Starting phenix.real_space_refine on Fri Jan 16 21:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cye_27076/01_2026/8cye_27076.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cye_27076/01_2026/8cye_27076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cye_27076/01_2026/8cye_27076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cye_27076/01_2026/8cye_27076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cye_27076/01_2026/8cye_27076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cye_27076/01_2026/8cye_27076.map" } resolution = 3.9 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= 0.001 sd= 0.022 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 44 5.16 5 C 26510 2.51 5 N 8074 2.21 5 O 9570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44198 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "A" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "M" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "C" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "N" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "D" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "O" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "E" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "P" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "F" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "Q" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "G" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "R" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "H" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "S" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "I" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "T" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "J" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "U" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "K" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "V" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Chain: "L" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 269, 2001 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 2, 'TRANS': 266} Chain breaks: 1 bond proxies already assigned to first conformer: 1997 Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" N AILE B 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 38 " occ=0.50 residue: pdb=" N AILE A 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 38 " occ=0.50 residue: pdb=" N AILE M 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE M 38 " occ=0.50 residue: pdb=" N AILE C 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE C 38 " occ=0.50 residue: pdb=" N AILE N 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE N 38 " occ=0.50 residue: pdb=" N AILE D 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE D 38 " occ=0.50 residue: pdb=" N AILE O 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE O 38 " occ=0.50 residue: pdb=" N AILE E 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE E 38 " occ=0.50 residue: pdb=" N AILE P 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE P 38 " occ=0.50 residue: pdb=" N AILE F 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE F 38 " occ=0.50 residue: pdb=" N AILE Q 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE Q 38 " occ=0.50 residue: pdb=" N AILE G 38 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE G 38 " occ=0.50 ... (remaining 10 not shown) Time building chain proxies: 17.56, per 1000 atoms: 0.40 Number of scatterers: 44198 At special positions: 0 Unit cell: (142.56, 143.64, 257.04, 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 44 16.00 O 9570 8.00 N 8074 7.00 C 26510 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: 3.88 Conformation dependent library (CDL) restraints added in 3.4 seconds 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11176 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 25 sheets defined 73.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 8 through 34 removed outlier: 3.746A pdb=" N ALA B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 100 removed outlier: 3.758A pdb=" N GLU B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 130 Processing helix chain 'B' and resid 459 through 507 removed outlier: 3.621A pdb=" N ASN B 498 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 538 removed outlier: 4.058A pdb=" N SER B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 517 " --> pdb=" O THR B 513 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.025A pdb=" N SER B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 34 removed outlier: 3.594A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 100 removed outlier: 4.061A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 130 removed outlier: 4.417A pdb=" N GLU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 459 through 507 removed outlier: 3.643A pdb=" N ASN A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 538 removed outlier: 4.160A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.213A pdb=" N SER A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 34 removed outlier: 3.553A pdb=" N SER M 23 " --> pdb=" O ASN M 19 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER M 34 " --> pdb=" O GLU M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 100 removed outlier: 3.682A pdb=" N ASP M 70 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN M 87 " --> pdb=" O SER M 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN M 88 " --> pdb=" O GLU M 84 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL M 97 " --> pdb=" O ARG M 93 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 130 Processing helix chain 'M' and resid 164 through 169 Processing helix chain 'M' and resid 459 through 507 Processing helix chain 'M' and resid 510 through 538 removed outlier: 3.808A pdb=" N SER M 516 " --> pdb=" O ALA M 512 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS M 534 " --> pdb=" O SER M 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 539 through 547 removed outlier: 4.108A pdb=" N LEU M 543 " --> pdb=" O PRO M 539 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN M 547 " --> pdb=" O LEU M 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 34 removed outlier: 3.616A pdb=" N LYS C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 100 removed outlier: 3.841A pdb=" N ILE C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 130 Processing helix chain 'C' and resid 459 through 507 removed outlier: 3.676A pdb=" N THR C 497 " --> pdb=" O ASN C 493 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 538 removed outlier: 4.099A pdb=" N GLU C 514 " --> pdb=" O ASP C 510 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 547 removed outlier: 3.761A pdb=" N GLN C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 34 removed outlier: 3.555A pdb=" N SER N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 101 removed outlier: 3.602A pdb=" N ARG N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA N 81 " --> pdb=" O THR N 77 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.664A pdb=" N THR N 130 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 169 removed outlier: 3.860A pdb=" N GLY N 169 " --> pdb=" O SER N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 507 removed outlier: 3.714A pdb=" N ALA N 463 " --> pdb=" O ASP N 459 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN N 494 " --> pdb=" O THR N 490 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG N 505 " --> pdb=" O GLU N 501 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE N 506 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 537 removed outlier: 4.375A pdb=" N SER N 516 " --> pdb=" O ALA N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 538 through 540 No H-bonds generated for 'chain 'N' and resid 538 through 540' Processing helix chain 'N' and resid 541 through 547 removed outlier: 3.539A pdb=" N LEU N 545 " --> pdb=" O GLN N 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 34 removed outlier: 3.662A pdb=" N ALA D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 101 removed outlier: 3.703A pdb=" N ASN D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 130 Processing helix chain 'D' and resid 459 through 507 removed outlier: 3.614A pdb=" N GLN D 482 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 537 removed outlier: 4.033A pdb=" N SER D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 3.740A pdb=" N SER D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 34 removed outlier: 3.916A pdb=" N SER O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER O 34 " --> pdb=" O GLU O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 101 removed outlier: 3.708A pdb=" N GLN O 48 " --> pdb=" O ASP O 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN O 88 " --> pdb=" O GLU O 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU O 95 " --> pdb=" O ARG O 91 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR O 101 " --> pdb=" O VAL O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 130 removed outlier: 3.539A pdb=" N ASP O 110 " --> pdb=" O ASP O 106 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 459 through 507 removed outlier: 3.665A pdb=" N ALA O 463 " --> pdb=" O ASP O 459 " (cutoff:3.500A) Processing helix chain 'O' and resid 510 through 538 removed outlier: 4.263A pdb=" N SER O 516 " --> pdb=" O ALA O 512 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA O 533 " --> pdb=" O ASN O 529 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 547 removed outlier: 4.410A pdb=" N LEU O 543 " --> pdb=" O PRO O 539 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN O 547 " --> pdb=" O LEU O 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 34 removed outlier: 3.707A pdb=" N SER E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 100 removed outlier: 3.818A pdb=" N GLN E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 95 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 130 removed outlier: 3.521A pdb=" N GLU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 459 through 507 removed outlier: 3.760A pdb=" N ALA E 463 " --> pdb=" O ASP E 459 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE E 506 " --> pdb=" O ALA E 502 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 507 " --> pdb=" O GLN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 538 removed outlier: 3.747A pdb=" N SER E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 547 removed outlier: 3.547A pdb=" N GLN E 547 " --> pdb=" O LEU E 543 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.509A pdb=" N LEU P 12 " --> pdb=" O ASN P 8 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN P 17 " --> pdb=" O ILE P 13 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA P 24 " --> pdb=" O LYS P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 101 removed outlier: 4.351A pdb=" N GLN P 48 " --> pdb=" O ASP P 44 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER P 73 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN P 87 " --> pdb=" O SER P 83 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR P 101 " --> pdb=" O VAL P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 130 removed outlier: 3.527A pdb=" N THR P 130 " --> pdb=" O VAL P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 507 removed outlier: 3.730A pdb=" N VAL P 481 " --> pdb=" O SER P 477 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN P 482 " --> pdb=" O LEU P 478 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN P 483 " --> pdb=" O GLY P 479 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG P 484 " --> pdb=" O ALA P 480 " (cutoff:3.500A) Processing helix chain 'P' and resid 510 through 536 removed outlier: 4.264A pdb=" N SER P 516 " --> pdb=" O ALA P 512 " (cutoff:3.500A) Processing helix chain 'P' and resid 539 through 547 removed outlier: 4.176A pdb=" N LEU P 543 " --> pdb=" O PRO P 539 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER P 544 " --> pdb=" O GLN P 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 34 removed outlier: 3.900A pdb=" N ALA F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 100 removed outlier: 3.814A pdb=" N ASN F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 130 removed outlier: 3.561A pdb=" N ASP F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 459 through 507 removed outlier: 3.728A pdb=" N ALA F 463 " --> pdb=" O ASP F 459 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 481 " --> pdb=" O SER F 477 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN F 483 " --> pdb=" O GLY F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 536 removed outlier: 4.045A pdb=" N SER F 516 " --> pdb=" O ALA F 512 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN F 517 " --> pdb=" O THR F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 547 removed outlier: 4.209A pdb=" N LEU F 543 " --> pdb=" O PRO F 539 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 545 " --> pdb=" O GLN F 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 546 " --> pdb=" O VAL F 542 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN F 547 " --> pdb=" O LEU F 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 539 through 547' Processing helix chain 'Q' and resid 8 through 34 removed outlier: 3.860A pdb=" N LEU Q 12 " --> pdb=" O ASN Q 8 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR Q 14 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER Q 23 " --> pdb=" O ASN Q 19 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA Q 24 " --> pdb=" O LYS Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 101 removed outlier: 3.929A pdb=" N GLN Q 48 " --> pdb=" O ASP Q 44 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN Q 69 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP Q 70 " --> pdb=" O ARG Q 66 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY Q 71 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU Q 84 " --> pdb=" O GLY Q 80 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR Q 101 " --> pdb=" O VAL Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 130 removed outlier: 3.514A pdb=" N GLU Q 115 " --> pdb=" O SER Q 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR Q 130 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 169 Processing helix chain 'Q' and resid 459 through 507 removed outlier: 3.781A pdb=" N ALA Q 463 " --> pdb=" O ASP Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 510 through 536 removed outlier: 3.550A pdb=" N GLU Q 514 " --> pdb=" O ASP Q 510 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER Q 516 " --> pdb=" O ALA Q 512 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN Q 517 " --> pdb=" O THR Q 513 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET Q 518 " --> pdb=" O GLU Q 514 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER Q 519 " --> pdb=" O VAL Q 515 " (cutoff:3.500A) Processing helix chain 'Q' and resid 537 through 539 No H-bonds generated for 'chain 'Q' and resid 537 through 539' Processing helix chain 'Q' and resid 540 through 547 removed outlier: 3.875A pdb=" N SER Q 544 " --> pdb=" O GLN Q 540 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN Q 547 " --> pdb=" O LEU Q 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 34 removed outlier: 4.003A pdb=" N THR G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN G 17 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 101 removed outlier: 3.811A pdb=" N GLN G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR G 101 " --> pdb=" O VAL G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 130 removed outlier: 3.570A pdb=" N GLU G 115 " --> pdb=" O SER G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 507 removed outlier: 3.968A pdb=" N ALA G 463 " --> pdb=" O ASP G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 536 removed outlier: 3.916A pdb=" N GLU G 514 " --> pdb=" O ASP G 510 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 517 " --> pdb=" O THR G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 540 Processing helix chain 'G' and resid 541 through 547 removed outlier: 3.895A pdb=" N LEU G 545 " --> pdb=" O GLN G 541 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN G 547 " --> pdb=" O LEU G 543 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 34 removed outlier: 3.776A pdb=" N ASN R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS R 20 " --> pdb=" O ASN R 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN R 21 " --> pdb=" O ASN R 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA R 24 " --> pdb=" O LYS R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 101 removed outlier: 4.221A pdb=" N GLN R 48 " --> pdb=" O ASP R 44 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG R 66 " --> pdb=" O THR R 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN R 88 " --> pdb=" O GLU R 84 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 130 removed outlier: 3.513A pdb=" N THR R 130 " --> pdb=" O VAL R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 169 Processing helix chain 'R' and resid 459 through 507 removed outlier: 3.862A pdb=" N ALA R 463 " --> pdb=" O ASP R 459 " (cutoff:3.500A) Processing helix chain 'R' and resid 510 through 537 removed outlier: 4.282A pdb=" N GLN R 537 " --> pdb=" O ALA R 533 " (cutoff:3.500A) Processing helix chain 'R' and resid 540 through 547 removed outlier: 4.269A pdb=" N SER R 544 " --> pdb=" O GLN R 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 34 removed outlier: 4.004A pdb=" N SER H 23 " --> pdb=" O ASN H 19 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 101 removed outlier: 3.530A pdb=" N GLN H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL H 97 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 130 Processing helix chain 'H' and resid 164 through 169 removed outlier: 3.507A pdb=" N GLY H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 459 through 507 removed outlier: 3.542A pdb=" N ALA H 463 " --> pdb=" O ASP H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 536 Processing helix chain 'H' and resid 537 through 540 removed outlier: 3.846A pdb=" N GLN H 540 " --> pdb=" O GLN H 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 537 through 540' Processing helix chain 'H' and resid 541 through 547 removed outlier: 3.883A pdb=" N LEU H 545 " --> pdb=" O GLN H 541 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 34 removed outlier: 3.643A pdb=" N ASN S 16 " --> pdb=" O LEU S 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN S 17 " --> pdb=" O ILE S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 101 removed outlier: 3.804A pdb=" N GLN S 48 " --> pdb=" O ASP S 44 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU S 84 " --> pdb=" O GLY S 80 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE S 85 " --> pdb=" O ALA S 81 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR S 101 " --> pdb=" O VAL S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 130 Processing helix chain 'S' and resid 164 through 169 Processing helix chain 'S' and resid 459 through 507 removed outlier: 3.562A pdb=" N ARG S 505 " --> pdb=" O GLU S 501 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE S 506 " --> pdb=" O ALA S 502 " (cutoff:3.500A) Processing helix chain 'S' and resid 510 through 538 removed outlier: 4.108A pdb=" N SER S 516 " --> pdb=" O ALA S 512 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL S 538 " --> pdb=" O LYS S 534 " (cutoff:3.500A) Processing helix chain 'S' and resid 541 through 547 removed outlier: 4.067A pdb=" N LEU S 545 " --> pdb=" O GLN S 541 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU S 546 " --> pdb=" O VAL S 542 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN S 547 " --> pdb=" O LEU S 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 541 through 547' Processing helix chain 'I' and resid 8 through 34 removed outlier: 4.031A pdb=" N ASN I 16 " --> pdb=" O LEU I 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN I 17 " --> pdb=" O ILE I 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 100 removed outlier: 3.582A pdb=" N GLN I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU I 84 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL I 97 " --> pdb=" O ARG I 93 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 130 removed outlier: 3.511A pdb=" N GLU I 115 " --> pdb=" O SER I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 169 Processing helix chain 'I' and resid 459 through 507 Processing helix chain 'I' and resid 510 through 537 removed outlier: 4.013A pdb=" N SER I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 547 removed outlier: 4.410A pdb=" N SER I 544 " --> pdb=" O GLN I 540 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 34 removed outlier: 4.076A pdb=" N LEU T 12 " --> pdb=" O ASN T 8 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER T 34 " --> pdb=" O GLU T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 101 removed outlier: 3.522A pdb=" N ILE T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN T 69 " --> pdb=" O ALA T 65 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP T 70 " --> pdb=" O ARG T 66 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN T 88 " --> pdb=" O GLU T 84 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN T 98 " --> pdb=" O GLU T 94 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR T 101 " --> pdb=" O VAL T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 130 Processing helix chain 'T' and resid 459 through 507 Processing helix chain 'T' and resid 510 through 538 removed outlier: 4.106A pdb=" N SER T 516 " --> pdb=" O ALA T 512 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 547 removed outlier: 4.266A pdb=" N SER T 544 " --> pdb=" O GLN T 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 34 removed outlier: 4.020A pdb=" N LEU J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE J 13 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 100 removed outlier: 3.969A pdb=" N GLN J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE J 50 " --> pdb=" O ALA J 46 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG J 66 " --> pdb=" O THR J 62 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 130 removed outlier: 3.586A pdb=" N THR J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 507 Processing helix chain 'J' and resid 510 through 537 removed outlier: 3.502A pdb=" N GLU J 514 " --> pdb=" O ASP J 510 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 547 removed outlier: 3.862A pdb=" N SER J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 13 Processing helix chain 'U' and resid 13 through 34 removed outlier: 4.102A pdb=" N ASN U 17 " --> pdb=" O ILE U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 101 removed outlier: 3.905A pdb=" N SER U 73 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL U 74 " --> pdb=" O ASP U 70 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA U 75 " --> pdb=" O GLY U 71 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN U 76 " --> pdb=" O ILE U 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA U 81 " --> pdb=" O THR U 77 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR U 101 " --> pdb=" O VAL U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 130 Processing helix chain 'U' and resid 459 through 507 removed outlier: 3.517A pdb=" N ARG U 505 " --> pdb=" O GLU U 501 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE U 506 " --> pdb=" O ALA U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 510 through 538 removed outlier: 4.069A pdb=" N SER U 516 " --> pdb=" O ALA U 512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA U 533 " --> pdb=" O ASN U 529 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS U 534 " --> pdb=" O SER U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 547 removed outlier: 3.982A pdb=" N SER U 544 " --> pdb=" O GLN U 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 34 removed outlier: 4.222A pdb=" N THR K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN K 15 " --> pdb=" O SER K 11 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER K 34 " --> pdb=" O GLU K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 101 removed outlier: 3.564A pdb=" N GLN K 48 " --> pdb=" O ASP K 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLN K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA K 99 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 130 Processing helix chain 'K' and resid 459 through 507 removed outlier: 3.606A pdb=" N ALA K 463 " --> pdb=" O ASP K 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 537 removed outlier: 4.194A pdb=" N SER K 516 " --> pdb=" O ALA K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 547 removed outlier: 4.006A pdb=" N SER K 544 " --> pdb=" O GLN K 540 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 34 removed outlier: 3.535A pdb=" N LEU V 12 " --> pdb=" O ASN V 8 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER V 23 " --> pdb=" O ASN V 19 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA V 24 " --> pdb=" O LYS V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 100 removed outlier: 3.649A pdb=" N GLN V 48 " --> pdb=" O ASP V 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 130 Processing helix chain 'V' and resid 459 through 507 removed outlier: 4.142A pdb=" N ALA V 463 " --> pdb=" O ASP V 459 " (cutoff:3.500A) Processing helix chain 'V' and resid 510 through 536 removed outlier: 4.369A pdb=" N SER V 516 " --> pdb=" O ALA V 512 " (cutoff:3.500A) Processing helix chain 'V' and resid 539 through 547 removed outlier: 3.743A pdb=" N LEU V 543 " --> pdb=" O PRO V 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 34 removed outlier: 3.581A pdb=" N SER L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 101 removed outlier: 3.914A pdb=" N SER L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA L 75 " --> pdb=" O GLY L 71 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL L 97 " --> pdb=" O ARG L 93 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR L 101 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 130 removed outlier: 3.739A pdb=" N THR L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 507 Processing helix chain 'L' and resid 510 through 537 removed outlier: 3.728A pdb=" N SER L 516 " --> pdb=" O ALA L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 547 removed outlier: 3.911A pdb=" N SER L 544 " --> pdb=" O GLN L 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 147 Processing sheet with id=AA4, first strand: chain 'M' and resid 142 through 147 removed outlier: 3.669A pdb=" N GLY M 142 " --> pdb=" O LEU M 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 146 Processing sheet with id=AA7, first strand: chain 'N' and resid 142 through 147 removed outlier: 3.563A pdb=" N ILE N 156 " --> pdb=" O ILE N 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 142 through 146 removed outlier: 3.544A pdb=" N ILE D 146 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 156 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 142 through 147 Processing sheet with id=AB1, first strand: chain 'E' and resid 142 through 147 Processing sheet with id=AB2, first strand: chain 'P' and resid 143 through 147 removed outlier: 3.610A pdb=" N MET P 144 " --> pdb=" O ILE P 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AB4, first strand: chain 'Q' and resid 143 through 147 Processing sheet with id=AB5, first strand: chain 'G' and resid 142 through 147 removed outlier: 3.525A pdb=" N GLY G 142 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 160 " --> pdb=" O GLY G 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET G 144 " --> pdb=" O ILE G 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 142 through 147 removed outlier: 3.613A pdb=" N GLY R 142 " --> pdb=" O LEU R 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 142 through 147 Processing sheet with id=AB8, first strand: chain 'S' and resid 142 through 147 Processing sheet with id=AB9, first strand: chain 'I' and resid 142 through 147 Processing sheet with id=AC1, first strand: chain 'T' and resid 142 through 147 Processing sheet with id=AC2, first strand: chain 'J' and resid 142 through 147 Processing sheet with id=AC3, first strand: chain 'U' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'U' and resid 142 through 146 Processing sheet with id=AC5, first strand: chain 'K' and resid 142 through 147 Processing sheet with id=AC6, first strand: chain 'V' and resid 142 through 147 removed outlier: 3.887A pdb=" N GLY V 142 " --> pdb=" O LEU V 160 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE V 146 " --> pdb=" O ILE V 156 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE V 156 " --> pdb=" O ILE V 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 142 through 146 3615 hydrogen bonds defined for protein. 10776 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: 7.35 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8738 1.32 - 1.44: 9323 1.44 - 1.56: 26181 1.56 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 44330 Sorted by residual: bond pdb=" C SER B 34 " pdb=" O SER B 34 " ideal model delta sigma weight residual 1.234 1.204 0.031 1.22e-02 6.72e+03 6.30e+00 bond pdb=" C ASN B 39 " pdb=" O ASN B 39 " ideal model delta sigma weight residual 1.243 1.220 0.024 9.50e-03 1.11e+04 6.21e+00 bond pdb=" CA SER B 34 " pdb=" C SER B 34 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.30e-02 5.92e+03 6.02e+00 bond pdb=" C VAL Q 538 " pdb=" N PRO Q 539 " ideal model delta sigma weight residual 1.331 1.349 -0.018 7.90e-03 1.60e+04 5.01e+00 bond pdb=" C LEU B 32 " pdb=" O LEU B 32 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.16e-02 7.43e+03 4.90e+00 ... (remaining 44325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 58775 2.07 - 4.14: 992 4.14 - 6.20: 185 6.20 - 8.27: 36 8.27 - 10.34: 6 Bond angle restraints: 59994 Sorted by residual: angle pdb=" N AILE B 38 " pdb=" CA AILE B 38 " pdb=" C AILE B 38 " ideal model delta sigma weight residual 110.62 118.02 -7.40 1.02e+00 9.61e-01 5.27e+01 angle pdb=" N BILE B 38 " pdb=" CA BILE B 38 " pdb=" C BILE B 38 " ideal model delta sigma weight residual 110.62 117.91 -7.29 1.02e+00 9.61e-01 5.11e+01 angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 113.53 107.80 5.73 9.80e-01 1.04e+00 3.41e+01 angle pdb=" N LYS B 42 " pdb=" CA LYS B 42 " pdb=" C LYS B 42 " ideal model delta sigma weight residual 111.71 105.42 6.29 1.15e+00 7.56e-01 2.99e+01 angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 110.20 118.32 -8.12 1.58e+00 4.01e-01 2.64e+01 ... (remaining 59989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 25080 17.95 - 35.91: 2138 35.91 - 53.86: 323 53.86 - 71.81: 91 71.81 - 89.77: 66 Dihedral angle restraints: 27698 sinusoidal: 10582 harmonic: 17116 Sorted by residual: dihedral pdb=" CA GLY D 169 " pdb=" C GLY D 169 " pdb=" N LEU D 170 " pdb=" CA LEU D 170 " ideal model delta harmonic sigma weight residual -180.00 -140.88 -39.12 0 5.00e+00 4.00e-02 6.12e+01 dihedral pdb=" CA SER E 40 " pdb=" C SER E 40 " pdb=" N ALA E 41 " pdb=" CA ALA E 41 " ideal model delta harmonic sigma weight residual -180.00 -142.86 -37.14 0 5.00e+00 4.00e-02 5.52e+01 dihedral pdb=" CA SER H 40 " pdb=" C SER H 40 " pdb=" N ALA H 41 " pdb=" CA ALA H 41 " ideal model delta harmonic sigma weight residual 180.00 -142.98 -37.02 0 5.00e+00 4.00e-02 5.48e+01 ... (remaining 27695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 7057 0.082 - 0.163: 305 0.163 - 0.245: 5 0.245 - 0.326: 2 0.326 - 0.408: 1 Chirality restraints: 7370 Sorted by residual: chirality pdb=" CG LEU D 170 " pdb=" CB LEU D 170 " pdb=" CD1 LEU D 170 " pdb=" CD2 LEU D 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA LEU B 36 " pdb=" N LEU B 36 " pdb=" C LEU B 36 " pdb=" CB LEU B 36 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE M 163 " pdb=" CA ILE M 163 " pdb=" CG1 ILE M 163 " pdb=" CG2 ILE M 163 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 7367 not shown) Planarity restraints: 8140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 37 " -0.025 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C ARG B 37 " 0.087 2.00e-02 2.50e+03 pdb=" O ARG B 37 " -0.033 2.00e-02 2.50e+03 pdb=" N BILE B 38 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AILE B 38 " -0.024 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C AILE B 38 " 0.086 2.00e-02 2.50e+03 pdb=" O AILE B 38 " -0.032 2.00e-02 2.50e+03 pdb=" N ASN B 39 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 37 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C ARG B 37 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG B 37 " -0.032 2.00e-02 2.50e+03 pdb=" N AILE B 38 " -0.028 2.00e-02 2.50e+03 ... (remaining 8137 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 838 2.64 - 3.21: 47183 3.21 - 3.77: 72732 3.77 - 4.34: 89659 4.34 - 4.90: 150725 Nonbonded interactions: 361137 Sorted by model distance: nonbonded pdb=" O LYS B 42 " pdb=" NZ LYS B 42 " model vdw 2.075 3.120 nonbonded pdb=" NE2 GLN T 147 " pdb=" O GLY T 149 " model vdw 2.097 3.120 nonbonded pdb=" NE2 GLN C 147 " pdb=" O GLY C 149 " model vdw 2.109 3.120 nonbonded pdb=" O GLY H 80 " pdb=" OG SER H 83 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASN L 8 " pdb=" OG SER L 11 " model vdw 2.115 3.040 ... (remaining 361132 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'B' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'C' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'D' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'E' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'F' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'G' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'H' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'I' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'J' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'K' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'L' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'M' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'N' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'O' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'P' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'Q' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'R' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'S' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'T' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'U' and (resid 2 through 37 or resid 39 through 547)) selection = (chain 'V' and (resid 2 through 37 or resid 39 through 547)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.420 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: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 48.820 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.003 0.068 44330 Z= 0.169 Angle : 0.679 10.338 59994 Z= 0.398 Chirality : 0.037 0.408 7370 Planarity : 0.004 0.057 8140 Dihedral : 14.344 89.767 16522 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.11), residues: 5896 helix: 3.20 (0.08), residues: 4180 sheet: 2.50 (0.24), residues: 352 loop : -1.75 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 484 TYR 0.019 0.001 TYR N 511 PHE 0.034 0.003 PHE D 173 Details of bonding type rmsd covalent geometry : bond 0.00325 (44330) covalent geometry : angle 0.67909 (59994) hydrogen bonds : bond 0.13109 ( 3615) hydrogen bonds : angle 4.72906 (10776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1261 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8794 (mttm) cc_final: 0.8259 (tmtt) REVERT: B 484 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7304 (ttt-90) REVERT: A 117 LYS cc_start: 0.9137 (tptt) cc_final: 0.8908 (tppt) REVERT: A 121 ASP cc_start: 0.8813 (m-30) cc_final: 0.8436 (m-30) REVERT: M 106 ASP cc_start: 0.8558 (m-30) cc_final: 0.8061 (m-30) REVERT: M 114 ASP cc_start: 0.8882 (t0) cc_final: 0.8637 (t0) REVERT: M 117 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8108 (pttm) REVERT: M 122 GLU cc_start: 0.8777 (tp30) cc_final: 0.7983 (tp30) REVERT: M 484 ARG cc_start: 0.7700 (ttt180) cc_final: 0.6915 (mmt180) REVERT: M 518 MET cc_start: 0.8298 (tmm) cc_final: 0.8084 (tmm) REVERT: C 104 ASN cc_start: 0.8895 (m110) cc_final: 0.8564 (m110) REVERT: C 110 ASP cc_start: 0.7996 (t0) cc_final: 0.7246 (t0) REVERT: C 114 ASP cc_start: 0.8344 (m-30) cc_final: 0.7836 (m-30) REVERT: C 115 GLU cc_start: 0.9073 (tp30) cc_final: 0.8723 (tp30) REVERT: C 131 GLN cc_start: 0.8434 (pp30) cc_final: 0.8184 (pp30) REVERT: C 164 ASP cc_start: 0.8594 (p0) cc_final: 0.7807 (p0) REVERT: C 482 GLN cc_start: 0.8478 (mp10) cc_final: 0.8255 (mp10) REVERT: C 514 GLU cc_start: 0.7031 (mp0) cc_final: 0.6754 (mp0) REVERT: C 523 ILE cc_start: 0.9208 (mm) cc_final: 0.9005 (tp) REVERT: N 126 VAL cc_start: 0.8887 (t) cc_final: 0.7850 (t) REVERT: N 520 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8229 (mmtt) REVERT: D 36 LEU cc_start: 0.8963 (tp) cc_final: 0.8695 (tp) REVERT: D 115 GLU cc_start: 0.8576 (tp30) cc_final: 0.8338 (tp30) REVERT: D 117 LYS cc_start: 0.9140 (tppt) cc_final: 0.8525 (ttpt) REVERT: D 520 LYS cc_start: 0.7970 (mttt) cc_final: 0.7403 (mmmt) REVERT: O 20 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8237 (tttp) REVERT: O 66 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8480 (mmm-85) REVERT: O 117 LYS cc_start: 0.9054 (tppp) cc_final: 0.8578 (tptp) REVERT: O 473 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8575 (mtmm) REVERT: O 508 ASP cc_start: 0.6965 (m-30) cc_final: 0.6740 (t0) REVERT: O 534 LYS cc_start: 0.9087 (pttt) cc_final: 0.8855 (tttp) REVERT: E 93 ARG cc_start: 0.8363 (tpt-90) cc_final: 0.7420 (ttt180) REVERT: E 110 ASP cc_start: 0.8272 (m-30) cc_final: 0.7803 (m-30) REVERT: E 167 THR cc_start: 0.8106 (m) cc_final: 0.7877 (m) REVERT: P 20 LYS cc_start: 0.8949 (mppt) cc_final: 0.8721 (mptt) REVERT: P 534 LYS cc_start: 0.8570 (mttm) cc_final: 0.8321 (tptp) REVERT: F 79 GLU cc_start: 0.8245 (tt0) cc_final: 0.7704 (tp30) REVERT: F 117 LYS cc_start: 0.8915 (tptm) cc_final: 0.8699 (ttmt) REVERT: F 135 VAL cc_start: 0.8971 (t) cc_final: 0.8648 (t) REVERT: F 520 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8525 (mmtt) REVERT: Q 505 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7305 (ttt180) REVERT: Q 514 GLU cc_start: 0.7805 (pp20) cc_final: 0.7029 (pp20) REVERT: G 78 THR cc_start: 0.9426 (m) cc_final: 0.9197 (t) REVERT: G 79 GLU cc_start: 0.9050 (pp20) cc_final: 0.8811 (pp20) REVERT: G 91 ARG cc_start: 0.8766 (tpt170) cc_final: 0.8546 (tpt170) REVERT: G 108 ASP cc_start: 0.8872 (m-30) cc_final: 0.8579 (t0) REVERT: G 472 ASP cc_start: 0.8573 (t0) cc_final: 0.8107 (t0) REVERT: R 145 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8543 (mtpt) REVERT: R 155 THR cc_start: 0.8547 (p) cc_final: 0.8231 (p) REVERT: R 503 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7217 (tm-30) REVERT: H 67 ASN cc_start: 0.8308 (m-40) cc_final: 0.8048 (m-40) REVERT: H 91 ARG cc_start: 0.8809 (tpt90) cc_final: 0.8367 (tpp80) REVERT: H 93 ARG cc_start: 0.8975 (ttt-90) cc_final: 0.7907 (ttp80) REVERT: H 110 ASP cc_start: 0.8786 (m-30) cc_final: 0.8367 (m-30) REVERT: H 115 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8195 (tm-30) REVERT: H 520 LYS cc_start: 0.8436 (pttm) cc_final: 0.8087 (tptt) REVERT: H 525 GLN cc_start: 0.8298 (tm130) cc_final: 0.7969 (tm-30) REVERT: H 541 GLN cc_start: 0.8873 (mp10) cc_final: 0.8297 (mp10) REVERT: S 124 ASP cc_start: 0.9164 (m-30) cc_final: 0.8861 (m-30) REVERT: S 164 ASP cc_start: 0.7783 (p0) cc_final: 0.7499 (p0) REVERT: S 518 MET cc_start: 0.8565 (tmm) cc_final: 0.8316 (tmm) REVERT: I 117 LYS cc_start: 0.8904 (tppt) cc_final: 0.8519 (tppt) REVERT: I 161 LYS cc_start: 0.8585 (mttp) cc_final: 0.8305 (mttp) REVERT: T 122 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8456 (tm-30) REVERT: T 147 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7167 (mt0) REVERT: J 94 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7456 (mm-30) REVERT: J 98 GLN cc_start: 0.5931 (mm110) cc_final: 0.5681 (mm110) REVERT: J 110 ASP cc_start: 0.8790 (t0) cc_final: 0.8541 (t0) REVERT: J 500 SER cc_start: 0.9211 (m) cc_final: 0.8975 (m) REVERT: U 122 GLU cc_start: 0.8447 (tt0) cc_final: 0.7879 (tt0) REVERT: K 30 GLU cc_start: 0.8502 (pt0) cc_final: 0.8295 (pt0) REVERT: K 484 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7885 (mtp180) REVERT: K 520 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9061 (tttt) REVERT: V 131 GLN cc_start: 0.8524 (pp30) cc_final: 0.8030 (pp30) REVERT: L 39 ASN cc_start: 0.8221 (t0) cc_final: 0.7866 (p0) REVERT: L 115 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8306 (tm-30) outliers start: 5 outliers final: 2 residues processed: 1264 average time/residue: 0.2598 time to fit residues: 540.5323 Evaluate side-chains 907 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 905 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain P residue 21 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 0.6980 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 0.5980 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN B 39 ASN B 86 ASN B 98 GLN B 104 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 491 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN M 19 ASN M 69 ASN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 ASN N 491 ASN ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 ASN D 19 ASN O 76 GLN O 86 ASN O 133 ASN O 503 GLN O 537 GLN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 491 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN F 171 ASN F 491 ASN Q 171 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN G 76 GLN G 536 ASN R 17 ASN ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN R 498 ASN ** R 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 86 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN S 22 GLN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN I 21 ASN I 88 ASN I 129 GLN ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN T 483 ASN T 498 ASN T 503 GLN T 507 GLN T 536 ASN J 17 ASN J 57 ASN J 491 ASN U 76 GLN U 90 GLN U 113 GLN U 491 ASN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 525 GLN ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 ASN K 498 ASN K 507 GLN ** K 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN L 526 GLN L 529 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.100533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084900 restraints weight = 685258.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089063 restraints weight = 214969.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091787 restraints weight = 108171.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.093614 restraints weight = 64454.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.094864 restraints weight = 42264.842| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 44330 Z= 0.163 Angle : 0.684 12.299 59994 Z= 0.372 Chirality : 0.041 0.256 7370 Planarity : 0.004 0.054 8140 Dihedral : 5.067 39.058 6187 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.90 % Allowed : 12.01 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.11), residues: 5896 helix: 3.20 (0.08), residues: 4224 sheet: 2.46 (0.24), residues: 352 loop : -1.71 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 505 TYR 0.021 0.002 TYR R 511 PHE 0.056 0.002 PHE G 54 Details of bonding type rmsd covalent geometry : bond 0.00340 (44330) covalent geometry : angle 0.68377 (59994) hydrogen bonds : bond 0.05826 ( 3615) hydrogen bonds : angle 4.11922 (10776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1039 time to evaluate : 1.765 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: B 159 ASP cc_start: 0.7904 (t0) cc_final: 0.7675 (t0) REVERT: B 484 ARG cc_start: 0.7935 (ttt180) cc_final: 0.7708 (ttp-170) REVERT: B 491 ASN cc_start: 0.8952 (t0) cc_final: 0.8645 (t0) REVERT: A 117 LYS cc_start: 0.9146 (tptt) cc_final: 0.8878 (tppt) REVERT: A 121 ASP cc_start: 0.8905 (m-30) cc_final: 0.8519 (m-30) REVERT: A 518 MET cc_start: 0.7950 (tmm) cc_final: 0.7020 (tmm) REVERT: A 522 GLN cc_start: 0.7655 (pt0) cc_final: 0.7244 (pt0) REVERT: M 114 ASP cc_start: 0.8749 (t0) cc_final: 0.8547 (t0) REVERT: M 484 ARG cc_start: 0.7756 (ttt180) cc_final: 0.6869 (mmt180) REVERT: C 110 ASP cc_start: 0.7880 (t0) cc_final: 0.7308 (t0) REVERT: C 114 ASP cc_start: 0.8277 (m-30) cc_final: 0.7903 (m-30) REVERT: C 115 GLU cc_start: 0.9224 (tp30) cc_final: 0.9023 (tp30) REVERT: C 131 GLN cc_start: 0.8361 (pp30) cc_final: 0.8007 (pp30) REVERT: C 164 ASP cc_start: 0.8062 (p0) cc_final: 0.7744 (p0) REVERT: D 8 ASN cc_start: 0.8695 (t0) cc_final: 0.8330 (t0) REVERT: D 31 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7977 (mtt90) REVERT: D 36 LEU cc_start: 0.8889 (tp) cc_final: 0.8629 (tp) REVERT: D 117 LYS cc_start: 0.9123 (tppt) cc_final: 0.8470 (ttpt) REVERT: D 520 LYS cc_start: 0.8128 (mttt) cc_final: 0.7535 (mmmt) REVERT: O 20 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8168 (tttp) REVERT: O 115 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7843 (tm-30) REVERT: O 117 LYS cc_start: 0.9005 (tppp) cc_final: 0.8574 (tptp) REVERT: O 508 ASP cc_start: 0.6989 (m-30) cc_final: 0.6766 (t0) REVERT: O 534 LYS cc_start: 0.9181 (pttt) cc_final: 0.8923 (tttp) REVERT: E 93 ARG cc_start: 0.8371 (tpt-90) cc_final: 0.7400 (ttt180) REVERT: E 110 ASP cc_start: 0.7904 (m-30) cc_final: 0.7699 (m-30) REVERT: P 534 LYS cc_start: 0.8499 (mttm) cc_final: 0.8135 (tptp) REVERT: P 537 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: F 79 GLU cc_start: 0.8165 (tt0) cc_final: 0.7742 (tp30) REVERT: F 117 LYS cc_start: 0.8905 (tptm) cc_final: 0.8669 (ttpt) REVERT: F 520 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8553 (tttt) REVERT: Q 514 GLU cc_start: 0.7545 (pp20) cc_final: 0.7170 (pp20) REVERT: Q 520 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8635 (mtpt) REVERT: G 78 THR cc_start: 0.9417 (m) cc_final: 0.9204 (t) REVERT: G 79 GLU cc_start: 0.9025 (pp20) cc_final: 0.8780 (pp20) REVERT: G 91 ARG cc_start: 0.8773 (tpt170) cc_final: 0.8431 (tpt170) REVERT: G 124 ASP cc_start: 0.8819 (m-30) cc_final: 0.8485 (m-30) REVERT: G 472 ASP cc_start: 0.8486 (t0) cc_final: 0.8066 (t0) REVERT: R 20 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: R 79 GLU cc_start: 0.7948 (tp30) cc_final: 0.7646 (tp30) REVERT: R 503 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7510 (tm-30) REVERT: H 21 ASN cc_start: 0.8617 (t0) cc_final: 0.8154 (t0) REVERT: H 110 ASP cc_start: 0.8593 (m-30) cc_final: 0.8289 (m-30) REVERT: H 115 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8026 (tm-30) REVERT: H 520 LYS cc_start: 0.8564 (pttm) cc_final: 0.8104 (tptt) REVERT: H 525 GLN cc_start: 0.8441 (tm130) cc_final: 0.8158 (tm-30) REVERT: S 124 ASP cc_start: 0.9151 (m-30) cc_final: 0.8860 (m-30) REVERT: S 518 MET cc_start: 0.8775 (tmm) cc_final: 0.8316 (tmm) REVERT: I 31 ARG cc_start: 0.7320 (mtp85) cc_final: 0.7058 (mtp85) REVERT: T 122 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8689 (tm-30) REVERT: T 147 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7099 (mt0) REVERT: T 498 ASN cc_start: 0.9218 (m-40) cc_final: 0.9005 (m110) REVERT: J 94 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7474 (tp30) REVERT: K 484 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8013 (mtp180) REVERT: K 520 LYS cc_start: 0.9364 (ttmt) cc_final: 0.9065 (tttt) REVERT: V 30 GLU cc_start: 0.8300 (pt0) cc_final: 0.8096 (pt0) REVERT: V 94 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: V 131 GLN cc_start: 0.8489 (pp30) cc_final: 0.7990 (pp30) REVERT: L 39 ASN cc_start: 0.8260 (t0) cc_final: 0.8017 (p0) REVERT: L 108 ASP cc_start: 0.8544 (m-30) cc_final: 0.8019 (t0) REVERT: L 115 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8434 (tm-30) REVERT: L 474 PHE cc_start: 0.8765 (t80) cc_final: 0.8543 (t80) outliers start: 95 outliers final: 49 residues processed: 1082 average time/residue: 0.2488 time to fit residues: 449.0282 Evaluate side-chains 950 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 898 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 133 ASN Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 76 GLN Chi-restraints excluded: chain U residue 90 GLN Chi-restraints excluded: chain U residue 525 GLN Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 466 ASP Chi-restraints excluded: chain L residue 458 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 272 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 502 optimal weight: 0.7980 chunk 253 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 461 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 90 GLN A 52 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 151 ASN M 98 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN C 498 ASN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 ASN N 503 GLN ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 470 GLN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 ASN P 76 GLN P 129 GLN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 491 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN F 507 GLN Q 171 ASN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN H 525 GLN H 529 ASN S 22 GLN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 ASN J 57 ASN J 470 GLN U 22 GLN U 76 GLN U 87 ASN U 90 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 ASN K 537 GLN V 76 GLN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.100575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.085044 restraints weight = 641925.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.089138 restraints weight = 210413.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091813 restraints weight = 107598.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.093619 restraints weight = 64740.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094866 restraints weight = 42764.336| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 44330 Z= 0.155 Angle : 0.648 12.080 59994 Z= 0.355 Chirality : 0.040 0.381 7370 Planarity : 0.003 0.049 8140 Dihedral : 4.938 40.260 6182 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.16 % Allowed : 15.10 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.11), residues: 5896 helix: 3.17 (0.08), residues: 4224 sheet: 2.28 (0.24), residues: 352 loop : -1.67 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 31 TYR 0.021 0.002 TYR N 511 PHE 0.055 0.002 PHE G 54 Details of bonding type rmsd covalent geometry : bond 0.00326 (44330) covalent geometry : angle 0.64800 (59994) hydrogen bonds : bond 0.05468 ( 3615) hydrogen bonds : angle 3.96307 (10776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 977 time to evaluate : 1.646 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 117 LYS cc_start: 0.9133 (tptt) cc_final: 0.8879 (tppt) REVERT: A 121 ASP cc_start: 0.8902 (m-30) cc_final: 0.8523 (m-30) REVERT: A 514 GLU cc_start: 0.8866 (pm20) cc_final: 0.8507 (mp0) REVERT: M 61 LEU cc_start: 0.8982 (mm) cc_final: 0.8779 (mm) REVERT: M 79 GLU cc_start: 0.8647 (pp20) cc_final: 0.8445 (pp20) REVERT: M 122 GLU cc_start: 0.9018 (tp30) cc_final: 0.8640 (tp30) REVERT: M 484 ARG cc_start: 0.7722 (ttt180) cc_final: 0.6841 (mmt180) REVERT: C 110 ASP cc_start: 0.7961 (t0) cc_final: 0.7347 (t0) REVERT: C 114 ASP cc_start: 0.8239 (m-30) cc_final: 0.7891 (m-30) REVERT: C 117 LYS cc_start: 0.9007 (tptp) cc_final: 0.8782 (tptp) REVERT: C 164 ASP cc_start: 0.8032 (p0) cc_final: 0.7680 (p0) REVERT: C 514 GLU cc_start: 0.7172 (mp0) cc_final: 0.6967 (mp0) REVERT: C 541 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7253 (tm-30) REVERT: N 514 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8630 (mm-30) REVERT: D 20 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8224 (mmmt) REVERT: D 36 LEU cc_start: 0.8922 (tp) cc_final: 0.8685 (tp) REVERT: D 117 LYS cc_start: 0.9104 (tppt) cc_final: 0.8432 (ttpt) REVERT: D 520 LYS cc_start: 0.8101 (mttt) cc_final: 0.7458 (mmmt) REVERT: O 20 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8131 (tttp) REVERT: O 115 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7849 (tm-30) REVERT: O 117 LYS cc_start: 0.9008 (tppp) cc_final: 0.8633 (tptp) REVERT: O 473 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8260 (ptmt) REVERT: O 534 LYS cc_start: 0.9171 (pttt) cc_final: 0.8957 (tttt) REVERT: E 93 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.7277 (ttt180) REVERT: E 94 GLU cc_start: 0.8289 (tt0) cc_final: 0.8047 (tt0) REVERT: P 129 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7605 (pp30) REVERT: P 534 LYS cc_start: 0.8486 (mttm) cc_final: 0.8121 (tptp) REVERT: P 537 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: F 79 GLU cc_start: 0.8164 (tt0) cc_final: 0.7748 (tp30) REVERT: F 105 SER cc_start: 0.8454 (t) cc_final: 0.8227 (p) REVERT: F 478 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8960 (mm) REVERT: F 520 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8588 (tttt) REVERT: F 522 GLN cc_start: 0.8635 (mt0) cc_final: 0.8120 (mm110) REVERT: Q 514 GLU cc_start: 0.7427 (pp20) cc_final: 0.7145 (pp20) REVERT: G 78 THR cc_start: 0.9407 (m) cc_final: 0.9189 (t) REVERT: G 79 GLU cc_start: 0.9034 (pp20) cc_final: 0.8756 (pp20) REVERT: G 91 ARG cc_start: 0.8819 (tpt170) cc_final: 0.8544 (tpt170) REVERT: G 124 ASP cc_start: 0.8854 (m-30) cc_final: 0.8526 (m-30) REVERT: G 472 ASP cc_start: 0.8515 (t0) cc_final: 0.8078 (t0) REVERT: R 79 GLU cc_start: 0.7929 (tp30) cc_final: 0.7590 (tp30) REVERT: R 503 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7580 (tm-30) REVERT: H 21 ASN cc_start: 0.8607 (t0) cc_final: 0.8085 (t0) REVERT: H 110 ASP cc_start: 0.8592 (m-30) cc_final: 0.8296 (m-30) REVERT: H 115 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8064 (tm-30) REVERT: H 520 LYS cc_start: 0.8621 (pttm) cc_final: 0.8142 (tptt) REVERT: H 525 GLN cc_start: 0.8400 (tm-30) cc_final: 0.8176 (tm-30) REVERT: S 124 ASP cc_start: 0.9176 (m-30) cc_final: 0.8919 (m-30) REVERT: S 518 MET cc_start: 0.8742 (tmm) cc_final: 0.8257 (tmm) REVERT: S 540 GLN cc_start: 0.8891 (mm110) cc_final: 0.8601 (mm-40) REVERT: I 465 ASP cc_start: 0.8150 (m-30) cc_final: 0.7872 (m-30) REVERT: T 122 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8678 (tm-30) REVERT: T 147 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7301 (mt0) REVERT: T 498 ASN cc_start: 0.9321 (m-40) cc_final: 0.8962 (m-40) REVERT: U 491 ASN cc_start: 0.9012 (t0) cc_final: 0.8597 (t0) REVERT: K 520 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9066 (tttt) REVERT: V 94 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: V 115 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8097 (tp30) REVERT: V 131 GLN cc_start: 0.8457 (pp30) cc_final: 0.7984 (pp30) REVERT: V 514 GLU cc_start: 0.8345 (tp30) cc_final: 0.7843 (tp30) REVERT: L 108 ASP cc_start: 0.8568 (m-30) cc_final: 0.8022 (t0) REVERT: L 115 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8404 (tm-30) REVERT: L 126 VAL cc_start: 0.9088 (t) cc_final: 0.8814 (p) REVERT: L 474 PHE cc_start: 0.8798 (t80) cc_final: 0.8519 (t80) outliers start: 108 outliers final: 57 residues processed: 1021 average time/residue: 0.2523 time to fit residues: 428.4039 Evaluate side-chains 958 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 897 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 486 ASP Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 21 ASN Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 491 ASN Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 489 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 466 ASP Chi-restraints excluded: chain L residue 173 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 44 optimal weight: 0.9990 chunk 286 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 494 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 ASN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 151 ASN A 154 GLN A 522 GLN ** M 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 498 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 ASN ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 129 GLN P 171 ASN P 491 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN F 522 GLN Q 171 ASN ** G 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 GLN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN S 22 GLN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 507 GLN I 547 GLN T 90 GLN J 470 GLN U 76 GLN U 87 ASN U 90 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.085178 restraints weight = 608000.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089225 restraints weight = 206041.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.091853 restraints weight = 106116.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.093624 restraints weight = 64342.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.094856 restraints weight = 42491.789| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 44330 Z= 0.153 Angle : 0.648 13.622 59994 Z= 0.352 Chirality : 0.040 0.348 7370 Planarity : 0.003 0.047 8140 Dihedral : 4.882 40.616 6182 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.52 % Allowed : 15.90 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.11), residues: 5896 helix: 3.10 (0.08), residues: 4290 sheet: 2.20 (0.24), residues: 352 loop : -1.65 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 31 TYR 0.017 0.002 TYR P 511 PHE 0.056 0.002 PHE G 54 Details of bonding type rmsd covalent geometry : bond 0.00326 (44330) covalent geometry : angle 0.64815 (59994) hydrogen bonds : bond 0.05291 ( 3615) hydrogen bonds : angle 3.90909 (10776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 974 time to evaluate : 1.743 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 117 LYS cc_start: 0.9126 (tptt) cc_final: 0.8880 (tppt) REVERT: A 121 ASP cc_start: 0.8925 (m-30) cc_final: 0.8559 (m-30) REVERT: M 61 LEU cc_start: 0.8989 (mm) cc_final: 0.8782 (mm) REVERT: M 94 GLU cc_start: 0.9376 (tm-30) cc_final: 0.8919 (tm-30) REVERT: M 122 GLU cc_start: 0.9129 (tp30) cc_final: 0.8878 (tp30) REVERT: M 484 ARG cc_start: 0.7717 (ttt180) cc_final: 0.6819 (mmt180) REVERT: M 541 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: C 110 ASP cc_start: 0.7868 (t0) cc_final: 0.7315 (t0) REVERT: C 114 ASP cc_start: 0.8213 (m-30) cc_final: 0.7893 (m-30) REVERT: C 117 LYS cc_start: 0.8924 (tptp) cc_final: 0.8694 (tptp) REVERT: C 131 GLN cc_start: 0.8314 (pp30) cc_final: 0.8031 (pp30) REVERT: C 164 ASP cc_start: 0.8021 (p0) cc_final: 0.7577 (p0) REVERT: C 514 GLU cc_start: 0.7245 (mp0) cc_final: 0.6914 (mp0) REVERT: C 541 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7217 (tm-30) REVERT: N 31 ARG cc_start: 0.8274 (mtt90) cc_final: 0.7865 (mtt-85) REVERT: N 94 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8268 (mm-30) REVERT: N 514 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8595 (mm-30) REVERT: D 20 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8204 (mmmt) REVERT: D 36 LEU cc_start: 0.8930 (tp) cc_final: 0.8711 (tp) REVERT: D 117 LYS cc_start: 0.9115 (tppt) cc_final: 0.8438 (ttpt) REVERT: D 520 LYS cc_start: 0.8091 (mttt) cc_final: 0.7518 (mtpt) REVERT: O 20 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8124 (tttp) REVERT: O 115 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7932 (tm-30) REVERT: O 117 LYS cc_start: 0.8944 (tppp) cc_final: 0.8594 (tptp) REVERT: O 518 MET cc_start: 0.8266 (ppp) cc_final: 0.8059 (ppp) REVERT: E 93 ARG cc_start: 0.8431 (tpt-90) cc_final: 0.7294 (ttt180) REVERT: E 162 LYS cc_start: 0.8549 (ptmm) cc_final: 0.7892 (ptmm) REVERT: P 534 LYS cc_start: 0.8484 (mttm) cc_final: 0.8112 (tptp) REVERT: P 537 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: F 79 GLU cc_start: 0.8110 (tt0) cc_final: 0.7658 (tp30) REVERT: F 98 GLN cc_start: 0.9002 (tt0) cc_final: 0.8534 (mm110) REVERT: F 478 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8987 (mm) REVERT: F 520 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8568 (tttt) REVERT: F 522 GLN cc_start: 0.8583 (mt0) cc_final: 0.8156 (mm110) REVERT: Q 122 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8417 (tm-30) REVERT: Q 526 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8597 (mm-40) REVERT: G 79 GLU cc_start: 0.9053 (pp20) cc_final: 0.8787 (pp20) REVERT: G 91 ARG cc_start: 0.8790 (tpt170) cc_final: 0.8573 (tpt170) REVERT: G 124 ASP cc_start: 0.8876 (m-30) cc_final: 0.8511 (m-30) REVERT: G 472 ASP cc_start: 0.8514 (t0) cc_final: 0.8077 (t0) REVERT: R 16 ASN cc_start: 0.7905 (m110) cc_final: 0.6998 (t0) REVERT: R 79 GLU cc_start: 0.7962 (tp30) cc_final: 0.7568 (tp30) REVERT: R 108 ASP cc_start: 0.8127 (t70) cc_final: 0.7860 (t0) REVERT: R 164 ASP cc_start: 0.8043 (t0) cc_final: 0.7582 (p0) REVERT: R 503 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7601 (tm-30) REVERT: H 84 GLU cc_start: 0.6693 (mp0) cc_final: 0.6249 (mp0) REVERT: H 110 ASP cc_start: 0.8574 (m-30) cc_final: 0.8333 (m-30) REVERT: H 115 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8091 (tm-30) REVERT: H 162 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8319 (ttpp) REVERT: H 520 LYS cc_start: 0.8619 (pttm) cc_final: 0.8133 (tptt) REVERT: H 525 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8159 (tm-30) REVERT: S 19 ASN cc_start: 0.8931 (m110) cc_final: 0.8716 (m110) REVERT: S 124 ASP cc_start: 0.9133 (m-30) cc_final: 0.8908 (m-30) REVERT: S 540 GLN cc_start: 0.8918 (mm110) cc_final: 0.8641 (mm-40) REVERT: I 465 ASP cc_start: 0.8246 (m-30) cc_final: 0.7943 (m-30) REVERT: T 122 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8526 (tm-30) REVERT: T 147 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7307 (mt0) REVERT: T 498 ASN cc_start: 0.9272 (m-40) cc_final: 0.8955 (m-40) REVERT: J 94 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7427 (tp30) REVERT: U 491 ASN cc_start: 0.8975 (t0) cc_final: 0.8608 (t0) REVERT: K 520 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9064 (tttt) REVERT: V 94 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: V 131 GLN cc_start: 0.8451 (pp30) cc_final: 0.7956 (pp30) REVERT: V 514 GLU cc_start: 0.8424 (tp30) cc_final: 0.7831 (tp30) REVERT: L 61 LEU cc_start: 0.8994 (mp) cc_final: 0.8668 (mp) REVERT: L 91 ARG cc_start: 0.7499 (tpt170) cc_final: 0.7241 (tpt170) REVERT: L 108 ASP cc_start: 0.8573 (m-30) cc_final: 0.8028 (t0) REVERT: L 115 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8408 (tm-30) REVERT: L 474 PHE cc_start: 0.8783 (t80) cc_final: 0.8533 (t80) outliers start: 126 outliers final: 88 residues processed: 1028 average time/residue: 0.2548 time to fit residues: 434.1268 Evaluate side-chains 979 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 887 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 486 ASP Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 173 PHE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 491 ASN Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 171 ASN Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 506 ILE Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 489 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 76 GLN Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 466 ASP Chi-restraints excluded: chain L residue 173 PHE Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 428 optimal weight: 0.9980 chunk 519 optimal weight: 0.5980 chunk 346 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 531 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 434 optimal weight: 2.9990 chunk 527 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 424 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN B 507 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 151 ASN A 522 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 498 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 ASN N 491 ASN ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 129 GLN P 491 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 104 ASN F 113 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 39 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN S 22 GLN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 547 GLN J 470 GLN U 76 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 ASN K 494 ASN ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 104 ASN ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.084990 restraints weight = 662436.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089066 restraints weight = 214855.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.091791 restraints weight = 109704.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093609 restraints weight = 65731.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.094858 restraints weight = 43261.012| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 44330 Z= 0.153 Angle : 0.651 14.418 59994 Z= 0.352 Chirality : 0.040 0.333 7370 Planarity : 0.003 0.045 8140 Dihedral : 4.852 39.283 6182 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.64 % Allowed : 16.90 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.11), residues: 5896 helix: 3.05 (0.08), residues: 4312 sheet: 2.19 (0.24), residues: 352 loop : -1.64 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 125 TYR 0.020 0.002 TYR P 511 PHE 0.035 0.002 PHE O 474 Details of bonding type rmsd covalent geometry : bond 0.00327 (44330) covalent geometry : angle 0.65066 (59994) hydrogen bonds : bond 0.05206 ( 3615) hydrogen bonds : angle 3.86065 (10776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 940 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8103 (tmm) cc_final: 0.7536 (tmm) REVERT: A 117 LYS cc_start: 0.9109 (tptt) cc_final: 0.8861 (tppt) REVERT: A 121 ASP cc_start: 0.8926 (m-30) cc_final: 0.8556 (m-30) REVERT: A 514 GLU cc_start: 0.8892 (pm20) cc_final: 0.8474 (mp0) REVERT: M 94 GLU cc_start: 0.9379 (tm-30) cc_final: 0.8895 (tm-30) REVERT: M 122 GLU cc_start: 0.9123 (tp30) cc_final: 0.8840 (tp30) REVERT: M 484 ARG cc_start: 0.7712 (ttt180) cc_final: 0.6804 (mmt180) REVERT: M 541 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: C 89 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8824 (mp) REVERT: C 110 ASP cc_start: 0.7805 (t0) cc_final: 0.7239 (t0) REVERT: C 114 ASP cc_start: 0.8231 (m-30) cc_final: 0.7896 (m-30) REVERT: C 131 GLN cc_start: 0.8230 (pp30) cc_final: 0.7975 (pp30) REVERT: C 164 ASP cc_start: 0.7999 (p0) cc_final: 0.7643 (p0) REVERT: C 498 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.9007 (m-40) REVERT: C 541 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7172 (tm-30) REVERT: N 31 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7782 (mtt-85) REVERT: N 514 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8558 (mm-30) REVERT: D 20 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8191 (mmmt) REVERT: D 36 LEU cc_start: 0.8951 (tp) cc_final: 0.8738 (tp) REVERT: D 173 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: D 520 LYS cc_start: 0.8086 (mttt) cc_final: 0.7518 (mtpt) REVERT: O 20 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8105 (tttp) REVERT: O 52 ASN cc_start: 0.8959 (t0) cc_final: 0.8709 (t0) REVERT: O 115 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8013 (tm-30) REVERT: O 117 LYS cc_start: 0.8919 (tppp) cc_final: 0.8613 (tptp) REVERT: O 122 GLU cc_start: 0.8765 (tp30) cc_final: 0.8547 (tp30) REVERT: E 93 ARG cc_start: 0.8440 (tpt-90) cc_final: 0.7294 (ttt180) REVERT: P 534 LYS cc_start: 0.8478 (mttm) cc_final: 0.8107 (tptp) REVERT: P 537 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8635 (tm-30) REVERT: F 79 GLU cc_start: 0.8038 (tt0) cc_final: 0.7646 (tp30) REVERT: F 98 GLN cc_start: 0.8991 (tt0) cc_final: 0.8532 (mm110) REVERT: F 478 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9048 (mm) REVERT: F 520 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8592 (tttt) REVERT: F 522 GLN cc_start: 0.8611 (mt0) cc_final: 0.8223 (mm110) REVERT: Q 122 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8394 (tm-30) REVERT: Q 144 MET cc_start: 0.4982 (OUTLIER) cc_final: 0.4702 (ttt) REVERT: G 79 GLU cc_start: 0.9037 (pp20) cc_final: 0.8752 (pp20) REVERT: G 124 ASP cc_start: 0.8842 (m-30) cc_final: 0.8482 (m-30) REVERT: G 147 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: G 472 ASP cc_start: 0.8509 (t0) cc_final: 0.8075 (t0) REVERT: R 16 ASN cc_start: 0.7901 (m110) cc_final: 0.7154 (t0) REVERT: R 79 GLU cc_start: 0.7920 (tp30) cc_final: 0.7431 (tp30) REVERT: R 108 ASP cc_start: 0.8175 (t70) cc_final: 0.7888 (t70) REVERT: R 164 ASP cc_start: 0.8007 (t0) cc_final: 0.7635 (p0) REVERT: H 84 GLU cc_start: 0.6716 (mp0) cc_final: 0.6211 (mp0) REVERT: H 110 ASP cc_start: 0.8605 (m-30) cc_final: 0.8310 (m-30) REVERT: H 115 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8129 (tm-30) REVERT: H 162 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8276 (ttpp) REVERT: H 520 LYS cc_start: 0.8626 (pttm) cc_final: 0.8124 (tptt) REVERT: S 19 ASN cc_start: 0.8924 (m110) cc_final: 0.8704 (m110) REVERT: S 124 ASP cc_start: 0.9119 (m-30) cc_final: 0.8888 (m-30) REVERT: S 518 MET cc_start: 0.8734 (tmm) cc_final: 0.8397 (tmm) REVERT: I 465 ASP cc_start: 0.8144 (m-30) cc_final: 0.7922 (m-30) REVERT: T 122 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8559 (tm-30) REVERT: T 147 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7236 (mt0) REVERT: T 498 ASN cc_start: 0.9263 (m-40) cc_final: 0.8993 (m110) REVERT: J 87 ASN cc_start: 0.8968 (m-40) cc_final: 0.8576 (m-40) REVERT: J 122 GLU cc_start: 0.9191 (tp30) cc_final: 0.8980 (tp30) REVERT: U 491 ASN cc_start: 0.8964 (t0) cc_final: 0.8647 (t0) REVERT: K 520 LYS cc_start: 0.9375 (ttmt) cc_final: 0.9058 (tttt) REVERT: V 94 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: V 131 GLN cc_start: 0.8514 (pp30) cc_final: 0.8040 (pp30) REVERT: L 61 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8681 (mp) REVERT: L 91 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7151 (tpp-160) REVERT: L 108 ASP cc_start: 0.8568 (m-30) cc_final: 0.8029 (t0) REVERT: L 115 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8339 (tm-30) outliers start: 132 outliers final: 97 residues processed: 1000 average time/residue: 0.2496 time to fit residues: 416.6075 Evaluate side-chains 1006 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 899 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 486 ASP Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 6 ASN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 482 GLN Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 145 LYS Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 458 SER Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 506 ILE Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 489 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 76 GLN Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 466 ASP Chi-restraints excluded: chain V residue 525 GLN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 173 PHE Chi-restraints excluded: chain L residue 458 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 476 optimal weight: 0.6980 chunk 536 optimal weight: 0.1980 chunk 490 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 549 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 395 optimal weight: 0.8980 chunk 509 optimal weight: 1.9990 chunk 402 optimal weight: 3.9990 chunk 480 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN A 522 GLN M 19 ASN M 113 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 498 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 171 ASN ** N 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 536 ASN O 133 ASN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 491 ASN P 503 GLN P 507 GLN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN S 22 GLN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 547 GLN U 76 GLN U 90 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 GLN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084630 restraints weight = 607973.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.088617 restraints weight = 208224.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091242 restraints weight = 107427.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092998 restraints weight = 64888.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.094216 restraints weight = 42940.841| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 44330 Z= 0.159 Angle : 0.658 15.381 59994 Z= 0.355 Chirality : 0.041 0.431 7370 Planarity : 0.003 0.044 8140 Dihedral : 4.840 39.668 6182 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.76 % Allowed : 17.66 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.11), residues: 5896 helix: 3.02 (0.08), residues: 4312 sheet: 2.20 (0.24), residues: 352 loop : -1.67 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 31 TYR 0.017 0.002 TYR Q 511 PHE 0.037 0.002 PHE O 474 Details of bonding type rmsd covalent geometry : bond 0.00346 (44330) covalent geometry : angle 0.65845 (59994) hydrogen bonds : bond 0.05192 ( 3615) hydrogen bonds : angle 3.87121 (10776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 938 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8250 (tmm) cc_final: 0.7827 (tmm) REVERT: A 117 LYS cc_start: 0.9111 (tptt) cc_final: 0.8851 (tppt) REVERT: A 121 ASP cc_start: 0.8889 (m-30) cc_final: 0.8521 (m-30) REVERT: A 514 GLU cc_start: 0.8892 (pm20) cc_final: 0.8551 (mp0) REVERT: M 79 GLU cc_start: 0.8659 (pp20) cc_final: 0.8437 (pp20) REVERT: M 94 GLU cc_start: 0.9357 (tm-30) cc_final: 0.8906 (tm-30) REVERT: M 124 ASP cc_start: 0.7937 (m-30) cc_final: 0.7698 (m-30) REVERT: M 484 ARG cc_start: 0.7726 (ttt180) cc_final: 0.6784 (mmt180) REVERT: M 510 ASP cc_start: 0.7618 (t0) cc_final: 0.7402 (t0) REVERT: M 541 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: C 110 ASP cc_start: 0.7807 (t0) cc_final: 0.7249 (t0) REVERT: C 114 ASP cc_start: 0.8249 (m-30) cc_final: 0.7918 (m-30) REVERT: C 117 LYS cc_start: 0.9063 (tptp) cc_final: 0.8715 (tptp) REVERT: C 131 GLN cc_start: 0.8183 (pp30) cc_final: 0.7927 (pp30) REVERT: C 514 GLU cc_start: 0.7138 (mp0) cc_final: 0.6832 (mp0) REVERT: C 541 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7495 (tm-30) REVERT: N 31 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7951 (tpp80) REVERT: D 20 LYS cc_start: 0.8578 (mtmm) cc_final: 0.8197 (mmmt) REVERT: D 173 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: D 459 ASP cc_start: 0.8284 (t0) cc_final: 0.7967 (m-30) REVERT: D 520 LYS cc_start: 0.8114 (mttt) cc_final: 0.7534 (mtpt) REVERT: O 20 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8094 (tttp) REVERT: O 52 ASN cc_start: 0.8959 (t0) cc_final: 0.8695 (t0) REVERT: O 91 ARG cc_start: 0.8731 (tpt170) cc_final: 0.8010 (tpp-160) REVERT: O 117 LYS cc_start: 0.8907 (tppp) cc_final: 0.8593 (tptp) REVERT: O 510 ASP cc_start: 0.7288 (t70) cc_final: 0.7083 (t0) REVERT: E 93 ARG cc_start: 0.8459 (tpt-90) cc_final: 0.7313 (ttt180) REVERT: E 162 LYS cc_start: 0.8590 (ptmm) cc_final: 0.8031 (ptmm) REVERT: P 534 LYS cc_start: 0.8456 (mttm) cc_final: 0.8066 (tptp) REVERT: P 537 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: P 541 GLN cc_start: 0.9005 (pm20) cc_final: 0.8647 (pm20) REVERT: F 79 GLU cc_start: 0.8067 (tt0) cc_final: 0.7687 (tp30) REVERT: F 98 GLN cc_start: 0.8969 (tt0) cc_final: 0.8528 (mm110) REVERT: F 478 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9065 (mm) REVERT: F 520 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8592 (tttt) REVERT: F 522 GLN cc_start: 0.8667 (mt0) cc_final: 0.8269 (mm110) REVERT: Q 122 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8474 (tm-30) REVERT: Q 144 MET cc_start: 0.4988 (OUTLIER) cc_final: 0.4778 (ttt) REVERT: G 79 GLU cc_start: 0.9046 (pp20) cc_final: 0.8768 (pp20) REVERT: G 124 ASP cc_start: 0.8881 (m-30) cc_final: 0.8525 (m-30) REVERT: G 472 ASP cc_start: 0.8514 (t0) cc_final: 0.8063 (t0) REVERT: G 485 LEU cc_start: 0.9211 (mm) cc_final: 0.8955 (mp) REVERT: R 16 ASN cc_start: 0.7904 (m110) cc_final: 0.7069 (t0) REVERT: R 79 GLU cc_start: 0.7864 (tp30) cc_final: 0.7353 (tp30) REVERT: R 108 ASP cc_start: 0.8170 (t70) cc_final: 0.7892 (t70) REVERT: R 164 ASP cc_start: 0.7873 (t0) cc_final: 0.7512 (p0) REVERT: R 536 ASN cc_start: 0.8343 (m110) cc_final: 0.8045 (m110) REVERT: H 84 GLU cc_start: 0.6717 (mp0) cc_final: 0.6181 (mp0) REVERT: H 110 ASP cc_start: 0.8598 (m-30) cc_final: 0.8329 (m-30) REVERT: H 115 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8115 (tm-30) REVERT: H 145 LYS cc_start: 0.8914 (mttm) cc_final: 0.8461 (mtpt) REVERT: H 161 LYS cc_start: 0.8958 (pttt) cc_final: 0.8272 (tptt) REVERT: H 162 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8212 (ttpp) REVERT: H 520 LYS cc_start: 0.8750 (pttm) cc_final: 0.8164 (tptt) REVERT: S 19 ASN cc_start: 0.8904 (m110) cc_final: 0.8673 (m110) REVERT: S 124 ASP cc_start: 0.9121 (m-30) cc_final: 0.8892 (m-30) REVERT: S 518 MET cc_start: 0.8719 (tmm) cc_final: 0.8319 (tmm) REVERT: I 465 ASP cc_start: 0.8146 (m-30) cc_final: 0.7924 (m-30) REVERT: I 518 MET cc_start: 0.8346 (ppp) cc_final: 0.8128 (tmm) REVERT: T 115 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7338 (tm-30) REVERT: T 122 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8559 (tm-30) REVERT: T 147 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7130 (mt0) REVERT: T 498 ASN cc_start: 0.9267 (m-40) cc_final: 0.8992 (m110) REVERT: J 87 ASN cc_start: 0.8957 (m-40) cc_final: 0.8561 (m-40) REVERT: J 122 GLU cc_start: 0.9217 (tp30) cc_final: 0.8935 (tp30) REVERT: K 520 LYS cc_start: 0.9383 (ttmt) cc_final: 0.9072 (tttt) REVERT: K 537 GLN cc_start: 0.7611 (pt0) cc_final: 0.6654 (pp30) REVERT: V 94 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: V 131 GLN cc_start: 0.8531 (pp30) cc_final: 0.8046 (pp30) REVERT: L 61 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8709 (mp) REVERT: L 91 ARG cc_start: 0.7514 (tpt170) cc_final: 0.7264 (tpt170) REVERT: L 108 ASP cc_start: 0.8566 (m-30) cc_final: 0.8042 (t0) REVERT: L 115 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8400 (tm-30) outliers start: 138 outliers final: 98 residues processed: 1004 average time/residue: 0.2478 time to fit residues: 414.9968 Evaluate side-chains 1000 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 895 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 486 ASP Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 482 GLN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 32 LEU Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 145 LYS Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 538 VAL Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 144 MET Chi-restraints excluded: chain Q residue 458 SER Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 506 ILE Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain J residue 489 VAL Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 76 GLN Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 466 ASP Chi-restraints excluded: chain V residue 525 GLN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 458 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 542 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 305 optimal weight: 0.9990 chunk 568 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 540 GLN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 491 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN S 22 GLN ** S 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 491 ASN ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 GLN U 90 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.100568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.085063 restraints weight = 626834.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.089138 restraints weight = 212205.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.091819 restraints weight = 109376.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093615 restraints weight = 66093.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.094856 restraints weight = 43811.814| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 44330 Z= 0.150 Angle : 0.661 15.453 59994 Z= 0.354 Chirality : 0.040 0.393 7370 Planarity : 0.003 0.043 8140 Dihedral : 4.793 39.225 6182 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.50 % Allowed : 18.52 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.11), residues: 5896 helix: 3.01 (0.08), residues: 4312 sheet: 2.22 (0.25), residues: 352 loop : -1.69 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 475 TYR 0.019 0.002 TYR P 511 PHE 0.030 0.002 PHE S 132 Details of bonding type rmsd covalent geometry : bond 0.00321 (44330) covalent geometry : angle 0.66104 (59994) hydrogen bonds : bond 0.05093 ( 3615) hydrogen bonds : angle 3.82373 (10776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 944 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8362 (tmm) cc_final: 0.7935 (tmm) REVERT: A 117 LYS cc_start: 0.9094 (tptt) cc_final: 0.8846 (tppt) REVERT: A 121 ASP cc_start: 0.8886 (m-30) cc_final: 0.8519 (m-30) REVERT: M 124 ASP cc_start: 0.7911 (m-30) cc_final: 0.7660 (m-30) REVERT: M 484 ARG cc_start: 0.7701 (ttt180) cc_final: 0.6768 (mmt180) REVERT: M 510 ASP cc_start: 0.7645 (t0) cc_final: 0.7423 (t0) REVERT: M 541 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: C 110 ASP cc_start: 0.7747 (t0) cc_final: 0.7188 (t0) REVERT: C 114 ASP cc_start: 0.8224 (m-30) cc_final: 0.7863 (m-30) REVERT: C 117 LYS cc_start: 0.9075 (tptp) cc_final: 0.8799 (tptp) REVERT: C 164 ASP cc_start: 0.7960 (p0) cc_final: 0.7564 (p0) REVERT: C 514 GLU cc_start: 0.7130 (mp0) cc_final: 0.6705 (mp0) REVERT: C 541 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7485 (tm-30) REVERT: N 9 SER cc_start: 0.8901 (p) cc_final: 0.8479 (m) REVERT: N 31 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7951 (tpp80) REVERT: N 514 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8613 (mm-30) REVERT: D 20 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8190 (mmmt) REVERT: D 170 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5043 (pp) REVERT: D 173 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: D 520 LYS cc_start: 0.8111 (mttt) cc_final: 0.7531 (mtpt) REVERT: O 20 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8061 (tttp) REVERT: O 52 ASN cc_start: 0.8959 (t0) cc_final: 0.8693 (t0) REVERT: O 91 ARG cc_start: 0.8646 (tpt170) cc_final: 0.8053 (tpp-160) REVERT: O 94 GLU cc_start: 0.8550 (pm20) cc_final: 0.8323 (pm20) REVERT: O 117 LYS cc_start: 0.8865 (tppp) cc_final: 0.8548 (tptp) REVERT: O 473 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8338 (ptmt) REVERT: E 93 ARG cc_start: 0.8446 (tpt-90) cc_final: 0.7298 (ttt180) REVERT: E 162 LYS cc_start: 0.8637 (ptmm) cc_final: 0.8373 (ptmm) REVERT: P 534 LYS cc_start: 0.8449 (mttm) cc_final: 0.7986 (tptp) REVERT: P 537 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: P 541 GLN cc_start: 0.8964 (pm20) cc_final: 0.8635 (pm20) REVERT: F 79 GLU cc_start: 0.7994 (tt0) cc_final: 0.7576 (tp30) REVERT: F 98 GLN cc_start: 0.8933 (tt0) cc_final: 0.8523 (mm110) REVERT: F 129 GLN cc_start: 0.8541 (mp10) cc_final: 0.7737 (mt0) REVERT: F 478 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9053 (mm) REVERT: F 520 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8643 (tttt) REVERT: F 522 GLN cc_start: 0.8676 (mt0) cc_final: 0.8285 (mm110) REVERT: Q 122 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8451 (tm-30) REVERT: G 79 GLU cc_start: 0.9028 (pp20) cc_final: 0.8753 (pp20) REVERT: G 124 ASP cc_start: 0.8883 (m-30) cc_final: 0.8524 (m-30) REVERT: G 455 GLU cc_start: 0.7316 (pm20) cc_final: 0.6827 (pm20) REVERT: G 472 ASP cc_start: 0.8518 (t0) cc_final: 0.8067 (t0) REVERT: G 485 LEU cc_start: 0.9202 (mm) cc_final: 0.8947 (mp) REVERT: R 16 ASN cc_start: 0.7865 (m110) cc_final: 0.7051 (t0) REVERT: R 108 ASP cc_start: 0.8177 (t70) cc_final: 0.7895 (t70) REVERT: R 164 ASP cc_start: 0.7856 (t0) cc_final: 0.7513 (p0) REVERT: R 536 ASN cc_start: 0.8339 (m110) cc_final: 0.8054 (m110) REVERT: H 21 ASN cc_start: 0.8415 (t0) cc_final: 0.7919 (t0) REVERT: H 84 GLU cc_start: 0.6726 (mp0) cc_final: 0.6218 (mp0) REVERT: H 110 ASP cc_start: 0.8595 (m-30) cc_final: 0.8341 (m-30) REVERT: H 115 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8128 (tm-30) REVERT: H 145 LYS cc_start: 0.8920 (mttm) cc_final: 0.8442 (mtpt) REVERT: H 161 LYS cc_start: 0.8936 (pttt) cc_final: 0.8271 (tptt) REVERT: H 520 LYS cc_start: 0.8749 (pttm) cc_final: 0.8157 (tptt) REVERT: S 19 ASN cc_start: 0.8857 (m110) cc_final: 0.8602 (m110) REVERT: S 124 ASP cc_start: 0.9114 (m-30) cc_final: 0.8882 (m-30) REVERT: S 518 MET cc_start: 0.8670 (tmm) cc_final: 0.8240 (tmm) REVERT: I 465 ASP cc_start: 0.8137 (m-30) cc_final: 0.7917 (m-30) REVERT: I 518 MET cc_start: 0.8347 (ppp) cc_final: 0.8116 (tmm) REVERT: T 122 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8593 (tm-30) REVERT: T 498 ASN cc_start: 0.9229 (m-40) cc_final: 0.9007 (m110) REVERT: J 87 ASN cc_start: 0.8924 (m-40) cc_final: 0.8524 (m-40) REVERT: J 122 GLU cc_start: 0.9173 (tp30) cc_final: 0.8749 (tp30) REVERT: K 475 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.7758 (tpt170) REVERT: K 518 MET cc_start: 0.7356 (tmm) cc_final: 0.7055 (tmm) REVERT: K 520 LYS cc_start: 0.9375 (ttmt) cc_final: 0.9074 (tttt) REVERT: K 537 GLN cc_start: 0.7572 (pt0) cc_final: 0.6636 (pp30) REVERT: V 94 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: V 131 GLN cc_start: 0.8495 (pp30) cc_final: 0.8029 (pp30) REVERT: L 31 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8367 (ttm170) REVERT: L 61 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8733 (mp) REVERT: L 91 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7169 (tpp-160) REVERT: L 108 ASP cc_start: 0.8558 (m-30) cc_final: 0.8037 (t0) REVERT: L 115 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8361 (tm-30) outliers start: 125 outliers final: 89 residues processed: 1000 average time/residue: 0.2539 time to fit residues: 421.8064 Evaluate side-chains 984 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 888 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 486 ASP Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 482 GLN Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 478 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 145 LYS Chi-restraints excluded: chain P residue 491 ASN Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 458 SER Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain Q residue 543 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain H residue 151 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 491 ASN Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain T residue 546 LEU Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 173 PHE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 525 GLN Chi-restraints excluded: chain V residue 543 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 458 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 103 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 399 optimal weight: 0.7980 chunk 191 optimal weight: 0.0670 chunk 309 optimal weight: 0.6980 chunk 258 optimal weight: 3.9990 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 ASN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 129 GLN P 491 ASN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 GLN ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.101129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085393 restraints weight = 667356.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089549 restraints weight = 217422.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092298 restraints weight = 111005.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094130 restraints weight = 66770.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095401 restraints weight = 44099.349| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 44330 Z= 0.147 Angle : 0.671 15.281 59994 Z= 0.358 Chirality : 0.041 0.390 7370 Planarity : 0.003 0.043 8140 Dihedral : 4.752 39.125 6182 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.16 % Allowed : 19.14 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.11), residues: 5896 helix: 2.99 (0.08), residues: 4312 sheet: 2.22 (0.25), residues: 352 loop : -1.67 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 505 TYR 0.016 0.002 TYR P 511 PHE 0.031 0.002 PHE S 132 Details of bonding type rmsd covalent geometry : bond 0.00310 (44330) covalent geometry : angle 0.67060 (59994) hydrogen bonds : bond 0.05001 ( 3615) hydrogen bonds : angle 3.79291 (10776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 919 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8443 (tmm) cc_final: 0.8014 (tmm) REVERT: A 117 LYS cc_start: 0.9057 (tptt) cc_final: 0.8838 (tppt) REVERT: A 121 ASP cc_start: 0.8896 (m-30) cc_final: 0.8534 (m-30) REVERT: A 496 THR cc_start: 0.9215 (m) cc_final: 0.8881 (p) REVERT: A 534 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7874 (mtpt) REVERT: M 124 ASP cc_start: 0.7890 (m-30) cc_final: 0.7646 (m-30) REVERT: M 484 ARG cc_start: 0.7644 (ttt180) cc_final: 0.6726 (mmt180) REVERT: M 510 ASP cc_start: 0.7649 (t0) cc_final: 0.7436 (t0) REVERT: M 541 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: C 110 ASP cc_start: 0.7703 (t0) cc_final: 0.7150 (t0) REVERT: C 114 ASP cc_start: 0.8195 (m-30) cc_final: 0.7820 (m-30) REVERT: C 117 LYS cc_start: 0.9054 (tptp) cc_final: 0.8808 (tptp) REVERT: C 164 ASP cc_start: 0.7933 (p0) cc_final: 0.7524 (p0) REVERT: C 501 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7292 (mm-30) REVERT: C 514 GLU cc_start: 0.6944 (mp0) cc_final: 0.6649 (mp0) REVERT: C 541 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7463 (tm-30) REVERT: N 9 SER cc_start: 0.8803 (p) cc_final: 0.8411 (m) REVERT: N 31 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7524 (mmm-85) REVERT: N 514 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8613 (mm-30) REVERT: D 20 LYS cc_start: 0.8511 (mtmm) cc_final: 0.8125 (mmmt) REVERT: D 36 LEU cc_start: 0.9043 (tt) cc_final: 0.8800 (tp) REVERT: D 170 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.5042 (pp) REVERT: D 173 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: D 520 LYS cc_start: 0.8098 (mttt) cc_final: 0.7524 (mtpt) REVERT: O 20 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8062 (tttp) REVERT: O 52 ASN cc_start: 0.8960 (t0) cc_final: 0.8690 (t0) REVERT: O 117 LYS cc_start: 0.8850 (tppp) cc_final: 0.8494 (tptm) REVERT: O 122 GLU cc_start: 0.8766 (tp30) cc_final: 0.8565 (tp30) REVERT: O 473 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8250 (ptmt) REVERT: E 93 ARG cc_start: 0.8448 (tpt-90) cc_final: 0.7301 (ttt180) REVERT: E 140 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8693 (tptt) REVERT: P 491 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8159 (t0) REVERT: P 514 GLU cc_start: 0.8526 (tp30) cc_final: 0.8125 (tp30) REVERT: P 534 LYS cc_start: 0.8435 (mttm) cc_final: 0.7977 (tptp) REVERT: P 537 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: P 541 GLN cc_start: 0.8959 (pm20) cc_final: 0.8647 (pm20) REVERT: F 79 GLU cc_start: 0.7996 (tt0) cc_final: 0.7568 (tp30) REVERT: F 98 GLN cc_start: 0.8886 (tt0) cc_final: 0.8494 (mm110) REVERT: F 129 GLN cc_start: 0.8546 (mp10) cc_final: 0.7666 (mt0) REVERT: F 478 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9042 (mm) REVERT: F 520 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8629 (tttt) REVERT: F 522 GLN cc_start: 0.8682 (mt0) cc_final: 0.8288 (mm110) REVERT: Q 94 GLU cc_start: 0.8393 (tp30) cc_final: 0.7928 (tp30) REVERT: Q 122 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8285 (tm-30) REVERT: G 63 GLN cc_start: 0.8831 (mm110) cc_final: 0.8529 (mp10) REVERT: G 79 GLU cc_start: 0.9031 (pp20) cc_final: 0.8759 (pp20) REVERT: G 124 ASP cc_start: 0.8885 (m-30) cc_final: 0.8513 (m-30) REVERT: G 455 GLU cc_start: 0.7288 (pm20) cc_final: 0.6857 (pm20) REVERT: G 472 ASP cc_start: 0.8514 (t0) cc_final: 0.8057 (t0) REVERT: R 16 ASN cc_start: 0.7840 (m110) cc_final: 0.7018 (t0) REVERT: R 108 ASP cc_start: 0.8162 (t70) cc_final: 0.7882 (t70) REVERT: R 122 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8035 (tp30) REVERT: R 164 ASP cc_start: 0.7853 (t0) cc_final: 0.7544 (p0) REVERT: R 536 ASN cc_start: 0.8391 (m110) cc_final: 0.8111 (m110) REVERT: H 21 ASN cc_start: 0.8381 (t0) cc_final: 0.7871 (t0) REVERT: H 110 ASP cc_start: 0.8598 (m-30) cc_final: 0.8344 (m-30) REVERT: H 115 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8131 (tm-30) REVERT: H 145 LYS cc_start: 0.8891 (mttm) cc_final: 0.8440 (mtpt) REVERT: H 161 LYS cc_start: 0.8958 (pttt) cc_final: 0.8282 (tptt) REVERT: H 162 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8095 (ttpp) REVERT: H 520 LYS cc_start: 0.8756 (pttm) cc_final: 0.8121 (tptt) REVERT: S 19 ASN cc_start: 0.8848 (m110) cc_final: 0.8625 (m110) REVERT: S 124 ASP cc_start: 0.9110 (m-30) cc_final: 0.8871 (m-30) REVERT: S 518 MET cc_start: 0.8666 (tmm) cc_final: 0.8213 (tmm) REVERT: I 30 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7673 (tm-30) REVERT: I 465 ASP cc_start: 0.8144 (m-30) cc_final: 0.7922 (m-30) REVERT: I 518 MET cc_start: 0.8388 (ppp) cc_final: 0.8159 (tmm) REVERT: T 122 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8580 (tm-30) REVERT: J 87 ASN cc_start: 0.8914 (m-40) cc_final: 0.8526 (m-40) REVERT: J 94 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7419 (tp30) REVERT: J 122 GLU cc_start: 0.9158 (tp30) cc_final: 0.8748 (tp30) REVERT: U 117 LYS cc_start: 0.9220 (tppt) cc_final: 0.8898 (tttt) REVERT: K 475 ARG cc_start: 0.8494 (mtt-85) cc_final: 0.7732 (tpt170) REVERT: K 518 MET cc_start: 0.7358 (tmm) cc_final: 0.7027 (tmm) REVERT: K 520 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9012 (tttt) REVERT: K 537 GLN cc_start: 0.7568 (pt0) cc_final: 0.6605 (pp30) REVERT: V 131 GLN cc_start: 0.8486 (pp30) cc_final: 0.8006 (pp30) REVERT: L 61 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8700 (mp) REVERT: L 91 ARG cc_start: 0.7448 (tpt170) cc_final: 0.7089 (tpp-160) REVERT: L 115 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8365 (tm-30) outliers start: 108 outliers final: 86 residues processed: 970 average time/residue: 0.2526 time to fit residues: 408.8721 Evaluate side-chains 972 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 879 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 482 GLN Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 478 LEU Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 145 LYS Chi-restraints excluded: chain P residue 491 ASN Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 458 SER Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 173 PHE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 525 GLN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 506 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 39 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 394 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 294 optimal weight: 0.8980 chunk 234 optimal weight: 0.0020 chunk 163 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 418 optimal weight: 10.0000 chunk 127 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 470 GLN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 491 ASN ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 498 ASN ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.101052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.085327 restraints weight = 667887.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.089478 restraints weight = 218238.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092215 restraints weight = 111621.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094056 restraints weight = 67171.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095316 restraints weight = 44266.507| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 44330 Z= 0.181 Angle : 0.785 59.195 59994 Z= 0.440 Chirality : 0.041 0.401 7370 Planarity : 0.003 0.096 8140 Dihedral : 4.740 39.209 6182 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.02 % Allowed : 19.76 % Favored : 78.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.11), residues: 5896 helix: 2.98 (0.08), residues: 4312 sheet: 2.21 (0.25), residues: 352 loop : -1.67 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG G 505 TYR 0.011 0.002 TYR P 511 PHE 0.029 0.002 PHE S 132 Details of bonding type rmsd covalent geometry : bond 0.00393 (44330) covalent geometry : angle 0.78489 (59994) hydrogen bonds : bond 0.05003 ( 3615) hydrogen bonds : angle 3.80271 (10776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 878 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8455 (tmm) cc_final: 0.8032 (tmm) REVERT: A 117 LYS cc_start: 0.9058 (tptt) cc_final: 0.8839 (tppt) REVERT: A 121 ASP cc_start: 0.8895 (m-30) cc_final: 0.8541 (m-30) REVERT: A 496 THR cc_start: 0.9215 (m) cc_final: 0.8878 (p) REVERT: A 514 GLU cc_start: 0.8851 (pm20) cc_final: 0.8382 (mp0) REVERT: A 534 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7825 (mtpt) REVERT: M 484 ARG cc_start: 0.7655 (ttt180) cc_final: 0.6729 (mmt180) REVERT: M 510 ASP cc_start: 0.7642 (t0) cc_final: 0.7410 (t0) REVERT: M 541 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: C 110 ASP cc_start: 0.7696 (t0) cc_final: 0.7146 (t0) REVERT: C 114 ASP cc_start: 0.8192 (m-30) cc_final: 0.7817 (m-30) REVERT: C 164 ASP cc_start: 0.7922 (p0) cc_final: 0.7524 (p0) REVERT: C 514 GLU cc_start: 0.6929 (mp0) cc_final: 0.6651 (mp0) REVERT: C 541 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7462 (tm-30) REVERT: N 9 SER cc_start: 0.8798 (p) cc_final: 0.8407 (m) REVERT: N 31 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7527 (mmm-85) REVERT: N 514 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8616 (mm-30) REVERT: D 20 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8133 (mmmt) REVERT: D 36 LEU cc_start: 0.9032 (tt) cc_final: 0.8805 (tp) REVERT: D 170 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.5060 (pp) REVERT: D 173 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: D 459 ASP cc_start: 0.8191 (t0) cc_final: 0.7858 (m-30) REVERT: D 520 LYS cc_start: 0.8107 (mttt) cc_final: 0.7532 (mtpt) REVERT: O 20 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8062 (tttp) REVERT: O 52 ASN cc_start: 0.8952 (t0) cc_final: 0.8684 (t0) REVERT: O 117 LYS cc_start: 0.8859 (tppp) cc_final: 0.8495 (tptm) REVERT: O 473 LYS cc_start: 0.8544 (mmtt) cc_final: 0.8251 (ptmt) REVERT: E 93 ARG cc_start: 0.8449 (tpt-90) cc_final: 0.7302 (ttt180) REVERT: E 140 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8692 (tptt) REVERT: P 514 GLU cc_start: 0.8511 (tp30) cc_final: 0.8113 (tp30) REVERT: P 534 LYS cc_start: 0.8436 (mttm) cc_final: 0.7976 (tptp) REVERT: P 537 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: P 541 GLN cc_start: 0.8958 (pm20) cc_final: 0.8642 (pm20) REVERT: F 79 GLU cc_start: 0.7998 (tt0) cc_final: 0.7568 (tp30) REVERT: F 98 GLN cc_start: 0.8885 (tt0) cc_final: 0.8494 (mm110) REVERT: F 129 GLN cc_start: 0.8545 (mp10) cc_final: 0.7657 (mt0) REVERT: F 478 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9039 (mm) REVERT: F 520 LYS cc_start: 0.8999 (mtmm) cc_final: 0.8633 (tttt) REVERT: F 522 GLN cc_start: 0.8687 (mt0) cc_final: 0.8289 (mm110) REVERT: Q 94 GLU cc_start: 0.8387 (tp30) cc_final: 0.7909 (tp30) REVERT: Q 122 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8328 (tm-30) REVERT: G 63 GLN cc_start: 0.8828 (mm110) cc_final: 0.8524 (mp10) REVERT: G 79 GLU cc_start: 0.9033 (pp20) cc_final: 0.8764 (pp20) REVERT: G 124 ASP cc_start: 0.8867 (m-30) cc_final: 0.8499 (m-30) REVERT: G 455 GLU cc_start: 0.7282 (pm20) cc_final: 0.6876 (pm20) REVERT: G 472 ASP cc_start: 0.8523 (t0) cc_final: 0.8067 (t0) REVERT: R 16 ASN cc_start: 0.7867 (m110) cc_final: 0.7019 (t0) REVERT: R 108 ASP cc_start: 0.8157 (t70) cc_final: 0.7880 (t70) REVERT: R 122 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8040 (tp30) REVERT: R 164 ASP cc_start: 0.7866 (t0) cc_final: 0.7548 (p0) REVERT: R 536 ASN cc_start: 0.8391 (m110) cc_final: 0.8108 (m110) REVERT: H 21 ASN cc_start: 0.8385 (t0) cc_final: 0.7867 (t0) REVERT: H 110 ASP cc_start: 0.8583 (m-30) cc_final: 0.8318 (m-30) REVERT: H 115 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8135 (tm-30) REVERT: H 145 LYS cc_start: 0.8880 (mttm) cc_final: 0.8439 (mtpt) REVERT: H 161 LYS cc_start: 0.8962 (pttt) cc_final: 0.8285 (tptt) REVERT: H 162 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8091 (ttpp) REVERT: H 520 LYS cc_start: 0.8759 (pttm) cc_final: 0.8124 (tptt) REVERT: S 19 ASN cc_start: 0.8844 (m110) cc_final: 0.8623 (m110) REVERT: S 124 ASP cc_start: 0.9116 (m-30) cc_final: 0.8880 (m-30) REVERT: S 518 MET cc_start: 0.8667 (tmm) cc_final: 0.8220 (tmm) REVERT: I 30 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7666 (tm-30) REVERT: I 465 ASP cc_start: 0.8140 (m-30) cc_final: 0.7917 (m-30) REVERT: I 518 MET cc_start: 0.8391 (ppp) cc_final: 0.8161 (tmm) REVERT: T 122 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8590 (tm-30) REVERT: J 87 ASN cc_start: 0.8915 (m-40) cc_final: 0.8528 (m-40) REVERT: J 94 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7422 (tp30) REVERT: J 122 GLU cc_start: 0.9156 (tp30) cc_final: 0.8750 (tp30) REVERT: K 475 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.7738 (tpt170) REVERT: K 518 MET cc_start: 0.7358 (tmm) cc_final: 0.7028 (tmm) REVERT: K 520 LYS cc_start: 0.9366 (ttmt) cc_final: 0.9008 (tttt) REVERT: K 537 GLN cc_start: 0.7567 (pt0) cc_final: 0.6608 (pp30) REVERT: V 95 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8312 (mp) REVERT: V 131 GLN cc_start: 0.8489 (pp30) cc_final: 0.8004 (pp30) REVERT: V 466 ASP cc_start: 0.8246 (m-30) cc_final: 0.7878 (m-30) REVERT: L 61 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8697 (mp) REVERT: L 91 ARG cc_start: 0.7432 (tpt170) cc_final: 0.7087 (tpp-160) REVERT: L 108 ASP cc_start: 0.8567 (m-30) cc_final: 0.7997 (t0) REVERT: L 115 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8357 (tm-30) outliers start: 101 outliers final: 88 residues processed: 928 average time/residue: 0.2463 time to fit residues: 384.0301 Evaluate side-chains 966 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 871 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 482 GLN Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 478 LEU Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 145 LYS Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 173 PHE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 525 GLN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 347 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 301 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 455 optimal weight: 0.5980 chunk 437 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 470 GLN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.101102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.085506 restraints weight = 634384.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.089619 restraints weight = 213315.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092304 restraints weight = 109877.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.094115 restraints weight = 66778.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095359 restraints weight = 44152.176| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 44330 Z= 0.181 Angle : 0.785 59.200 59994 Z= 0.440 Chirality : 0.041 0.401 7370 Planarity : 0.003 0.096 8140 Dihedral : 4.740 39.209 6182 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.90 % Allowed : 19.88 % Favored : 78.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.11), residues: 5896 helix: 2.98 (0.08), residues: 4312 sheet: 2.21 (0.25), residues: 352 loop : -1.67 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG G 505 TYR 0.011 0.002 TYR P 511 PHE 0.029 0.002 PHE S 132 Details of bonding type rmsd covalent geometry : bond 0.00392 (44330) covalent geometry : angle 0.78477 (59994) hydrogen bonds : bond 0.05003 ( 3615) hydrogen bonds : angle 3.80272 (10776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11792 Ramachandran restraints generated. 5896 Oldfield, 0 Emsley, 5896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 871 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 518 MET cc_start: 0.8458 (tmm) cc_final: 0.8033 (tmm) REVERT: A 117 LYS cc_start: 0.9056 (tptt) cc_final: 0.8835 (tppt) REVERT: A 121 ASP cc_start: 0.8895 (m-30) cc_final: 0.8542 (m-30) REVERT: A 496 THR cc_start: 0.9214 (m) cc_final: 0.8876 (p) REVERT: A 514 GLU cc_start: 0.8855 (pm20) cc_final: 0.8386 (mp0) REVERT: A 534 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7822 (mtpt) REVERT: M 484 ARG cc_start: 0.7654 (ttt180) cc_final: 0.6730 (mmt180) REVERT: M 510 ASP cc_start: 0.7649 (t0) cc_final: 0.7414 (t0) REVERT: M 541 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: C 110 ASP cc_start: 0.7708 (t0) cc_final: 0.7154 (t0) REVERT: C 114 ASP cc_start: 0.8195 (m-30) cc_final: 0.7819 (m-30) REVERT: C 164 ASP cc_start: 0.7936 (p0) cc_final: 0.7533 (p0) REVERT: C 514 GLU cc_start: 0.6935 (mp0) cc_final: 0.6656 (mp0) REVERT: C 541 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7451 (tm-30) REVERT: N 9 SER cc_start: 0.8799 (p) cc_final: 0.8408 (m) REVERT: N 31 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7525 (mmm-85) REVERT: N 514 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8619 (mm-30) REVERT: D 20 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8130 (mmmt) REVERT: D 36 LEU cc_start: 0.9034 (tt) cc_final: 0.8806 (tp) REVERT: D 170 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.5052 (pp) REVERT: D 173 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: D 459 ASP cc_start: 0.8227 (t0) cc_final: 0.7894 (m-30) REVERT: D 520 LYS cc_start: 0.8109 (mttt) cc_final: 0.7535 (mtpt) REVERT: O 20 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8061 (tttp) REVERT: O 52 ASN cc_start: 0.8955 (t0) cc_final: 0.8686 (t0) REVERT: O 117 LYS cc_start: 0.8862 (tppp) cc_final: 0.8495 (tptm) REVERT: O 473 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8249 (ptmt) REVERT: E 93 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.7301 (ttt180) REVERT: E 140 LYS cc_start: 0.9025 (mtmm) cc_final: 0.8692 (tptt) REVERT: P 514 GLU cc_start: 0.8522 (tp30) cc_final: 0.8122 (tp30) REVERT: P 534 LYS cc_start: 0.8437 (mttm) cc_final: 0.7976 (tptp) REVERT: P 537 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8561 (tm-30) REVERT: P 541 GLN cc_start: 0.8955 (pm20) cc_final: 0.8640 (pm20) REVERT: F 79 GLU cc_start: 0.7997 (tt0) cc_final: 0.7567 (tp30) REVERT: F 98 GLN cc_start: 0.8893 (tt0) cc_final: 0.8492 (mm110) REVERT: F 129 GLN cc_start: 0.8543 (mp10) cc_final: 0.7656 (mt0) REVERT: F 478 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9041 (mm) REVERT: F 520 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8635 (tttt) REVERT: F 522 GLN cc_start: 0.8695 (mt0) cc_final: 0.8292 (mm110) REVERT: Q 94 GLU cc_start: 0.8366 (tp30) cc_final: 0.7914 (tp30) REVERT: Q 122 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8325 (tm-30) REVERT: G 63 GLN cc_start: 0.8835 (mm110) cc_final: 0.8525 (mp10) REVERT: G 79 GLU cc_start: 0.9034 (pp20) cc_final: 0.8765 (pp20) REVERT: G 124 ASP cc_start: 0.8870 (m-30) cc_final: 0.8501 (m-30) REVERT: G 455 GLU cc_start: 0.7276 (pm20) cc_final: 0.6872 (pm20) REVERT: G 472 ASP cc_start: 0.8518 (t0) cc_final: 0.8063 (t0) REVERT: R 16 ASN cc_start: 0.7870 (m110) cc_final: 0.7020 (t0) REVERT: R 108 ASP cc_start: 0.8170 (t70) cc_final: 0.7892 (t70) REVERT: R 122 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8043 (tp30) REVERT: R 164 ASP cc_start: 0.7872 (t0) cc_final: 0.7551 (p0) REVERT: R 536 ASN cc_start: 0.8396 (m110) cc_final: 0.8113 (m110) REVERT: H 21 ASN cc_start: 0.8391 (t0) cc_final: 0.7869 (t0) REVERT: H 110 ASP cc_start: 0.8543 (m-30) cc_final: 0.8321 (m-30) REVERT: H 115 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8143 (tm-30) REVERT: H 145 LYS cc_start: 0.8879 (mttm) cc_final: 0.8440 (mtpt) REVERT: H 161 LYS cc_start: 0.8962 (pttt) cc_final: 0.8280 (tptt) REVERT: H 162 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8093 (ttpp) REVERT: H 520 LYS cc_start: 0.8761 (pttm) cc_final: 0.8124 (tptt) REVERT: S 19 ASN cc_start: 0.8845 (m110) cc_final: 0.8624 (m110) REVERT: S 124 ASP cc_start: 0.9120 (m-30) cc_final: 0.8882 (m-30) REVERT: S 518 MET cc_start: 0.8666 (tmm) cc_final: 0.8219 (tmm) REVERT: I 30 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7665 (tm-30) REVERT: I 465 ASP cc_start: 0.8147 (m-30) cc_final: 0.7921 (m-30) REVERT: I 518 MET cc_start: 0.8393 (ppp) cc_final: 0.8162 (tmm) REVERT: T 122 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8585 (tm-30) REVERT: J 87 ASN cc_start: 0.8916 (m-40) cc_final: 0.8531 (m-40) REVERT: J 94 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7422 (tp30) REVERT: J 122 GLU cc_start: 0.9160 (tp30) cc_final: 0.8754 (tp30) REVERT: K 475 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.7736 (tpt170) REVERT: K 518 MET cc_start: 0.7365 (tmm) cc_final: 0.7031 (tmm) REVERT: K 520 LYS cc_start: 0.9363 (ttmt) cc_final: 0.9006 (tttt) REVERT: K 537 GLN cc_start: 0.7560 (pt0) cc_final: 0.6603 (pp30) REVERT: V 95 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8314 (mp) REVERT: V 131 GLN cc_start: 0.8487 (pp30) cc_final: 0.8002 (pp30) REVERT: V 466 ASP cc_start: 0.8246 (m-30) cc_final: 0.7878 (m-30) REVERT: L 61 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8696 (mp) REVERT: L 91 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7085 (tpp-160) REVERT: L 108 ASP cc_start: 0.8563 (m-30) cc_final: 0.7992 (t0) REVERT: L 115 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8362 (tm-30) outliers start: 95 outliers final: 88 residues processed: 916 average time/residue: 0.2443 time to fit residues: 375.4737 Evaluate side-chains 963 residues out of total 4950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 868 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 499 LEU Chi-restraints excluded: chain M residue 541 GLN Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 482 GLN Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain O residue 471 ILE Chi-restraints excluded: chain O residue 478 LEU Chi-restraints excluded: chain O residue 546 LEU Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 129 GLN Chi-restraints excluded: chain P residue 145 LYS Chi-restraints excluded: chain P residue 504 SER Chi-restraints excluded: chain P residue 537 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 143 SER Chi-restraints excluded: chain Q residue 470 GLN Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 122 GLU Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 166 ASP Chi-restraints excluded: chain R residue 542 VAL Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 157 THR Chi-restraints excluded: chain S residue 173 PHE Chi-restraints excluded: chain S residue 537 GLN Chi-restraints excluded: chain S residue 544 SER Chi-restraints excluded: chain I residue 70 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 471 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain T residue 11 SER Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 489 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 170 LEU Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 170 LEU Chi-restraints excluded: chain U residue 173 PHE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain V residue 82 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 171 ASN Chi-restraints excluded: chain V residue 173 PHE Chi-restraints excluded: chain V residue 525 GLN Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 458 SER Chi-restraints excluded: chain L residue 506 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 31 optimal weight: 0.9980 chunk 126 optimal weight: 0.1980 chunk 527 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 560 optimal weight: 5.9990 chunk 524 optimal weight: 3.9990 chunk 234 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 470 GLN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.101103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085229 restraints weight = 698783.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089393 restraints weight = 223303.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092186 restraints weight = 113935.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094041 restraints weight = 68301.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.095304 restraints weight = 44990.677| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 44330 Z= 0.181 Angle : 0.785 59.200 59994 Z= 0.440 Chirality : 0.041 0.401 7370 Planarity : 0.003 0.096 8140 Dihedral : 4.740 39.209 6182 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.90 % Allowed : 19.90 % Favored : 78.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.11), residues: 5896 helix: 2.98 (0.08), residues: 4312 sheet: 2.21 (0.25), residues: 352 loop : -1.67 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG G 505 TYR 0.011 0.002 TYR P 511 PHE 0.029 0.002 PHE S 132 Details of bonding type rmsd covalent geometry : bond 0.00392 (44330) covalent geometry : angle 0.78477 (59994) hydrogen bonds : bond 0.05003 ( 3615) hydrogen bonds : angle 3.80272 (10776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9315.43 seconds wall clock time: 161 minutes 28.48 seconds (9688.48 seconds total)