_start: 0.8200 (m-30) cc_final: 0.7863 (m-30) REVERT: O 439 ASP cc_start: 0.8173 (p0) cc_final: 0.7915 (p0) REVERT: O 450 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8347 (mt-10) REVERT: O 458 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8684 (mmpt) REVERT: O 486 ASN cc_start: 0.8688 (t0) cc_final: 0.8448 (t0) REVERT: O 516 HIS cc_start: 0.8624 (p-80) cc_final: 0.8339 (p90) REVERT: o 4 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8595 (mm-40) REVERT: o 7 GLU cc_start: 0.7967 (mp0) cc_final: 0.7716 (mp0) REVERT: o 14 GLN cc_start: 0.8712 (pm20) cc_final: 0.8281 (mp10) REVERT: o 73 ASP cc_start: 0.8409 (t0) cc_final: 0.7861 (t0) REVERT: o 87 LYS cc_start: 0.7612 (mmtt) cc_final: 0.6864 (ttmm) REVERT: o 89 GLU cc_start: 0.9051 (pm20) cc_final: 0.8709 (pm20) REVERT: o 90 ASP cc_start: 0.8086 (m-30) cc_final: 0.7322 (m-30) REVERT: o 102 THR cc_start: 0.8683 (p) cc_final: 0.8428 (t) REVERT: o 105 GLN cc_start: 0.8362 (mp10) cc_final: 0.7749 (pm20) REVERT: P 450 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8321 (mt-10) REVERT: P 458 LYS cc_start: 0.9080 (mtmm) cc_final: 0.8746 (mmpt) REVERT: P 486 ASN cc_start: 0.8931 (t0) cc_final: 0.8522 (t0) REVERT: P 517 ARG cc_start: 0.9183 (ptt180) cc_final: 0.8740 (ptp-110) REVERT: p 4 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8586 (mm-40) REVERT: p 73 ASP cc_start: 0.8037 (t0) cc_final: 0.7404 (t0) REVERT: p 76 LYS cc_start: 0.9217 (pmmt) cc_final: 0.8932 (pmmt) REVERT: p 77 ASN cc_start: 0.8960 (m-40) cc_final: 0.8367 (m110) REVERT: p 86 LEU cc_start: 0.9185 (mt) cc_final: 0.8852 (mm) REVERT: p 87 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7476 (ttmm) REVERT: p 89 GLU cc_start: 0.8919 (pm20) cc_final: 0.8398 (pm20) outliers start: 94 outliers final: 72 residues processed: 987 average time/residue: 0.6867 time to fit residues: 824.2692 Evaluate side-chains 993 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 910 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain I residue 517 ARG Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 76 LYS Chi-restraints excluded: chain i residue 83 MET Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 83 MET Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 458 LYS Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain O residue 517 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain O residue 544 GLU Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.0170 chunk 270 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 333 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 497 optimal weight: 20.0000 chunk 284 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 422 optimal weight: 0.0970 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.147786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092888 restraints weight = 64388.493| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.68 r_work: 0.3161 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43344 Z= 0.135 Angle : 0.610 11.828 58608 Z= 0.302 Chirality : 0.040 0.159 6608 Planarity : 0.004 0.043 7536 Dihedral : 4.490 21.424 6016 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.89 % Allowed : 20.96 % Favored : 77.15 % 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 aren not related in a simple way. whole: 0.28 (0.12), residues: 5360 helix: 1.29 (0.11), residues: 2224 sheet: -0.31 (0.18), residues: 864 loop : -0.66 (0.14), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 543 TYR 0.011 0.001 TYR m 80 PHE 0.006 0.001 PHE f 68 TRP 0.009 0.001 TRP c 103 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00324 (43328) covalent geometry : angle 0.61031 (58576) SS BOND : bond 0.00122 ( 16) SS BOND : angle 0.64870 ( 32) hydrogen bonds : bond 0.03190 ( 1921) hydrogen bonds : angle 3.83587 ( 5190) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 926 time to evaluate : 1.464 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: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8440 (ptmt) cc_final: 0.7884 (ptpp) REVERT: A 450 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 489 ASP cc_start: 0.8776 (m-30) cc_final: 0.8422 (p0) REVERT: a 4 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8593 (mm-40) REVERT: a 7 GLU cc_start: 0.7636 (mp0) cc_final: 0.7074 (mp0) REVERT: a 44 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8265 (mtmm) REVERT: a 59 ASN cc_start: 0.8134 (m-40) cc_final: 0.7888 (m-40) REVERT: a 73 ASP cc_start: 0.7979 (t0) cc_final: 0.7073 (t0) REVERT: a 76 LYS cc_start: 0.9081 (pmtt) cc_final: 0.8746 (pmtt) REVERT: a 77 ASN cc_start: 0.8886 (m-40) cc_final: 0.8442 (m-40) REVERT: a 86 LEU cc_start: 0.9208 (mt) cc_final: 0.8942 (mm) REVERT: a 87 LYS cc_start: 0.7425 (mmtt) cc_final: 0.7004 (ttmm) REVERT: a 89 GLU cc_start: 0.8918 (pm20) cc_final: 0.8375 (pm20) REVERT: a 90 ASP cc_start: 0.8081 (m-30) cc_final: 0.7820 (m-30) REVERT: a 105 GLN cc_start: 0.7835 (pm20) cc_final: 0.7253 (pm20) REVERT: B 472 GLU cc_start: 0.8893 (tt0) cc_final: 0.8393 (tp30) REVERT: B 489 ASP cc_start: 0.8933 (m-30) cc_final: 0.8712 (m-30) REVERT: b 73 ASP cc_start: 0.8141 (t70) cc_final: 0.7553 (t0) REVERT: b 76 LYS cc_start: 0.9122 (pmmt) cc_final: 0.8842 (pmtt) REVERT: b 87 LYS cc_start: 0.7513 (mmtt) cc_final: 0.6910 (ttmm) REVERT: b 89 GLU cc_start: 0.8966 (pm20) cc_final: 0.8222 (pm20) REVERT: b 90 ASP cc_start: 0.8108 (m-30) cc_final: 0.7677 (m-30) REVERT: C 450 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8184 (mt-10) REVERT: C 486 ASN cc_start: 0.9012 (t0) cc_final: 0.8356 (t0) REVERT: C 489 ASP cc_start: 0.8857 (m-30) cc_final: 0.8529 (m-30) REVERT: C 517 ARG cc_start: 0.9112 (ptt180) cc_final: 0.8823 (ptp-110) REVERT: c 4 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8690 (mp10) REVERT: c 7 GLU cc_start: 0.7836 (mp0) cc_final: 0.7188 (mp0) REVERT: c 44 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8311 (mtmm) REVERT: c 59 ASN cc_start: 0.8144 (m-40) cc_final: 0.7902 (m-40) REVERT: c 77 ASN cc_start: 0.8857 (m-40) cc_final: 0.8422 (m-40) REVERT: c 86 LEU cc_start: 0.9210 (mt) cc_final: 0.8933 (mm) REVERT: c 87 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7008 (ttmm) REVERT: c 89 GLU cc_start: 0.8909 (pm20) cc_final: 0.8311 (pm20) REVERT: c 90 ASP cc_start: 0.8080 (m-30) cc_final: 0.7779 (m-30) REVERT: c 105 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: D 458 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8822 (mmpt) REVERT: D 472 GLU cc_start: 0.8917 (tt0) cc_final: 0.8427 (tp30) REVERT: D 486 ASN cc_start: 0.9013 (t0) cc_final: 0.8694 (t0) REVERT: D 517 ARG cc_start: 0.9188 (ptm160) cc_final: 0.8866 (ptp-110) REVERT: D 543 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8168 (mtt-85) REVERT: d 4 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8728 (mp10) REVERT: d 73 ASP cc_start: 0.8092 (t70) cc_final: 0.7548 (t0) REVERT: d 86 LEU cc_start: 0.9163 (mt) cc_final: 0.8825 (mm) REVERT: d 87 LYS cc_start: 0.7476 (mmtt) cc_final: 0.6856 (ttmm) REVERT: d 89 GLU cc_start: 0.8905 (pm20) cc_final: 0.8299 (pm20) REVERT: d 90 ASP cc_start: 0.8072 (m-30) cc_final: 0.7603 (m-30) REVERT: E 450 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8156 (mt-10) REVERT: E 472 GLU cc_start: 0.8888 (tt0) cc_final: 0.8396 (tp30) REVERT: E 486 ASN cc_start: 0.9061 (t0) cc_final: 0.8844 (t0) REVERT: E 544 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8479 (pp20) REVERT: e 4 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8674 (mm-40) REVERT: e 7 GLU cc_start: 0.7654 (mp0) cc_final: 0.6997 (mp0) REVERT: e 14 GLN cc_start: 0.8696 (pm20) cc_final: 0.8481 (mp-120) REVERT: e 44 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8354 (mppt) REVERT: e 59 ASN cc_start: 0.8180 (m-40) cc_final: 0.7957 (m-40) REVERT: e 73 ASP cc_start: 0.8226 (t0) cc_final: 0.7613 (OUTLIER) REVERT: e 77 ASN cc_start: 0.8884 (m-40) cc_final: 0.8436 (m-40) REVERT: e 87 LYS cc_start: 0.7441 (mmtt) cc_final: 0.7110 (ttmm) REVERT: e 89 GLU cc_start: 0.8933 (pm20) cc_final: 0.8489 (pm20) REVERT: e 105 GLN cc_start: 0.7947 (pm20) cc_final: 0.7289 (pm20) REVERT: F 403 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8511 (mmm-85) REVERT: F 472 GLU cc_start: 0.8886 (tt0) cc_final: 0.8420 (tp30) REVERT: F 489 ASP cc_start: 0.8820 (m-30) cc_final: 0.8564 (p0) REVERT: F 517 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8895 (ptp-110) REVERT: f 4 GLN cc_start: 0.8966 (mp10) cc_final: 0.8662 (mp10) REVERT: f 73 ASP cc_start: 0.8133 (t0) cc_final: 0.7530 (OUTLIER) REVERT: f 86 LEU cc_start: 0.9208 (mt) cc_final: 0.8870 (mm) REVERT: f 87 LYS cc_start: 0.7462 (mmtt) cc_final: 0.6851 (ttmm) REVERT: f 89 GLU cc_start: 0.8939 (pm20) cc_final: 0.8400 (pm20) REVERT: f 90 ASP cc_start: 0.8103 (m-30) cc_final: 0.7628 (m-30) REVERT: G 450 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8203 (mt-10) REVERT: G 457 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8860 (mtm) REVERT: G 472 GLU cc_start: 0.8862 (tt0) cc_final: 0.8411 (tp30) REVERT: G 486 ASN cc_start: 0.9050 (t0) cc_final: 0.8811 (t0) REVERT: G 517 ARG cc_start: 0.9087 (ptt180) cc_final: 0.8817 (ptp-110) REVERT: g 4 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8924 (mp10) REVERT: g 14 GLN cc_start: 0.8738 (pm20) cc_final: 0.8387 (mp10) REVERT: g 73 ASP cc_start: 0.8006 (t70) cc_final: 0.7511 (t0) REVERT: g 76 LYS cc_start: 0.9227 (pmtt) cc_final: 0.8966 (pmtt) REVERT: g 77 ASN cc_start: 0.8884 (m-40) cc_final: 0.8393 (m-40) REVERT: g 86 LEU cc_start: 0.9268 (mt) cc_final: 0.8988 (mm) REVERT: g 87 LYS cc_start: 0.7448 (mmtt) cc_final: 0.7006 (ttmm) REVERT: g 89 GLU cc_start: 0.8865 (pm20) cc_final: 0.8287 (pm20) REVERT: g 90 ASP cc_start: 0.8077 (m-30) cc_final: 0.7810 (m-30) REVERT: H 472 GLU cc_start: 0.8920 (tt0) cc_final: 0.8423 (tp30) REVERT: H 486 ASN cc_start: 0.9014 (t0) cc_final: 0.8711 (t0) REVERT: H 516 HIS cc_start: 0.8565 (p90) cc_final: 0.7925 (p90) REVERT: H 517 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8520 (ptp-110) REVERT: h 4 GLN cc_start: 0.8866 (mp10) cc_final: 0.8624 (mp10) REVERT: h 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7656 (t0) REVERT: h 76 LYS cc_start: 0.9178 (pmmt) cc_final: 0.8917 (pmmt) REVERT: h 86 LEU cc_start: 0.9119 (mt) cc_final: 0.8830 (mm) REVERT: h 87 LYS cc_start: 0.7410 (mmtt) cc_final: 0.6783 (ttmm) REVERT: h 89 GLU cc_start: 0.8967 (pm20) cc_final: 0.8220 (pm20) REVERT: h 90 ASP cc_start: 0.8110 (m-30) cc_final: 0.7629 (m-30) REVERT: I 450 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8368 (mt-10) REVERT: I 483 ASP cc_start: 0.8251 (t0) cc_final: 0.8002 (t0) REVERT: I 486 ASN cc_start: 0.8762 (t0) cc_final: 0.8381 (t0) REVERT: I 543 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8280 (mtt-85) REVERT: i 4 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8561 (mm-40) REVERT: i 73 ASP cc_start: 0.8380 (t0) cc_final: 0.7837 (t0) REVERT: i 76 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8893 (pmmt) REVERT: i 86 LEU cc_start: 0.9223 (mt) cc_final: 0.9010 (mm) REVERT: i 87 LYS cc_start: 0.7543 (mmtt) cc_final: 0.6976 (ttmm) REVERT: i 89 GLU cc_start: 0.8964 (pm20) cc_final: 0.8643 (pm20) REVERT: i 90 ASP cc_start: 0.7912 (m-30) cc_final: 0.7120 (m-30) REVERT: J 486 ASN cc_start: 0.8941 (t0) cc_final: 0.8538 (t0) REVERT: J 516 HIS cc_start: 0.8753 (p-80) cc_final: 0.8483 (p90) REVERT: J 517 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8747 (ptp-170) REVERT: j 4 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8579 (mm-40) REVERT: j 7 GLU cc_start: 0.7713 (mp0) cc_final: 0.7490 (mp0) REVERT: j 44 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8555 (mtmm) REVERT: j 73 ASP cc_start: 0.8139 (t0) cc_final: 0.7539 (t0) REVERT: j 76 LYS cc_start: 0.9180 (pmmt) cc_final: 0.8893 (pmmt) REVERT: j 86 LEU cc_start: 0.9186 (mt) cc_final: 0.8907 (mm) REVERT: j 87 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7217 (ttmm) REVERT: j 89 GLU cc_start: 0.8914 (pm20) cc_final: 0.8264 (pm20) REVERT: j 90 ASP cc_start: 0.8103 (m-30) cc_final: 0.7599 (m-30) REVERT: j 105 GLN cc_start: 0.7847 (pm20) cc_final: 0.7362 (pm20) REVERT: K 450 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8362 (mt-10) REVERT: K 483 ASP cc_start: 0.8290 (t0) cc_final: 0.8037 (t0) REVERT: K 484 ARG cc_start: 0.8986 (tpp-160) cc_final: 0.8775 (tpp-160) REVERT: K 486 ASN cc_start: 0.9028 (t0) cc_final: 0.8561 (t0) REVERT: K 517 ARG cc_start: 0.9197 (ptt180) cc_final: 0.8949 (ptp-110) REVERT: k 4 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8573 (mm-40) REVERT: k 14 GLN cc_start: 0.8673 (pm20) cc_final: 0.8189 (mp10) REVERT: k 73 ASP cc_start: 0.8416 (t0) cc_final: 0.7868 (t0) REVERT: k 86 LEU cc_start: 0.9310 (mt) cc_final: 0.9062 (mm) REVERT: k 87 LYS cc_start: 0.7563 (mmtt) cc_final: 0.6877 (ttmm) REVERT: k 89 GLU cc_start: 0.8990 (pm20) cc_final: 0.8535 (pm20) REVERT: k 90 ASP cc_start: 0.8092 (m-30) cc_final: 0.7284 (m-30) REVERT: k 105 GLN cc_start: 0.7851 (pm20) cc_final: 0.7441 (pm20) REVERT: L 450 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8321 (mt-10) REVERT: L 472 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8617 (tp30) REVERT: L 486 ASN cc_start: 0.8970 (t0) cc_final: 0.8469 (t0) REVERT: L 517 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8615 (ptp-110) REVERT: L 543 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8125 (mtt-85) REVERT: l 4 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8656 (mm-40) REVERT: l 44 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8451 (mtmm) REVERT: l 73 ASP cc_start: 0.8272 (t0) cc_final: 0.7685 (t0) REVERT: l 86 LEU cc_start: 0.9225 (mt) cc_final: 0.8900 (mm) REVERT: l 87 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7158 (ttmm) REVERT: l 89 GLU cc_start: 0.8829 (pm20) cc_final: 0.8142 (pm20) REVERT: l 90 ASP cc_start: 0.8129 (m-30) cc_final: 0.7678 (m-30) REVERT: M 450 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8330 (mt-10) REVERT: M 458 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8683 (mmpt) REVERT: M 486 ASN cc_start: 0.8867 (t0) cc_final: 0.8552 (t0) REVERT: M 516 HIS cc_start: 0.8537 (p90) cc_final: 0.8158 (p90) REVERT: M 543 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8234 (mtt-85) REVERT: m 4 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8619 (mm-40) REVERT: m 7 GLU cc_start: 0.7728 (mp0) cc_final: 0.7507 (mp0) REVERT: m 14 GLN cc_start: 0.8698 (pm20) cc_final: 0.8243 (mp10) REVERT: m 73 ASP cc_start: 0.8399 (t0) cc_final: 0.7885 (t0) REVERT: m 87 LYS cc_start: 0.7643 (mmtt) cc_final: 0.6937 (ttmm) REVERT: m 89 GLU cc_start: 0.9002 (pm20) cc_final: 0.8674 (pm20) REVERT: m 90 ASP cc_start: 0.8103 (m-30) cc_final: 0.7275 (m-30) REVERT: m 105 GLN cc_start: 0.8068 (pm20) cc_final: 0.7786 (pm20) REVERT: N 486 ASN cc_start: 0.8930 (t0) cc_final: 0.8498 (t0) REVERT: N 517 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8702 (ptp-110) REVERT: N 545 MET cc_start: 0.7598 (ttp) cc_final: 0.7223 (ttp) REVERT: n 4 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8606 (mm-40) REVERT: n 73 ASP cc_start: 0.8021 (t0) cc_final: 0.7248 (t0) REVERT: n 76 LYS cc_start: 0.9231 (pmtt) cc_final: 0.8939 (pmtt) REVERT: n 86 LEU cc_start: 0.9197 (mt) cc_final: 0.8858 (mm) REVERT: n 87 LYS cc_start: 0.7695 (mmtt) cc_final: 0.7391 (ttmm) REVERT: n 89 GLU cc_start: 0.8859 (pm20) cc_final: 0.8301 (pm20) REVERT: n 90 ASP cc_start: 0.8207 (m-30) cc_final: 0.7864 (m-30) REVERT: n 105 GLN cc_start: 0.7740 (pm20) cc_final: 0.7361 (pm20) REVERT: O 439 ASP cc_start: 0.8244 (p0) cc_final: 0.7978 (p0) REVERT: O 450 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8317 (mt-10) REVERT: O 458 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8687 (mmpt) REVERT: O 486 ASN cc_start: 0.8693 (t0) cc_final: 0.8452 (t0) REVERT: o 4 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8603 (mm-40) REVERT: o 14 GLN cc_start: 0.8726 (pm20) cc_final: 0.8298 (mp10) REVERT: o 73 ASP cc_start: 0.8412 (t0) cc_final: 0.7870 (t0) REVERT: o 87 LYS cc_start: 0.7661 (mmtt) cc_final: 0.6985 (ttmm) REVERT: o 89 GLU cc_start: 0.9037 (pm20) cc_final: 0.8702 (pm20) REVERT: o 90 ASP cc_start: 0.8154 (m-30) cc_final: 0.7397 (m-30) REVERT: o 102 THR cc_start: 0.8685 (p) cc_final: 0.8434 (t) REVERT: P 450 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8387 (mt-10) REVERT: P 458 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8726 (mmpt) REVERT: P 486 ASN cc_start: 0.8916 (t0) cc_final: 0.8477 (t0) REVERT: P 517 ARG cc_start: 0.9100 (ptt180) cc_final: 0.8780 (ptp-170) REVERT: p 4 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8580 (mm-40) REVERT: p 73 ASP cc_start: 0.8037 (t0) cc_final: 0.7405 (t0) REVERT: p 76 LYS cc_start: 0.9211 (pmmt) cc_final: 0.8925 (pmmt) REVERT: p 77 ASN cc_start: 0.8962 (m-40) cc_final: 0.8369 (m110) REVERT: p 86 LEU cc_start: 0.9170 (mt) cc_final: 0.8853 (mm) REVERT: p 87 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7424 (ttmm) REVERT: p 89 GLU cc_start: 0.8914 (pm20) cc_final: 0.8363 (pm20) REVERT: p 90 ASP cc_start: 0.7890 (m-30) cc_final: 0.7595 (m-30) outliers start: 88 outliers final: 75 residues processed: 968 average time/residue: 0.7018 time to fit residues: 823.1594 Evaluate side-chains 997 residues out of total 4656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 912 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 102 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain c residue 4 GLN Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 13 VAL Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 105 GLN Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain d residue 12 LEU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 102 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain F residue 385 THR Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain f residue 12 LEU Chi-restraints excluded: chain f residue 83 MET Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain G residue 378 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain g residue 12 LEU Chi-restraints excluded: chain g residue 34 VAL Chi-restraints excluded: chain g residue 102 THR Chi-restraints excluded: chain H residue 385 THR Chi-restraints excluded: chain H residue 517 ARG Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain i residue 12 LEU Chi-restraints excluded: chain i residue 76 LYS Chi-restraints excluded: chain i residue 83 MET Chi-restraints excluded: chain i residue 102 THR Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain J residue 385 THR Chi-restraints excluded: chain J residue 483 ASP Chi-restraints excluded: chain J residue 517 ARG Chi-restraints excluded: chain J residue 545 MET Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 83 MET Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain K residue 385 THR Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 83 MET Chi-restraints excluded: chain k residue 102 THR Chi-restraints excluded: chain L residue 385 THR Chi-restraints excluded: chain L residue 472 GLU Chi-restraints excluded: chain L residue 517 ARG Chi-restraints excluded: chain L residue 544 GLU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 102 THR Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 458 LYS Chi-restraints excluded: chain m residue 12 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 517 ARG Chi-restraints excluded: chain n residue 12 LEU Chi-restraints excluded: chain n residue 102 THR Chi-restraints excluded: chain O residue 458 LYS Chi-restraints excluded: chain O residue 517 ARG Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain o residue 12 LEU Chi-restraints excluded: chain P residue 385 THR Chi-restraints excluded: chain P residue 481 THR Chi-restraints excluded: chain P residue 544 GLU Chi-restraints excluded: chain p residue 12 LEU Chi-restraints excluded: chain p residue 83 MET Chi-restraints excluded: chain p residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 231 optimal weight: 40.0000 chunk 480 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 423 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 264 optimal weight: 30.0000 chunk 376 optimal weight: 0.7980 chunk 263 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 105 GLN ** I 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092721 restraints weight = 64525.899| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.63 r_work: 0.3154 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 43344 Z= 0.148 Angle : 0.621 11.830 58608 Z= 0.308 Chirality : 0.040 0.155 6608 Planarity : 0.004 0.045 7536 Dihedral : 4.509 21.526 6016 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.10 % Allowed : 20.94 % Favored : 76.95 % 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 aren not related in a simple way. whole: 0.30 (0.12), residues: 5360 helix: 1.31 (0.11), residues: 2224 sheet: -0.30 (0.18), residues: 864 loop : -0.65 (0.14), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 543 TYR 0.017 0.001 TYR c 80 PHE 0.006 0.001 PHE L 426 TRP 0.008 0.001 TRP c 103 HIS 0.004 0.001 HIS D 516 Details of bonding type rmsd covalent geometry : bond 0.00357 (43328) covalent geometry : angle 0.62125 (58576) SS BOND : bond 0.00114 ( 16) SS BOND : angle 0.65628 ( 32) hydrogen bonds : bond 0.03242 ( 1921) hydrogen bonds : angle 3.84198 ( 5190) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20009.33 seconds wall clock time: 339 minutes 54.06 seconds (20394.06 seconds total)