Starting phenix.real_space_refine on Sat Mar 7 02:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nhr_12338/03_2026/7nhr_12338.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhr_12338/03_2026/7nhr_12338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nhr_12338/03_2026/7nhr_12338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhr_12338/03_2026/7nhr_12338.map" model { file = "/net/cci-nas-00/data/ceres_data/7nhr_12338/03_2026/7nhr_12338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhr_12338/03_2026/7nhr_12338.cif" } resolution = 2.85 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= 0.007 sd= 0.078 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 113 5.16 5 C 23609 2.51 5 N 6305 2.21 5 O 6984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37011 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "B" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Chain: "D" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "E" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4050 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "G" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "H" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Time building chain proxies: 8.17, per 1000 atoms: 0.22 Number of scatterers: 37011 At special positions: 0 Unit cell: (159.168, 164.142, 173.261, 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 113 16.00 O 6984 8.00 N 6305 7.00 C 23609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 32 sheets defined 52.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.606A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.877A pdb=" N LYS A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.611A pdb=" N SER A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.821A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.582A pdb=" N SER A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 403 removed outlier: 3.646A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 452 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.926A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.778A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.686A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 596' Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.058A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.550A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.834A pdb=" N THR B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.731A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 425 through 452 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.068A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.596A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 removed outlier: 3.666A pdb=" N THR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.593A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 596' Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 636 removed outlier: 4.081A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 Processing helix chain 'B' and resid 701 through 708 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.872A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 240 through 263 removed outlier: 3.661A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 385 through 404 Processing helix chain 'C' and resid 425 through 452 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.039A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.692A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 554 removed outlier: 3.845A pdb=" N THR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 636 removed outlier: 4.156A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.578A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.545A pdb=" N TYR C 705 " --> pdb=" O LYS C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.587A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.924A pdb=" N LYS D 101 " --> pdb=" O MET D 97 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.712A pdb=" N SER D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 266 removed outlier: 3.712A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 Processing helix chain 'D' and resid 340 through 366 removed outlier: 3.529A pdb=" N SER D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 404 removed outlier: 3.917A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 452 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.087A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.511A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 554 removed outlier: 4.049A pdb=" N THR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.669A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 595' Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.102A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.616A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.671A pdb=" N TYR D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.731A pdb=" N THR E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 129 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.610A pdb=" N SER E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 425 through 451 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.056A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.704A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.531A pdb=" N PHE E 585 " --> pdb=" O GLY E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.616A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.154A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 672 through 686 Processing helix chain 'E' and resid 701 through 708 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.529A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.633A pdb=" N LYS F 101 " --> pdb=" O MET F 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 102 " --> pdb=" O ILE F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.598A pdb=" N SER F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 266 removed outlier: 3.798A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 297 Proline residue: F 279 - end of helix Processing helix chain 'F' and resid 305 through 336 Processing helix chain 'F' and resid 340 through 366 Processing helix chain 'F' and resid 368 through 403 removed outlier: 4.037A pdb=" N VAL F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 403 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 451 Processing helix chain 'F' and resid 457 through 464 removed outlier: 3.987A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.552A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.780A pdb=" N THR F 554 " --> pdb=" O THR F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 574 Processing helix chain 'F' and resid 581 through 587 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.526A pdb=" N ILE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 615 through 621 removed outlier: 3.551A pdb=" N MET F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 636 removed outlier: 4.151A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.530A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 708 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.847A pdb=" N THR G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.510A pdb=" N SER G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 277 removed outlier: 3.593A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN G 263 " --> pdb=" O ASN G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 404 Processing helix chain 'G' and resid 425 through 451 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.027A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.630A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 554 removed outlier: 3.802A pdb=" N THR G 554 " --> pdb=" O THR G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.922A pdb=" N ILE G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 595' Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 636 removed outlier: 4.135A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.517A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 708 Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.904A pdb=" N THR H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 240 through 278 removed outlier: 3.551A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 404 Processing helix chain 'H' and resid 425 through 452 Processing helix chain 'H' and resid 457 through 465 removed outlier: 4.037A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 Processing helix chain 'H' and resid 539 through 554 removed outlier: 3.799A pdb=" N THR H 554 " --> pdb=" O THR H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 588 Processing helix chain 'H' and resid 591 through 595 removed outlier: 3.829A pdb=" N ILE H 595 " --> pdb=" O ALA H 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 591 through 595' Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 636 removed outlier: 4.117A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.539A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 701 through 708 removed outlier: 3.549A pdb=" N TYR H 705 " --> pdb=" O LYS H 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 8.573A pdb=" N ILE A 54 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASP A 418 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.732A pdb=" N ILE A 156 " --> pdb=" O ASN A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.270A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 138 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.366A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 559 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP A 642 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 561 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.924A pdb=" N GLU B 56 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 12.266A pdb=" N ASP B 58 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 12.821A pdb=" N LEU B 60 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N THR B 417 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 14.610A pdb=" N GLN B 62 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 13.958A pdb=" N ALA B 415 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.256A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.270A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 559 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP B 642 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 561 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 224 removed outlier: 6.972A pdb=" N GLU C 56 " --> pdb=" O PRO C 421 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N ASP C 58 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 12.807A pdb=" N LEU C 60 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 13.046A pdb=" N THR C 417 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 14.497A pdb=" N GLN C 62 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 13.846A pdb=" N ALA C 415 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.737A pdb=" N ILE C 156 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.322A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.271A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 692 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.448A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.280A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.254A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 559 " --> pdb=" O ILE D 640 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP D 642 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE D 561 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 7.096A pdb=" N GLU E 56 " --> pdb=" O PRO E 421 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N ASP E 58 " --> pdb=" O PRO E 419 " (cutoff:3.500A) removed outlier: 12.583A pdb=" N LEU E 60 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 12.881A pdb=" N THR E 417 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 14.477A pdb=" N GLN E 62 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 13.888A pdb=" N ALA E 415 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.421A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.103A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU E 559 " --> pdb=" O ILE E 640 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASP E 642 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE E 561 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 6.887A pdb=" N GLU F 56 " --> pdb=" O PRO F 421 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N ASP F 58 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 12.823A pdb=" N LEU F 60 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 12.914A pdb=" N THR F 417 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 14.210A pdb=" N GLN F 62 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 13.603A pdb=" N ALA F 415 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 removed outlier: 3.574A pdb=" N ILE F 156 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.434A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.317A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU F 559 " --> pdb=" O ILE F 640 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP F 642 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE F 561 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 224 removed outlier: 7.001A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.158A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 7.324A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 224 removed outlier: 8.593A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 removed outlier: 4.034A pdb=" N ILE H 156 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.188A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.316A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) 2105 hydrogen bonds defined for protein. 6201 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: 8.91 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9779 1.33 - 1.45: 5703 1.45 - 1.57: 21873 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 37565 Sorted by residual: bond pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" N ILE G 260 " pdb=" CA ILE G 260 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.30e-02 5.92e+03 6.53e+00 bond pdb=" C GLN G 206 " pdb=" N LEU G 207 " ideal model delta sigma weight residual 1.331 1.282 0.049 2.07e-02 2.33e+03 5.63e+00 bond pdb=" N ARG G 262 " pdb=" CA ARG G 262 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.96e+00 bond pdb=" CA LYS D 580 " pdb=" C LYS D 580 " ideal model delta sigma weight residual 1.530 1.505 0.025 1.17e-02 7.31e+03 4.66e+00 ... (remaining 37560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 50084 2.30 - 4.61: 635 4.61 - 6.91: 104 6.91 - 9.22: 22 9.22 - 11.52: 3 Bond angle restraints: 50848 Sorted by residual: angle pdb=" N GLY B 575 " pdb=" CA GLY B 575 " pdb=" C GLY B 575 " ideal model delta sigma weight residual 112.68 101.32 11.36 1.26e+00 6.30e-01 8.13e+01 angle pdb=" N MET H 573 " pdb=" CA MET H 573 " pdb=" C MET H 573 " ideal model delta sigma weight residual 111.36 119.04 -7.68 1.09e+00 8.42e-01 4.97e+01 angle pdb=" N THR A 229 " pdb=" CA THR A 229 " pdb=" C THR A 229 " ideal model delta sigma weight residual 110.35 119.45 -9.10 1.36e+00 5.41e-01 4.48e+01 angle pdb=" N LYS H 580 " pdb=" CA LYS H 580 " pdb=" C LYS H 580 " ideal model delta sigma weight residual 111.52 120.07 -8.55 1.40e+00 5.10e-01 3.73e+01 angle pdb=" N GLY A 603 " pdb=" CA GLY A 603 " pdb=" C GLY A 603 " ideal model delta sigma weight residual 114.64 106.91 7.73 1.40e+00 5.10e-01 3.05e+01 ... (remaining 50843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 21540 17.94 - 35.88: 1262 35.88 - 53.82: 141 53.82 - 71.76: 35 71.76 - 89.70: 20 Dihedral angle restraints: 22998 sinusoidal: 9220 harmonic: 13778 Sorted by residual: dihedral pdb=" CA HIS F 576 " pdb=" C HIS F 576 " pdb=" N LYS F 577 " pdb=" CA LYS F 577 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA HIS D 576 " pdb=" C HIS D 576 " pdb=" N LYS D 577 " pdb=" CA LYS D 577 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA HIS G 576 " pdb=" C HIS G 576 " pdb=" N LYS G 577 " pdb=" CA LYS G 577 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 22995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5323 0.075 - 0.149: 686 0.149 - 0.224: 10 0.224 - 0.298: 5 0.298 - 0.373: 4 Chirality restraints: 6028 Sorted by residual: chirality pdb=" CA LYS H 580 " pdb=" N LYS H 580 " pdb=" C LYS H 580 " pdb=" CB LYS H 580 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA LYS D 580 " pdb=" N LYS D 580 " pdb=" C LYS D 580 " pdb=" CB LYS D 580 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA LYS B 580 " pdb=" N LYS B 580 " pdb=" C LYS B 580 " pdb=" CB LYS B 580 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 6025 not shown) Planarity restraints: 6509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 622 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO H 623 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 623 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 623 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 131 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 132 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 197 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B 198 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " -0.028 5.00e-02 4.00e+02 ... (remaining 6506 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 143 2.42 - 3.04: 23588 3.04 - 3.66: 55979 3.66 - 4.28: 86156 4.28 - 4.90: 142573 Nonbonded interactions: 308439 Sorted by model distance: nonbonded pdb=" OG SER D 86 " pdb=" OD2 ASP D 224 " model vdw 1.796 3.040 nonbonded pdb=" O ASP F 224 " pdb=" O MET F 231 " model vdw 1.924 3.040 nonbonded pdb=" O ASP B 224 " pdb=" O MET B 231 " model vdw 2.036 3.040 nonbonded pdb=" OE1 GLU H 89 " pdb=" OH TYR H 255 " model vdw 2.041 3.040 nonbonded pdb=" OE1 GLU B 89 " pdb=" OH TYR B 255 " model vdw 2.100 3.040 ... (remaining 308434 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 279 or resid 385 through 721)) selection = chain 'B' selection = (chain 'C' and (resid 17 through 279 or resid 385 through 721)) selection = (chain 'D' and (resid 17 through 279 or resid 385 through 721)) selection = (chain 'F' and (resid 17 through 279 or resid 385 through 721)) selection = chain 'G' selection = (chain 'H' and (resid 17 through 279 or resid 385 through 721)) } 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 32.950 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.080 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:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.006 0.073 37565 Z= 0.240 Angle : 0.700 11.520 50848 Z= 0.393 Chirality : 0.048 0.373 6028 Planarity : 0.004 0.073 6509 Dihedral : 11.665 89.700 14120 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.02 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4708 helix: 0.90 (0.11), residues: 2348 sheet: -0.03 (0.18), residues: 719 loop : -1.56 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 394 TYR 0.022 0.002 TYR B 606 PHE 0.030 0.002 PHE H 574 TRP 0.007 0.001 TRP H 631 HIS 0.006 0.001 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00553 (37565) covalent geometry : angle 0.69979 (50848) hydrogen bonds : bond 0.12430 ( 2105) hydrogen bonds : angle 5.85915 ( 6201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 627 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8295 (mp) cc_final: 0.7816 (mp) REVERT: A 193 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 177 VAL cc_start: 0.8635 (t) cc_final: 0.8229 (t) REVERT: D 185 LYS cc_start: 0.7798 (mppt) cc_final: 0.7408 (tptp) REVERT: D 187 ILE cc_start: 0.8599 (mt) cc_final: 0.8370 (mp) REVERT: D 394 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7464 (ttm-80) REVERT: D 621 MET cc_start: 0.8811 (mtp) cc_final: 0.8586 (mtm) REVERT: E 136 ASP cc_start: 0.8143 (t70) cc_final: 0.7749 (t0) REVERT: G 139 ARG cc_start: 0.7564 (ttt-90) cc_final: 0.7264 (ttt90) REVERT: G 174 LEU cc_start: 0.8331 (mp) cc_final: 0.7362 (mp) REVERT: H 101 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7944 (tttm) REVERT: H 177 VAL cc_start: 0.9189 (t) cc_final: 0.8967 (t) outliers start: 1 outliers final: 4 residues processed: 628 average time/residue: 0.5865 time to fit residues: 452.6071 Evaluate side-chains 467 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 463 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain H residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 470 optimal weight: 0.0970 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 323 ASN A 361 ASN A 393 ASN A 589 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN C 175 ASN D 320 ASN D 390 GLN E 258 GLN E 259 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN G 175 ASN G 206 GLN H 175 ASN H 420 ASN H 710 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.160718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114004 restraints weight = 50197.030| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.18 r_work: 0.3176 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 37565 Z= 0.207 Angle : 0.655 11.533 50848 Z= 0.331 Chirality : 0.046 0.357 6028 Planarity : 0.004 0.065 6509 Dihedral : 4.951 81.169 5118 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.16 % Allowed : 9.06 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4708 helix: 1.30 (0.11), residues: 2384 sheet: 0.21 (0.18), residues: 683 loop : -1.51 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 21 TYR 0.016 0.001 TYR D 388 PHE 0.022 0.002 PHE D 273 TRP 0.007 0.001 TRP C 631 HIS 0.006 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00492 (37565) covalent geometry : angle 0.65465 (50848) hydrogen bonds : bond 0.04354 ( 2105) hydrogen bonds : angle 4.77211 ( 6201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 531 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 321 GLN cc_start: 0.9212 (mt0) cc_final: 0.8854 (mp10) REVERT: A 323 ASN cc_start: 0.8650 (t0) cc_final: 0.8342 (t0) REVERT: B 89 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 193 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 707 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7488 (tpt-90) REVERT: C 164 ASN cc_start: 0.8557 (p0) cc_final: 0.8350 (p0) REVERT: C 446 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8110 (tp) REVERT: C 573 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7747 (ptp) REVERT: D 185 LYS cc_start: 0.7783 (mppt) cc_final: 0.7362 (tptp) REVERT: D 187 ILE cc_start: 0.8592 (mt) cc_final: 0.8373 (mp) REVERT: D 362 LYS cc_start: 0.9236 (mmpt) cc_final: 0.9030 (mmtm) REVERT: D 390 GLN cc_start: 0.7821 (tm130) cc_final: 0.7366 (tm-30) REVERT: D 594 MET cc_start: 0.8153 (mtp) cc_final: 0.7912 (ttm) REVERT: D 621 MET cc_start: 0.9082 (mtp) cc_final: 0.8873 (mtm) REVERT: E 136 ASP cc_start: 0.8617 (t70) cc_final: 0.7804 (p0) REVERT: E 408 ASN cc_start: 0.5204 (t0) cc_final: 0.4813 (t0) REVERT: E 680 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8982 (mtt) REVERT: E 707 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8131 (ttt-90) REVERT: F 103 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8663 (mp) REVERT: F 195 ASP cc_start: 0.8302 (t0) cc_final: 0.7792 (t0) REVERT: G 23 ILE cc_start: 0.8848 (mm) cc_final: 0.8569 (mp) REVERT: G 139 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8145 (ttp80) REVERT: G 174 LEU cc_start: 0.7140 (mp) cc_final: 0.6817 (tp) REVERT: G 181 LEU cc_start: 0.8587 (tt) cc_final: 0.8386 (tt) REVERT: H 89 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7702 (mm-30) REVERT: H 657 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8254 (mtm-85) outliers start: 88 outliers final: 29 residues processed: 566 average time/residue: 0.5811 time to fit residues: 404.9443 Evaluate side-chains 502 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 467 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 718 TYR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 680 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 152 optimal weight: 1.9990 chunk 357 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 402 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 301 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 359 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 268 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 393 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN E 408 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN H 175 ASN H 420 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117454 restraints weight = 50199.892| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.97 r_work: 0.3254 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37565 Z= 0.120 Angle : 0.588 13.338 50848 Z= 0.294 Chirality : 0.044 0.226 6028 Planarity : 0.004 0.055 6509 Dihedral : 4.404 58.705 5112 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.38 % Allowed : 10.72 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 4708 helix: 1.75 (0.11), residues: 2384 sheet: 0.43 (0.18), residues: 699 loop : -1.38 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 379 TYR 0.017 0.001 TYR D 388 PHE 0.022 0.001 PHE D 273 TRP 0.009 0.001 TRP C 631 HIS 0.004 0.001 HIS B 571 Details of bonding type rmsd covalent geometry : bond 0.00266 (37565) covalent geometry : angle 0.58812 (50848) hydrogen bonds : bond 0.03659 ( 2105) hydrogen bonds : angle 4.35452 ( 6201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 522 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7121 (tm-30) REVERT: A 262 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7241 (tmm-80) REVERT: A 321 GLN cc_start: 0.9121 (mt0) cc_final: 0.8813 (mp10) REVERT: A 323 ASN cc_start: 0.8609 (t0) cc_final: 0.8169 (t0) REVERT: A 394 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.7983 (ttp-170) REVERT: B 193 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 262 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7616 (mtm-85) REVERT: B 707 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7369 (tpt-90) REVERT: C 52 THR cc_start: 0.8922 (p) cc_final: 0.8642 (t) REVERT: C 410 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8064 (ptp90) REVERT: C 573 MET cc_start: 0.8184 (ttm) cc_final: 0.7702 (ptp) REVERT: C 621 MET cc_start: 0.8739 (mtp) cc_final: 0.8484 (mtp) REVERT: D 144 ASP cc_start: 0.8687 (t0) cc_final: 0.8429 (t0) REVERT: D 185 LYS cc_start: 0.7811 (mppt) cc_final: 0.7373 (tptp) REVERT: D 362 LYS cc_start: 0.9239 (mmpt) cc_final: 0.9027 (mmtm) REVERT: D 594 MET cc_start: 0.7903 (mtp) cc_final: 0.7699 (ttm) REVERT: D 621 MET cc_start: 0.8998 (mtp) cc_final: 0.8796 (mtm) REVERT: E 136 ASP cc_start: 0.8570 (t70) cc_final: 0.7908 (p0) REVERT: E 408 ASN cc_start: 0.5191 (t0) cc_final: 0.4595 (t0) REVERT: E 522 MET cc_start: 0.8047 (mtm) cc_final: 0.7847 (mtt) REVERT: E 680 MET cc_start: 0.9234 (mtm) cc_final: 0.8932 (mtt) REVERT: E 707 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: F 52 THR cc_start: 0.8966 (p) cc_final: 0.8743 (t) REVERT: F 103 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8503 (mp) REVERT: F 175 ASN cc_start: 0.8145 (m-40) cc_final: 0.7769 (t0) REVERT: F 195 ASP cc_start: 0.8436 (t0) cc_final: 0.7976 (t0) REVERT: F 221 SER cc_start: 0.8647 (t) cc_final: 0.8336 (m) REVERT: F 320 ASN cc_start: 0.8670 (m-40) cc_final: 0.8240 (m-40) REVERT: G 23 ILE cc_start: 0.8844 (mm) cc_final: 0.8551 (mp) REVERT: G 139 ARG cc_start: 0.8307 (ttt-90) cc_final: 0.8010 (ttp80) REVERT: G 173 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8205 (tp-100) REVERT: G 181 LEU cc_start: 0.8629 (tt) cc_final: 0.8373 (tt) REVERT: H 89 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7782 (mm-30) REVERT: H 657 ARG cc_start: 0.8379 (mmm-85) cc_final: 0.8100 (mtm-85) REVERT: H 670 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8187 (mmtp) outliers start: 97 outliers final: 30 residues processed: 562 average time/residue: 0.5655 time to fit residues: 393.1762 Evaluate side-chains 508 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 474 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 441 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 384 optimal weight: 1.9990 chunk 417 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 chunk 395 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 274 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 164 ASN H 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.161491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.113749 restraints weight = 50303.730| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.01 r_work: 0.3178 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 37565 Z= 0.258 Angle : 0.669 12.172 50848 Z= 0.333 Chirality : 0.047 0.239 6028 Planarity : 0.004 0.059 6509 Dihedral : 4.670 56.021 5112 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.85 % Allowed : 12.52 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.12), residues: 4708 helix: 1.56 (0.11), residues: 2383 sheet: 0.38 (0.19), residues: 699 loop : -1.39 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 376 TYR 0.016 0.002 TYR E 141 PHE 0.024 0.002 PHE D 273 TRP 0.007 0.001 TRP H 631 HIS 0.004 0.001 HIS D 571 Details of bonding type rmsd covalent geometry : bond 0.00623 (37565) covalent geometry : angle 0.66918 (50848) hydrogen bonds : bond 0.04239 ( 2105) hydrogen bonds : angle 4.49499 ( 6201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 501 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 321 GLN cc_start: 0.9212 (mt0) cc_final: 0.8895 (mp10) REVERT: A 323 ASN cc_start: 0.8710 (t0) cc_final: 0.8306 (t0) REVERT: A 376 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7362 (ttp80) REVERT: A 380 ASP cc_start: 0.8482 (m-30) cc_final: 0.8230 (m-30) REVERT: B 136 ASP cc_start: 0.7917 (t70) cc_final: 0.7460 (t0) REVERT: B 193 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 242 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8498 (mtmm) REVERT: B 707 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7414 (tpt-90) REVERT: D 144 ASP cc_start: 0.8842 (t0) cc_final: 0.8551 (t0) REVERT: D 185 LYS cc_start: 0.7792 (mppt) cc_final: 0.7506 (tptp) REVERT: D 707 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (ttm170) REVERT: E 136 ASP cc_start: 0.8606 (t70) cc_final: 0.7877 (p0) REVERT: E 408 ASN cc_start: 0.5408 (t0) cc_final: 0.4976 (t0) REVERT: E 680 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.9035 (mtt) REVERT: F 103 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8671 (mp) REVERT: F 136 ASP cc_start: 0.8430 (t70) cc_final: 0.7803 (t0) REVERT: F 195 ASP cc_start: 0.8545 (t0) cc_final: 0.8151 (t0) REVERT: F 320 ASN cc_start: 0.8663 (m-40) cc_final: 0.8057 (m-40) REVERT: G 23 ILE cc_start: 0.8841 (mm) cc_final: 0.8553 (mp) REVERT: G 139 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.7986 (ttp80) REVERT: G 174 LEU cc_start: 0.8479 (tm) cc_final: 0.7975 (mt) REVERT: G 181 LEU cc_start: 0.8733 (tt) cc_final: 0.8420 (tt) REVERT: G 523 GLU cc_start: 0.7906 (pp20) cc_final: 0.7696 (pp20) REVERT: H 63 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8233 (mm) REVERT: H 89 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7682 (mm-30) REVERT: H 657 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8254 (mtm-85) outliers start: 116 outliers final: 46 residues processed: 555 average time/residue: 0.5812 time to fit residues: 397.8852 Evaluate side-chains 515 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 463 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain B residue 718 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 707 ARG Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 107 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 397 optimal weight: 1.9990 chunk 347 optimal weight: 0.6980 chunk 337 optimal weight: 0.9980 chunk 466 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 293 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN C 175 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.163124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117105 restraints weight = 50051.089| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.05 r_work: 0.3230 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37565 Z= 0.131 Angle : 0.599 15.601 50848 Z= 0.297 Chirality : 0.044 0.281 6028 Planarity : 0.004 0.055 6509 Dihedral : 4.337 53.491 5112 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.43 % Allowed : 13.67 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 4708 helix: 1.88 (0.11), residues: 2379 sheet: 0.43 (0.19), residues: 679 loop : -1.31 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 379 TYR 0.011 0.001 TYR B 569 PHE 0.024 0.001 PHE D 273 TRP 0.008 0.001 TRP C 631 HIS 0.003 0.001 HIS D 710 Details of bonding type rmsd covalent geometry : bond 0.00303 (37565) covalent geometry : angle 0.59894 (50848) hydrogen bonds : bond 0.03548 ( 2105) hydrogen bonds : angle 4.24387 ( 6201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 507 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7910 (tm-30) cc_final: 0.6993 (tm-30) REVERT: A 210 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 262 ARG cc_start: 0.6868 (tmm-80) cc_final: 0.6658 (tmm-80) REVERT: A 321 GLN cc_start: 0.9166 (mt0) cc_final: 0.8877 (mp10) REVERT: A 323 ASN cc_start: 0.8691 (t0) cc_final: 0.8274 (t0) REVERT: A 444 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8555 (mt) REVERT: B 89 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 136 ASP cc_start: 0.7904 (t70) cc_final: 0.7452 (t0) REVERT: B 174 LEU cc_start: 0.8469 (mm) cc_final: 0.8211 (mp) REVERT: B 193 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7414 (tm-30) REVERT: B 707 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7411 (tpt-90) REVERT: C 52 THR cc_start: 0.8923 (p) cc_final: 0.8635 (t) REVERT: C 573 MET cc_start: 0.8232 (ttm) cc_final: 0.7773 (ptp) REVERT: C 708 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: D 144 ASP cc_start: 0.8790 (t0) cc_final: 0.8494 (t0) REVERT: D 185 LYS cc_start: 0.7781 (mppt) cc_final: 0.7468 (tptt) REVERT: D 195 ASP cc_start: 0.8642 (t70) cc_final: 0.8368 (t0) REVERT: D 355 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8236 (tm-30) REVERT: D 388 TYR cc_start: 0.8814 (t80) cc_final: 0.8593 (t80) REVERT: D 707 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8065 (ttm110) REVERT: E 136 ASP cc_start: 0.8527 (t70) cc_final: 0.7913 (p0) REVERT: E 161 ASP cc_start: 0.8585 (p0) cc_final: 0.8304 (p0) REVERT: E 408 ASN cc_start: 0.5448 (t0) cc_final: 0.4957 (t0) REVERT: E 680 MET cc_start: 0.9260 (mtm) cc_final: 0.9016 (mtt) REVERT: E 707 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7959 (ttp-170) REVERT: F 103 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8473 (mp) REVERT: F 175 ASN cc_start: 0.8345 (m-40) cc_final: 0.8075 (t0) REVERT: F 195 ASP cc_start: 0.8518 (t0) cc_final: 0.8182 (t0) REVERT: G 23 ILE cc_start: 0.8803 (mm) cc_final: 0.8515 (mp) REVERT: G 139 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.8007 (ttp80) REVERT: G 174 LEU cc_start: 0.8605 (tm) cc_final: 0.8178 (mt) REVERT: G 181 LEU cc_start: 0.8671 (tt) cc_final: 0.8345 (tt) REVERT: H 63 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7416 (pp) REVERT: H 190 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8266 (tm) REVERT: H 425 LYS cc_start: 0.7914 (mttt) cc_final: 0.7539 (mttp) REVERT: H 657 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8127 (mtm-85) outliers start: 99 outliers final: 35 residues processed: 558 average time/residue: 0.5701 time to fit residues: 393.7990 Evaluate side-chains 512 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 468 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 708 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 707 ARG Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 461 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 431 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 chunk 304 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 405 optimal weight: 8.9990 chunk 281 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 414 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 578 ASN ** G 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.161367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.114677 restraints weight = 50104.199| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.24 r_work: 0.3179 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 37565 Z= 0.199 Angle : 0.649 12.671 50848 Z= 0.323 Chirality : 0.046 0.330 6028 Planarity : 0.004 0.067 6509 Dihedral : 4.482 52.992 5112 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.87 % Allowed : 14.23 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.12), residues: 4708 helix: 1.80 (0.11), residues: 2379 sheet: 0.41 (0.19), residues: 674 loop : -1.29 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 376 TYR 0.017 0.001 TYR F 255 PHE 0.022 0.001 PHE D 273 TRP 0.007 0.001 TRP H 631 HIS 0.004 0.001 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00476 (37565) covalent geometry : angle 0.64905 (50848) hydrogen bonds : bond 0.03906 ( 2105) hydrogen bonds : angle 4.33245 ( 6201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 487 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7943 (tm-30) cc_final: 0.6941 (tm-30) REVERT: A 210 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 323 ASN cc_start: 0.8722 (t0) cc_final: 0.8187 (t0) REVERT: A 376 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7384 (ttp80) REVERT: A 394 ARG cc_start: 0.8655 (mtp85) cc_final: 0.7717 (ttp-170) REVERT: B 89 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 136 ASP cc_start: 0.7936 (t70) cc_final: 0.7491 (t0) REVERT: B 193 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7414 (tm-30) REVERT: B 707 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7424 (tpt-90) REVERT: D 144 ASP cc_start: 0.8817 (t0) cc_final: 0.8513 (t0) REVERT: D 185 LYS cc_start: 0.7823 (mppt) cc_final: 0.7527 (tptt) REVERT: D 195 ASP cc_start: 0.8720 (t70) cc_final: 0.8465 (t0) REVERT: D 225 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7743 (pt) REVERT: D 394 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7163 (ttm-80) REVERT: D 707 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8162 (ttm110) REVERT: E 136 ASP cc_start: 0.8537 (t70) cc_final: 0.7861 (p0) REVERT: E 161 ASP cc_start: 0.8556 (p0) cc_final: 0.8326 (p0) REVERT: E 195 ASP cc_start: 0.8931 (t0) cc_final: 0.8691 (t0) REVERT: E 408 ASN cc_start: 0.5443 (t0) cc_final: 0.5031 (t0) REVERT: E 680 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9048 (mtt) REVERT: F 103 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8648 (mp) REVERT: F 139 ARG cc_start: 0.8152 (tpt-90) cc_final: 0.7896 (tpt170) REVERT: F 195 ASP cc_start: 0.8560 (t0) cc_final: 0.8232 (OUTLIER) REVERT: G 23 ILE cc_start: 0.8826 (mm) cc_final: 0.8539 (mp) REVERT: G 139 ARG cc_start: 0.8387 (ttt-90) cc_final: 0.8040 (ttp80) REVERT: G 174 LEU cc_start: 0.8522 (tm) cc_final: 0.8212 (mt) REVERT: G 181 LEU cc_start: 0.8688 (tt) cc_final: 0.8345 (tt) REVERT: H 63 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8194 (mp) REVERT: H 89 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7442 (mm-30) REVERT: H 425 LYS cc_start: 0.7961 (mttt) cc_final: 0.7530 (mptt) REVERT: H 657 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8261 (mtm-85) outliers start: 117 outliers final: 54 residues processed: 543 average time/residue: 0.5455 time to fit residues: 367.8308 Evaluate side-chains 529 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 468 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain B residue 718 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 707 ARG Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 76 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 358 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 261 optimal weight: 0.6980 chunk 259 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 317 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN D 183 ASN D 351 GLN E 414 ASN F 259 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 578 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114681 restraints weight = 47719.676| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.23 r_work: 0.3067 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37565 Z= 0.134 Angle : 0.614 13.389 50848 Z= 0.303 Chirality : 0.045 0.317 6028 Planarity : 0.004 0.063 6509 Dihedral : 4.287 52.089 5112 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.21 % Allowed : 15.29 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.12), residues: 4708 helix: 1.97 (0.11), residues: 2379 sheet: 0.45 (0.19), residues: 674 loop : -1.25 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.014 0.001 TYR F 255 PHE 0.029 0.001 PHE D 327 TRP 0.007 0.001 TRP C 631 HIS 0.003 0.001 HIS D 710 Details of bonding type rmsd covalent geometry : bond 0.00310 (37565) covalent geometry : angle 0.61431 (50848) hydrogen bonds : bond 0.03548 ( 2105) hydrogen bonds : angle 4.19179 ( 6201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 501 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7831 (tm-30) cc_final: 0.6858 (tm-30) REVERT: A 210 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7840 (tp) REVERT: A 282 ARG cc_start: 0.8634 (tpt90) cc_final: 0.8326 (mmm160) REVERT: A 321 GLN cc_start: 0.9166 (mt0) cc_final: 0.8827 (mp10) REVERT: A 323 ASN cc_start: 0.8697 (t0) cc_final: 0.8157 (t0) REVERT: A 372 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: A 376 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7674 (ttp80) REVERT: A 380 ASP cc_start: 0.8469 (m-30) cc_final: 0.8132 (m-30) REVERT: A 394 ARG cc_start: 0.8651 (mtp85) cc_final: 0.7790 (ttp-170) REVERT: A 444 LEU cc_start: 0.8768 (mp) cc_final: 0.8538 (mt) REVERT: A 517 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8693 (mp) REVERT: B 89 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 136 ASP cc_start: 0.7835 (t70) cc_final: 0.7359 (t0) REVERT: B 137 ILE cc_start: 0.8715 (mt) cc_final: 0.8310 (mp) REVERT: B 193 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 52 THR cc_start: 0.8945 (p) cc_final: 0.8666 (t) REVERT: D 144 ASP cc_start: 0.8742 (t0) cc_final: 0.8444 (t0) REVERT: D 185 LYS cc_start: 0.7756 (mppt) cc_final: 0.7500 (tptt) REVERT: D 195 ASP cc_start: 0.8715 (t70) cc_final: 0.8483 (t0) REVERT: D 225 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7743 (pt) REVERT: D 707 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8025 (ttm110) REVERT: E 136 ASP cc_start: 0.8464 (t70) cc_final: 0.7915 (p0) REVERT: E 161 ASP cc_start: 0.8517 (p0) cc_final: 0.8254 (p0) REVERT: E 195 ASP cc_start: 0.8848 (t0) cc_final: 0.8600 (t0) REVERT: E 408 ASN cc_start: 0.5552 (t0) cc_final: 0.5090 (t0) REVERT: E 680 MET cc_start: 0.9338 (mtm) cc_final: 0.9113 (mtt) REVERT: F 89 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: F 103 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8534 (mp) REVERT: F 195 ASP cc_start: 0.8551 (t0) cc_final: 0.8263 (OUTLIER) REVERT: F 210 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7593 (tp) REVERT: G 23 ILE cc_start: 0.8848 (mm) cc_final: 0.8572 (mp) REVERT: G 139 ARG cc_start: 0.8333 (ttt-90) cc_final: 0.8058 (ttp80) REVERT: G 174 LEU cc_start: 0.8517 (tm) cc_final: 0.8299 (mt) REVERT: G 181 LEU cc_start: 0.8700 (tt) cc_final: 0.8376 (tt) REVERT: G 594 MET cc_start: 0.8334 (mtm) cc_final: 0.8118 (mtp) REVERT: H 63 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7418 (pp) REVERT: H 89 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7394 (mm-30) REVERT: H 425 LYS cc_start: 0.7917 (mttt) cc_final: 0.7525 (mptt) REVERT: H 657 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8198 (mtm-85) REVERT: H 670 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8111 (mmtp) outliers start: 90 outliers final: 53 residues processed: 547 average time/residue: 0.5587 time to fit residues: 379.1215 Evaluate side-chains 534 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 473 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 707 ARG Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 141 TYR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 101 LYS Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 146 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 471 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 221 optimal weight: 0.0020 chunk 70 optimal weight: 5.9990 chunk 134 optimal weight: 0.0470 chunk 353 optimal weight: 1.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN D 351 GLN E 164 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114798 restraints weight = 47332.120| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.22 r_work: 0.3048 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37565 Z= 0.138 Angle : 0.628 14.047 50848 Z= 0.310 Chirality : 0.045 0.313 6028 Planarity : 0.004 0.061 6509 Dihedral : 4.244 51.543 5112 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 15.80 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4708 helix: 2.00 (0.11), residues: 2382 sheet: 0.48 (0.19), residues: 668 loop : -1.19 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 379 TYR 0.023 0.001 TYR D 388 PHE 0.050 0.001 PHE D 273 TRP 0.007 0.001 TRP C 631 HIS 0.003 0.001 HIS D 710 Details of bonding type rmsd covalent geometry : bond 0.00321 (37565) covalent geometry : angle 0.62813 (50848) hydrogen bonds : bond 0.03553 ( 2105) hydrogen bonds : angle 4.17392 ( 6201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 502 time to evaluate : 1.268 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 23 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9003 (mp) REVERT: A 193 GLU cc_start: 0.7825 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 195 ASP cc_start: 0.8618 (t0) cc_final: 0.8057 (t0) REVERT: A 210 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7792 (tp) REVERT: A 323 ASN cc_start: 0.8685 (t0) cc_final: 0.8181 (t0) REVERT: A 372 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: A 376 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7622 (ttp80) REVERT: A 380 ASP cc_start: 0.8356 (m-30) cc_final: 0.7936 (m-30) REVERT: A 394 ARG cc_start: 0.8654 (mtp85) cc_final: 0.7800 (ttp-170) REVERT: A 444 LEU cc_start: 0.8760 (mp) cc_final: 0.8524 (mt) REVERT: B 89 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8283 (mm-30) REVERT: B 136 ASP cc_start: 0.7776 (t70) cc_final: 0.7297 (t0) REVERT: B 137 ILE cc_start: 0.8689 (mt) cc_final: 0.8303 (mp) REVERT: B 193 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7284 (tm-30) REVERT: C 52 THR cc_start: 0.8925 (p) cc_final: 0.8630 (t) REVERT: D 144 ASP cc_start: 0.8697 (t0) cc_final: 0.8403 (t0) REVERT: D 225 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7637 (pt) REVERT: E 136 ASP cc_start: 0.8461 (t70) cc_final: 0.7931 (p0) REVERT: E 161 ASP cc_start: 0.8474 (p0) cc_final: 0.8233 (p0) REVERT: E 195 ASP cc_start: 0.8898 (t0) cc_final: 0.8697 (t0) REVERT: E 408 ASN cc_start: 0.5543 (t0) cc_final: 0.5058 (t0) REVERT: E 606 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8694 (p90) REVERT: E 680 MET cc_start: 0.9342 (mtm) cc_final: 0.9114 (mtt) REVERT: F 89 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: F 103 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8459 (mp) REVERT: F 195 ASP cc_start: 0.8504 (t0) cc_final: 0.8241 (t0) REVERT: F 210 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7542 (tp) REVERT: F 221 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8317 (m) REVERT: G 23 ILE cc_start: 0.8804 (mm) cc_final: 0.8522 (mp) REVERT: G 139 ARG cc_start: 0.8280 (ttt-90) cc_final: 0.8027 (ttp80) REVERT: G 181 LEU cc_start: 0.8672 (tt) cc_final: 0.8357 (tt) REVERT: G 578 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7319 (t0) REVERT: G 594 MET cc_start: 0.8224 (mtm) cc_final: 0.8004 (mtp) REVERT: G 681 LYS cc_start: 0.9173 (mttt) cc_final: 0.8822 (mtmp) REVERT: H 63 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7401 (pp) REVERT: H 89 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7364 (mm-30) REVERT: H 161 ASP cc_start: 0.8721 (p0) cc_final: 0.8240 (p0) REVERT: H 425 LYS cc_start: 0.7857 (mttt) cc_final: 0.7470 (mptt) REVERT: H 657 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8181 (mtm-85) outliers start: 94 outliers final: 54 residues processed: 553 average time/residue: 0.5512 time to fit residues: 380.5906 Evaluate side-chains 544 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 479 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 708 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 606 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain G residue 578 ASN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 101 LYS Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 541 THR Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 259 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 301 optimal weight: 0.0770 chunk 181 optimal weight: 1.9990 chunk 297 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 227 optimal weight: 0.0370 chunk 267 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115981 restraints weight = 47816.274| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.23 r_work: 0.3119 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37565 Z= 0.124 Angle : 0.643 14.678 50848 Z= 0.318 Chirality : 0.045 0.340 6028 Planarity : 0.004 0.062 6509 Dihedral : 4.165 51.384 5112 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.87 % Allowed : 16.37 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 4708 helix: 2.05 (0.11), residues: 2385 sheet: 0.51 (0.19), residues: 668 loop : -1.15 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 379 TYR 0.023 0.001 TYR F 343 PHE 0.050 0.001 PHE D 273 TRP 0.007 0.001 TRP C 631 HIS 0.004 0.000 HIS G 576 Details of bonding type rmsd covalent geometry : bond 0.00284 (37565) covalent geometry : angle 0.64341 (50848) hydrogen bonds : bond 0.03434 ( 2105) hydrogen bonds : angle 4.13672 ( 6201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 504 time to evaluate : 1.333 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 23 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9027 (mp) REVERT: A 193 GLU cc_start: 0.7795 (tm-30) cc_final: 0.6827 (tm-30) REVERT: A 195 ASP cc_start: 0.8608 (t0) cc_final: 0.8105 (t0) REVERT: A 210 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.7795 (tp) REVERT: A 282 ARG cc_start: 0.8595 (mmm160) cc_final: 0.8323 (mmm160) REVERT: A 372 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: A 380 ASP cc_start: 0.8339 (m-30) cc_final: 0.8075 (m-30) REVERT: A 388 TYR cc_start: 0.8593 (t80) cc_final: 0.8358 (t80) REVERT: A 394 ARG cc_start: 0.8644 (mtp85) cc_final: 0.7806 (ttp-170) REVERT: A 444 LEU cc_start: 0.8747 (mp) cc_final: 0.8512 (mt) REVERT: B 89 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 136 ASP cc_start: 0.7777 (t70) cc_final: 0.7310 (t0) REVERT: B 137 ILE cc_start: 0.8693 (mt) cc_final: 0.8314 (mp) REVERT: B 193 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7258 (tm-30) REVERT: B 195 ASP cc_start: 0.8889 (t70) cc_final: 0.8372 (t0) REVERT: C 52 THR cc_start: 0.8938 (p) cc_final: 0.8678 (t) REVERT: C 163 GLU cc_start: 0.7906 (pp20) cc_final: 0.7192 (pp20) REVERT: C 164 ASN cc_start: 0.8604 (p0) cc_final: 0.8300 (p0) REVERT: C 573 MET cc_start: 0.8214 (ttm) cc_final: 0.7801 (ptp) REVERT: D 144 ASP cc_start: 0.8715 (t0) cc_final: 0.8415 (t0) REVERT: D 195 ASP cc_start: 0.8604 (t0) cc_final: 0.8386 (t0) REVERT: E 136 ASP cc_start: 0.8475 (t70) cc_final: 0.7989 (p0) REVERT: E 161 ASP cc_start: 0.8452 (p0) cc_final: 0.8185 (p0) REVERT: E 195 ASP cc_start: 0.8819 (t0) cc_final: 0.8552 (t0) REVERT: E 408 ASN cc_start: 0.5545 (t0) cc_final: 0.5047 (t0) REVERT: E 680 MET cc_start: 0.9309 (mtm) cc_final: 0.9086 (mtt) REVERT: F 103 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8472 (mp) REVERT: F 136 ASP cc_start: 0.8179 (t70) cc_final: 0.7505 (p0) REVERT: F 139 ARG cc_start: 0.8190 (tpt90) cc_final: 0.7709 (tpt170) REVERT: F 195 ASP cc_start: 0.8453 (t0) cc_final: 0.8225 (t0) REVERT: F 210 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7568 (tp) REVERT: G 23 ILE cc_start: 0.8831 (mm) cc_final: 0.8546 (mp) REVERT: G 174 LEU cc_start: 0.8381 (mt) cc_final: 0.7879 (tp) REVERT: G 181 LEU cc_start: 0.8678 (tt) cc_final: 0.8393 (tt) REVERT: G 578 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7465 (t0) REVERT: G 681 LYS cc_start: 0.9135 (mttt) cc_final: 0.8800 (mtmp) REVERT: H 63 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7411 (pp) REVERT: H 89 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7361 (mm-30) REVERT: H 103 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8865 (mp) REVERT: H 127 LEU cc_start: 0.8989 (mm) cc_final: 0.8647 (mm) REVERT: H 190 LEU cc_start: 0.8554 (tm) cc_final: 0.8244 (tm) REVERT: H 425 LYS cc_start: 0.7845 (mttt) cc_final: 0.7469 (mptt) REVERT: H 657 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8168 (mtm-85) outliers start: 76 outliers final: 46 residues processed: 543 average time/residue: 0.5240 time to fit residues: 356.8516 Evaluate side-chains 536 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 482 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain G residue 578 ASN Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 101 LYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 54 optimal weight: 0.7980 chunk 381 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 319 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 349 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 393 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 HIS E 164 ASN F 589 GLN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.159001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116000 restraints weight = 47585.043| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.26 r_work: 0.3117 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37565 Z= 0.129 Angle : 0.656 13.763 50848 Z= 0.322 Chirality : 0.045 0.325 6028 Planarity : 0.004 0.061 6509 Dihedral : 4.142 51.268 5112 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.60 % Allowed : 17.13 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4708 helix: 2.06 (0.11), residues: 2385 sheet: 0.57 (0.19), residues: 665 loop : -1.13 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 379 TYR 0.026 0.001 TYR F 141 PHE 0.050 0.001 PHE D 273 TRP 0.007 0.001 TRP C 631 HIS 0.003 0.000 HIS D 710 Details of bonding type rmsd covalent geometry : bond 0.00299 (37565) covalent geometry : angle 0.65574 (50848) hydrogen bonds : bond 0.03462 ( 2105) hydrogen bonds : angle 4.13905 ( 6201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 496 time to evaluate : 1.616 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 23 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9020 (mp) REVERT: A 193 GLU cc_start: 0.7799 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 195 ASP cc_start: 0.8597 (t0) cc_final: 0.8121 (t0) REVERT: A 210 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7793 (tp) REVERT: A 376 ARG cc_start: 0.8014 (tmm-80) cc_final: 0.7814 (ttp80) REVERT: A 380 ASP cc_start: 0.8361 (m-30) cc_final: 0.8013 (m-30) REVERT: A 394 ARG cc_start: 0.8622 (mtp85) cc_final: 0.7775 (ttp-170) REVERT: B 89 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 136 ASP cc_start: 0.7755 (t70) cc_final: 0.7290 (t0) REVERT: B 137 ILE cc_start: 0.8701 (mt) cc_final: 0.8330 (mp) REVERT: B 193 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7256 (tm-30) REVERT: B 195 ASP cc_start: 0.8860 (t70) cc_final: 0.8367 (t0) REVERT: B 463 GLU cc_start: 0.8368 (pt0) cc_final: 0.8089 (pt0) REVERT: C 52 THR cc_start: 0.8930 (p) cc_final: 0.8679 (t) REVERT: C 573 MET cc_start: 0.8254 (ttm) cc_final: 0.7775 (ptp) REVERT: D 144 ASP cc_start: 0.8737 (t0) cc_final: 0.8445 (t0) REVERT: E 136 ASP cc_start: 0.8453 (t70) cc_final: 0.7981 (p0) REVERT: E 161 ASP cc_start: 0.8404 (p0) cc_final: 0.8140 (p0) REVERT: E 408 ASN cc_start: 0.5555 (t0) cc_final: 0.5066 (t0) REVERT: E 521 MET cc_start: 0.8803 (mtp) cc_final: 0.8572 (mtp) REVERT: E 680 MET cc_start: 0.9320 (mtm) cc_final: 0.9106 (mtt) REVERT: F 89 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: F 103 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8466 (mp) REVERT: F 136 ASP cc_start: 0.8129 (t70) cc_final: 0.7534 (p0) REVERT: F 195 ASP cc_start: 0.8484 (t0) cc_final: 0.8250 (t0) REVERT: F 210 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7564 (tp) REVERT: G 23 ILE cc_start: 0.8832 (mm) cc_final: 0.8545 (mp) REVERT: G 139 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7722 (ttt90) REVERT: G 174 LEU cc_start: 0.8382 (mt) cc_final: 0.7881 (tp) REVERT: G 609 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8485 (ptt90) REVERT: G 681 LYS cc_start: 0.9127 (mttt) cc_final: 0.8785 (mtmp) REVERT: G 707 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8043 (ttp-170) REVERT: H 89 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7373 (mm-30) REVERT: H 103 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8856 (mp) REVERT: H 127 LEU cc_start: 0.8970 (mm) cc_final: 0.8644 (mm) REVERT: H 190 LEU cc_start: 0.8549 (tm) cc_final: 0.8301 (tm) REVERT: H 425 LYS cc_start: 0.7814 (mttt) cc_final: 0.7475 (mptt) REVERT: H 657 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8169 (mtm-85) outliers start: 65 outliers final: 47 residues processed: 535 average time/residue: 0.5312 time to fit residues: 355.1631 Evaluate side-chains 533 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 479 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 672 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 101 LYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 541 THR Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 101 optimal weight: 0.8980 chunk 334 optimal weight: 0.5980 chunk 430 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 230 optimal weight: 0.0770 chunk 418 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 166 optimal weight: 3.9990 chunk 390 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 164 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 576 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 = 0.3889 r_free = 0.3889 target = 0.158788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116080 restraints weight = 47739.270| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.25 r_work: 0.3105 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.342 37565 Z= 0.183 Angle : 0.750 61.586 50848 Z= 0.365 Chirality : 0.048 0.983 6028 Planarity : 0.004 0.114 6509 Dihedral : 4.142 51.262 5112 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.52 % Allowed : 17.23 % Favored : 81.25 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4708 helix: 2.07 (0.11), residues: 2385 sheet: 0.57 (0.19), residues: 665 loop : -1.14 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 282 TYR 0.060 0.001 TYR D 343 PHE 0.046 0.001 PHE D 273 TRP 0.007 0.001 TRP C 631 HIS 0.075 0.001 HIS G 576 Details of bonding type rmsd covalent geometry : bond 0.00432 (37565) covalent geometry : angle 0.74953 (50848) hydrogen bonds : bond 0.03489 ( 2105) hydrogen bonds : angle 4.15473 ( 6201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14841.42 seconds wall clock time: 252 minutes 24.24 seconds (15144.24 seconds total)