Starting phenix.real_space_refine on Wed Mar 4 10:38:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k7i_22700/03_2026/7k7i_22700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k7i_22700/03_2026/7k7i_22700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k7i_22700/03_2026/7k7i_22700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k7i_22700/03_2026/7k7i_22700.map" model { file = "/net/cci-nas-00/data/ceres_data/7k7i_22700/03_2026/7k7i_22700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k7i_22700/03_2026/7k7i_22700.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 55 5.16 5 C 8355 2.51 5 N 2210 2.21 5 O 2575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13195 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "J" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Y" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "X" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 2.58, per 1000 atoms: 0.20 Number of scatterers: 13195 At special positions: 0 Unit cell: (129.48, 126.99, 80.51, 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 55 16.00 O 2575 8.00 N 2210 7.00 C 8355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 133 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 95 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 21 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 21 " - pdb=" SG CYS P 95 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 21 " - pdb=" SG CYS X 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 624.9 milliseconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 44 sheets defined 6.5% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 82 through 96 removed outlier: 4.105A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.916A pdb=" N THR A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 117' Processing helix chain 'B' and resid 82 through 96 removed outlier: 4.100A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.607A pdb=" N PHE B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 removed outlier: 4.288A pdb=" N GLN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.877A pdb=" N THR C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 117' Processing helix chain 'D' and resid 82 through 96 removed outlier: 4.341A pdb=" N GLN D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.594A pdb=" N PHE D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 removed outlier: 4.091A pdb=" N GLN E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.657A pdb=" N PHE E 117 " --> pdb=" O PHE E 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 102 removed outlier: 3.600A pdb=" N SER J 102 " --> pdb=" O TYR J 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 removed outlier: 3.527A pdb=" N ALA A 69 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 52 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A 44 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS A 54 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A 42 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 56 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 36 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 99 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 124 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 72 removed outlier: 3.641A pdb=" N ALA B 69 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 56 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL B 58 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE B 39 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 36 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL B 99 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 124 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.835A pdb=" N THR C 57 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 69 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 55 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 56 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 58 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE C 39 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 102 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 124 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N VAL C 123 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN D 46 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 44 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU D 42 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE D 39 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL D 58 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 56 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 55 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 69 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.835A pdb=" N THR C 57 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 69 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 55 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 56 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 58 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE C 39 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 102 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 124 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N VAL C 123 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN D 46 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 44 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU D 42 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR D 33 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 103 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER D 35 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 101 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY D 124 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.503A pdb=" N ALA E 69 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 56 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL E 58 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE E 39 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR E 33 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL E 103 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER E 35 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 101 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY E 124 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.201A pdb=" N LEU L 11 " --> pdb=" O GLY L 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.731A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE L 33 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB2, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AB4, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.818A pdb=" N ARG H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.529A pdb=" N TYR H 58 " --> pdb=" O THR H 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.135A pdb=" N LEU K 11 " --> pdb=" O GLY K 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'K' and resid 35 through 36 removed outlier: 6.675A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AC2, first strand: chain 'J' and resid 16 through 19 removed outlier: 3.623A pdb=" N LEU J 17 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.765A pdb=" N VAL J 96 " --> pdb=" O SER J 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.209A pdb=" N LEU N 11 " --> pdb=" O GLY N 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AC8, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.642A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.705A pdb=" N LEU M 17 " --> pdb=" O MET M 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.256A pdb=" N LEU Q 11 " --> pdb=" O GLY Q 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AD5, first strand: chain 'Q' and resid 33 through 35 removed outlier: 3.515A pdb=" N HIS Q 34 " --> pdb=" O GLN Q 89 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 48 through 49 Processing sheet with id=AD7, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'P' and resid 10 through 11 Processing sheet with id=AD9, first strand: chain 'P' and resid 17 through 18 Processing sheet with id=AE1, first strand: chain 'P' and resid 45 through 47 removed outlier: 6.838A pdb=" N CYS P 95 " --> pdb=" O TRP P 110 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TRP P 110 " --> pdb=" O CYS P 95 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG P 97 " --> pdb=" O ASP P 108 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 49 through 50 Processing sheet with id=AE3, first strand: chain 'Y' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU Y 11 " --> pdb=" O GLY Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Y' and resid 19 through 20 Processing sheet with id=AE6, first strand: chain 'Y' and resid 35 through 36 removed outlier: 6.754A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 18 through 19 Processing sheet with id=AE8, first strand: chain 'X' and resid 57 through 58 removed outlier: 6.681A pdb=" N TRP X 35 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER X 34 " --> pdb=" O VAL X 96 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 660 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: 1.83 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4189 1.34 - 1.46: 3704 1.46 - 1.58: 5582 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 13545 Sorted by residual: bond pdb=" CA ASN H 104 " pdb=" C ASN H 104 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.38e-02 5.25e+03 1.81e+00 bond pdb=" N TYR H 105 " pdb=" CA TYR H 105 " ideal model delta sigma weight residual 1.455 1.469 -0.015 1.36e-02 5.41e+03 1.15e+00 bond pdb=" CB CYS J 95 " pdb=" SG CYS J 95 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 9.84e-01 bond pdb=" CA ILE N 83 " pdb=" CB ILE N 83 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.74e-01 bond pdb=" C VAL B 67 " pdb=" N VAL B 68 " ideal model delta sigma weight residual 1.330 1.320 0.010 1.42e-02 4.96e+03 5.18e-01 ... (remaining 13540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 17805 1.36 - 2.73: 514 2.73 - 4.09: 82 4.09 - 5.45: 9 5.45 - 6.82: 5 Bond angle restraints: 18415 Sorted by residual: angle pdb=" C ASN J 73 " pdb=" N ALA J 74 " pdb=" CA ALA J 74 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N VAL M 47 " pdb=" CA VAL M 47 " pdb=" C VAL M 47 " ideal model delta sigma weight residual 109.34 115.20 -5.86 2.08e+00 2.31e-01 7.92e+00 angle pdb=" C TYR K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.56e+00 angle pdb=" N ALA M 48 " pdb=" CA ALA M 48 " pdb=" C ALA M 48 " ideal model delta sigma weight residual 110.06 113.90 -3.84 1.43e+00 4.89e-01 7.19e+00 angle pdb=" N GLY J 25 " pdb=" CA GLY J 25 " pdb=" C GLY J 25 " ideal model delta sigma weight residual 113.18 118.79 -5.61 2.37e+00 1.78e-01 5.61e+00 ... (remaining 18410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7165 18.00 - 36.00: 616 36.00 - 54.01: 93 54.01 - 72.01: 7 72.01 - 90.01: 4 Dihedral angle restraints: 7885 sinusoidal: 3000 harmonic: 4885 Sorted by residual: dihedral pdb=" CB CYS J 21 " pdb=" SG CYS J 21 " pdb=" SG CYS J 95 " pdb=" CB CYS J 95 " ideal model delta sinusoidal sigma weight residual -86.00 -176.01 90.01 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS Y 23 " pdb=" SG CYS Y 23 " pdb=" SG CYS Y 88 " pdb=" CB CYS Y 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.60 -62.60 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.70 -56.70 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 7882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1221 0.032 - 0.063: 500 0.063 - 0.095: 143 0.095 - 0.127: 106 0.127 - 0.159: 5 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CB THR X 68 " pdb=" CA THR X 68 " pdb=" OG1 THR X 68 " pdb=" CG2 THR X 68 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA VAL H 47 " pdb=" N VAL H 47 " pdb=" C VAL H 47 " pdb=" CB VAL H 47 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE M 50 " pdb=" N ILE M 50 " pdb=" C ILE M 50 " pdb=" CB ILE M 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1972 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 39 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO J 40 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO J 40 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 40 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 39 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO M 40 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 99 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" C TYR M 99 " -0.021 2.00e-02 2.50e+03 pdb=" O TYR M 99 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR M 100 " 0.007 2.00e-02 2.50e+03 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1530 2.75 - 3.29: 12848 3.29 - 3.82: 21017 3.82 - 4.36: 25380 4.36 - 4.90: 45448 Nonbonded interactions: 106223 Sorted by model distance: nonbonded pdb=" O ARG M 66 " pdb=" OG SER M 83 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLU E 24 " pdb=" OH TYR X 100 " model vdw 2.222 3.040 nonbonded pdb=" O ARG H 66 " pdb=" OG SER H 83 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.239 3.040 nonbonded pdb=" OE1 GLU C 37 " pdb=" OG1 THR C 57 " model vdw 2.242 3.040 ... (remaining 106218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'Q' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 0.033 13565 Z= 0.135 Angle : 0.550 6.818 18455 Z= 0.307 Chirality : 0.042 0.159 1975 Planarity : 0.003 0.034 2350 Dihedral : 12.848 81.122 4735 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.32 (0.16), residues: 1675 helix: -3.91 (0.29), residues: 75 sheet: -3.64 (0.18), residues: 585 loop : -3.55 (0.15), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 97 TYR 0.011 0.001 TYR X 99 PHE 0.008 0.001 PHE D 117 TRP 0.011 0.001 TRP J 110 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00297 (13545) covalent geometry : angle 0.54951 (18415) SS BOND : bond 0.00283 ( 20) SS BOND : angle 0.79510 ( 40) hydrogen bonds : bond 0.31659 ( 254) hydrogen bonds : angle 12.84874 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.455 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: L 69 THR cc_start: 0.8725 (p) cc_final: 0.7089 (p) REVERT: L 82 ASP cc_start: 0.8033 (m-30) cc_final: 0.7091 (m-30) REVERT: L 85 ASP cc_start: 0.7836 (m-30) cc_final: 0.7143 (m-30) REVERT: H 72 ASP cc_start: 0.7141 (t70) cc_final: 0.6469 (t0) REVERT: K 69 THR cc_start: 0.8647 (p) cc_final: 0.8310 (m) REVERT: K 85 ASP cc_start: 0.7948 (m-30) cc_final: 0.7299 (m-30) REVERT: J 72 ASP cc_start: 0.7648 (t0) cc_final: 0.7254 (t0) REVERT: N 82 ASP cc_start: 0.8084 (m-30) cc_final: 0.7644 (m-30) REVERT: M 49 THR cc_start: 0.8035 (m) cc_final: 0.7798 (m) REVERT: Q 69 THR cc_start: 0.8592 (p) cc_final: 0.8085 (m) REVERT: Q 76 ASN cc_start: 0.8184 (p0) cc_final: 0.7586 (p0) REVERT: Q 82 ASP cc_start: 0.7747 (m-30) cc_final: 0.6452 (m-30) REVERT: P 31 TYR cc_start: 0.7608 (m-80) cc_final: 0.7207 (m-80) REVERT: X 45 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7126 (mt-10) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.1474 time to fit residues: 76.9559 Evaluate side-chains 291 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN C 120 ASN E 120 ASN L 37 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN M 98 GLN P 98 GLN ** Y 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN X 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.069870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053873 restraints weight = 43080.627| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.89 r_work: 0.2942 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 13565 Z= 0.364 Angle : 0.760 9.680 18455 Z= 0.401 Chirality : 0.047 0.145 1975 Planarity : 0.005 0.041 2350 Dihedral : 5.200 33.596 1860 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 2.00 % Allowed : 15.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.17), residues: 1675 helix: -1.49 (0.54), residues: 75 sheet: -3.26 (0.19), residues: 580 loop : -3.09 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 86 TYR 0.035 0.002 TYR X 109 PHE 0.022 0.002 PHE H 67 TRP 0.011 0.002 TRP X 110 HIS 0.009 0.002 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00825 (13545) covalent geometry : angle 0.75912 (18415) SS BOND : bond 0.00494 ( 20) SS BOND : angle 1.19143 ( 40) hydrogen bonds : bond 0.04853 ( 254) hydrogen bonds : angle 7.24356 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 307 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8767 (mp0) cc_final: 0.8478 (mp0) REVERT: B 41 GLU cc_start: 0.7810 (mp0) cc_final: 0.7577 (mp0) REVERT: C 101 ILE cc_start: 0.9120 (mt) cc_final: 0.8898 (mt) REVERT: D 36 ASP cc_start: 0.8934 (t0) cc_final: 0.8664 (t0) REVERT: E 36 ASP cc_start: 0.9013 (t0) cc_final: 0.8809 (t0) REVERT: L 24 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7792 (mmm160) REVERT: L 82 ASP cc_start: 0.8197 (m-30) cc_final: 0.7927 (m-30) REVERT: L 85 ASP cc_start: 0.8458 (m-30) cc_final: 0.8114 (m-30) REVERT: H 43 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8031 (ttp80) REVERT: H 45 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8516 (mt-10) REVERT: H 72 ASP cc_start: 0.7762 (t0) cc_final: 0.7315 (t0) REVERT: H 86 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8098 (mtm110) REVERT: H 99 TYR cc_start: 0.8791 (t80) cc_final: 0.8338 (t80) REVERT: K 2 ILE cc_start: 0.7799 (mt) cc_final: 0.7520 (mm) REVERT: K 24 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8226 (mtp85) REVERT: K 27 GLN cc_start: 0.8839 (mp10) cc_final: 0.8218 (mp10) REVERT: J 72 ASP cc_start: 0.8489 (t0) cc_final: 0.7492 (t0) REVERT: N 24 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8482 (mtp85) REVERT: N 27 GLN cc_start: 0.8897 (mp10) cc_final: 0.8667 (mp10) REVERT: N 78 VAL cc_start: 0.9101 (p) cc_final: 0.8759 (m) REVERT: N 79 GLU cc_start: 0.8211 (mp0) cc_final: 0.7932 (mp0) REVERT: N 82 ASP cc_start: 0.8497 (m-30) cc_final: 0.8098 (m-30) REVERT: M 43 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7957 (ptm-80) REVERT: M 79 TYR cc_start: 0.8273 (m-10) cc_final: 0.8035 (m-10) REVERT: M 97 ARG cc_start: 0.6990 (ptp-170) cc_final: 0.6609 (ptp-170) REVERT: P 31 TYR cc_start: 0.8458 (m-80) cc_final: 0.7968 (m-80) REVERT: P 45 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8102 (pt0) REVERT: P 75 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8584 (mpp80) REVERT: P 77 THR cc_start: 0.8563 (p) cc_final: 0.8150 (p) REVERT: P 97 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7638 (ptt90) REVERT: P 109 TYR cc_start: 0.8506 (t80) cc_final: 0.7956 (t80) REVERT: Y 79 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8110 (tm-30) REVERT: Y 82 ASP cc_start: 0.8496 (m-30) cc_final: 0.8290 (m-30) REVERT: Y 92 ASN cc_start: 0.8918 (t0) cc_final: 0.8686 (m-40) REVERT: X 72 ASP cc_start: 0.7897 (t0) cc_final: 0.7585 (t0) REVERT: X 108 ASP cc_start: 0.8595 (t0) cc_final: 0.8305 (m-30) outliers start: 29 outliers final: 17 residues processed: 320 average time/residue: 0.1417 time to fit residues: 61.6590 Evaluate side-chains 285 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 62 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 120 ASN E 61 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.068698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052553 restraints weight = 43511.330| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.89 r_work: 0.2905 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 13565 Z= 0.369 Angle : 0.751 11.383 18455 Z= 0.394 Chirality : 0.048 0.146 1975 Planarity : 0.005 0.049 2350 Dihedral : 5.440 31.533 1860 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 3.17 % Allowed : 17.45 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.18), residues: 1675 helix: -0.91 (0.52), residues: 75 sheet: -2.80 (0.18), residues: 640 loop : -2.94 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 86 TYR 0.018 0.002 TYR X 31 PHE 0.021 0.002 PHE H 67 TRP 0.023 0.002 TRP P 46 HIS 0.012 0.002 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00838 (13545) covalent geometry : angle 0.74966 (18415) SS BOND : bond 0.00473 ( 20) SS BOND : angle 1.09536 ( 40) hydrogen bonds : bond 0.04167 ( 254) hydrogen bonds : angle 6.44585 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8303 (mp0) cc_final: 0.7893 (mm-30) REVERT: B 41 GLU cc_start: 0.8024 (mp0) cc_final: 0.7657 (mp0) REVERT: C 61 ASN cc_start: 0.8538 (p0) cc_final: 0.7993 (p0) REVERT: D 36 ASP cc_start: 0.8883 (t0) cc_final: 0.8654 (t0) REVERT: E 36 ASP cc_start: 0.8903 (t0) cc_final: 0.8664 (t0) REVERT: L 27 GLN cc_start: 0.8839 (mp10) cc_final: 0.8522 (mp10) REVERT: L 82 ASP cc_start: 0.8289 (m-30) cc_final: 0.7884 (m-30) REVERT: L 103 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7803 (t70) REVERT: H 43 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7937 (ttp80) REVERT: H 45 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8432 (mt-10) REVERT: H 72 ASP cc_start: 0.7828 (t0) cc_final: 0.7433 (t0) REVERT: H 99 TYR cc_start: 0.8903 (t80) cc_final: 0.8565 (t80) REVERT: H 108 ASP cc_start: 0.8331 (t0) cc_final: 0.8018 (t0) REVERT: K 2 ILE cc_start: 0.8177 (mt) cc_final: 0.7882 (mt) REVERT: K 27 GLN cc_start: 0.8823 (mp10) cc_final: 0.8567 (mp10) REVERT: K 70 ASP cc_start: 0.8886 (t0) cc_final: 0.8243 (m-30) REVERT: K 79 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7999 (tm-30) REVERT: K 82 ASP cc_start: 0.8249 (m-30) cc_final: 0.7862 (m-30) REVERT: K 89 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: J 72 ASP cc_start: 0.8509 (t0) cc_final: 0.7551 (t0) REVERT: J 75 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8500 (mtp-110) REVERT: N 27 GLN cc_start: 0.8832 (mp10) cc_final: 0.8629 (mp10) REVERT: N 78 VAL cc_start: 0.9038 (p) cc_final: 0.8816 (m) REVERT: N 79 GLU cc_start: 0.8145 (mp0) cc_final: 0.7766 (mp0) REVERT: N 82 ASP cc_start: 0.8420 (m-30) cc_final: 0.7718 (m-30) REVERT: P 45 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8051 (pt0) REVERT: P 75 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8647 (mmm-85) REVERT: P 97 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7922 (ttt-90) REVERT: P 109 TYR cc_start: 0.8620 (t80) cc_final: 0.8420 (t80) REVERT: Y 24 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8034 (mtm-85) REVERT: Y 79 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8025 (tm-30) REVERT: Y 82 ASP cc_start: 0.8484 (m-30) cc_final: 0.8233 (m-30) REVERT: X 43 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8094 (ptm-80) REVERT: X 45 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8192 (mt-10) REVERT: X 72 ASP cc_start: 0.8022 (t0) cc_final: 0.7587 (t0) REVERT: X 108 ASP cc_start: 0.8558 (t0) cc_final: 0.8311 (m-30) outliers start: 46 outliers final: 29 residues processed: 308 average time/residue: 0.1376 time to fit residues: 57.0851 Evaluate side-chains 294 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.069715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053791 restraints weight = 43094.329| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.87 r_work: 0.2940 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13565 Z= 0.233 Angle : 0.667 9.522 18455 Z= 0.346 Chirality : 0.045 0.159 1975 Planarity : 0.005 0.050 2350 Dihedral : 5.189 28.058 1860 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 2.83 % Allowed : 18.90 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.18), residues: 1675 helix: -0.22 (0.54), residues: 75 sheet: -2.70 (0.19), residues: 650 loop : -2.80 (0.17), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 86 TYR 0.013 0.001 TYR X 99 PHE 0.015 0.002 PHE H 67 TRP 0.021 0.001 TRP P 46 HIS 0.012 0.002 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00535 (13545) covalent geometry : angle 0.66518 (18415) SS BOND : bond 0.00390 ( 20) SS BOND : angle 1.12401 ( 40) hydrogen bonds : bond 0.03156 ( 254) hydrogen bonds : angle 6.00619 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 0.431 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 41 GLU cc_start: 0.7951 (mp0) cc_final: 0.7599 (mp0) REVERT: C 61 ASN cc_start: 0.8533 (p0) cc_final: 0.8020 (p0) REVERT: D 36 ASP cc_start: 0.8890 (t0) cc_final: 0.8673 (t0) REVERT: D 61 ASN cc_start: 0.8522 (p0) cc_final: 0.8143 (p0) REVERT: D 84 GLU cc_start: 0.8840 (mp0) cc_final: 0.8570 (mp0) REVERT: E 36 ASP cc_start: 0.8896 (t0) cc_final: 0.8671 (t0) REVERT: L 27 GLN cc_start: 0.8890 (mp10) cc_final: 0.8670 (mp10) REVERT: L 82 ASP cc_start: 0.8287 (m-30) cc_final: 0.7732 (m-30) REVERT: L 103 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7757 (t70) REVERT: H 43 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7973 (ttp80) REVERT: H 45 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8495 (mt-10) REVERT: H 72 ASP cc_start: 0.7818 (t0) cc_final: 0.7410 (t0) REVERT: H 99 TYR cc_start: 0.8838 (t80) cc_final: 0.8396 (t80) REVERT: K 2 ILE cc_start: 0.8076 (mt) cc_final: 0.7800 (mt) REVERT: K 27 GLN cc_start: 0.8777 (mp10) cc_final: 0.8562 (mp10) REVERT: K 89 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: J 45 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8335 (mt-10) REVERT: J 72 ASP cc_start: 0.8516 (t0) cc_final: 0.7526 (t0) REVERT: J 75 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8452 (mtp-110) REVERT: J 112 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8111 (mm-40) REVERT: N 24 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8274 (ttm-80) REVERT: N 78 VAL cc_start: 0.9035 (p) cc_final: 0.8753 (m) REVERT: N 79 GLU cc_start: 0.8208 (mp0) cc_final: 0.7787 (mp0) REVERT: N 82 ASP cc_start: 0.8438 (m-30) cc_final: 0.7623 (m-30) REVERT: M 43 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7766 (ttp-110) REVERT: M 50 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7594 (mp) REVERT: M 100 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: Q 79 GLU cc_start: 0.8697 (mp0) cc_final: 0.8307 (mp0) REVERT: Q 103 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7346 (m-70) REVERT: P 31 TYR cc_start: 0.8336 (m-10) cc_final: 0.8100 (m-10) REVERT: P 45 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7968 (pt0) REVERT: P 75 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8689 (mmm-85) REVERT: P 97 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7994 (ttt-90) REVERT: P 109 TYR cc_start: 0.8609 (t80) cc_final: 0.8378 (t80) REVERT: Y 24 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.7959 (mtm-85) REVERT: Y 79 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8070 (tm-30) REVERT: Y 82 ASP cc_start: 0.8525 (m-30) cc_final: 0.8256 (m-30) REVERT: Y 92 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8600 (m-40) REVERT: X 43 ARG cc_start: 0.8416 (ttp80) cc_final: 0.8123 (ptm-80) REVERT: X 45 GLU cc_start: 0.8619 (mt-10) cc_final: 0.7857 (mt-10) REVERT: X 72 ASP cc_start: 0.8048 (t0) cc_final: 0.7597 (t0) REVERT: X 107 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7347 (mmt) outliers start: 41 outliers final: 28 residues processed: 311 average time/residue: 0.1416 time to fit residues: 59.3046 Evaluate side-chains 302 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 107 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 124 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Y 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.069326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053607 restraints weight = 42907.399| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.81 r_work: 0.2938 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13565 Z= 0.248 Angle : 0.669 10.240 18455 Z= 0.349 Chirality : 0.045 0.158 1975 Planarity : 0.005 0.070 2350 Dihedral : 5.198 28.899 1860 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 3.45 % Allowed : 19.66 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.19), residues: 1675 helix: 0.08 (0.54), residues: 75 sheet: -2.49 (0.19), residues: 660 loop : -2.71 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 86 TYR 0.021 0.001 TYR X 99 PHE 0.015 0.001 PHE H 67 TRP 0.016 0.001 TRP P 46 HIS 0.010 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00572 (13545) covalent geometry : angle 0.66807 (18415) SS BOND : bond 0.00417 ( 20) SS BOND : angle 1.06545 ( 40) hydrogen bonds : bond 0.03148 ( 254) hydrogen bonds : angle 5.79235 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8272 (mp0) cc_final: 0.7850 (mm-30) REVERT: B 41 GLU cc_start: 0.8002 (mp0) cc_final: 0.7627 (mp0) REVERT: C 61 ASN cc_start: 0.8532 (p0) cc_final: 0.7759 (p0) REVERT: D 36 ASP cc_start: 0.8856 (t0) cc_final: 0.8612 (t0) REVERT: D 61 ASN cc_start: 0.8550 (p0) cc_final: 0.8027 (p0) REVERT: E 36 ASP cc_start: 0.8871 (t0) cc_final: 0.8625 (t0) REVERT: L 24 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8659 (mmm160) REVERT: L 70 ASP cc_start: 0.8854 (t0) cc_final: 0.8470 (p0) REVERT: L 103 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7763 (t70) REVERT: H 43 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7811 (tmm-80) REVERT: H 45 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8470 (mt-10) REVERT: H 72 ASP cc_start: 0.7830 (t0) cc_final: 0.7437 (t0) REVERT: H 99 TYR cc_start: 0.8813 (t80) cc_final: 0.8426 (t80) REVERT: H 108 ASP cc_start: 0.8270 (t0) cc_final: 0.8025 (t0) REVERT: K 2 ILE cc_start: 0.8025 (mt) cc_final: 0.7587 (mt) REVERT: K 24 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8139 (ttm-80) REVERT: K 27 GLN cc_start: 0.8760 (mp10) cc_final: 0.8476 (mp10) REVERT: K 89 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: J 26 PHE cc_start: 0.6697 (m-80) cc_final: 0.5459 (m-80) REVERT: J 43 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7303 (tmm-80) REVERT: J 45 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8155 (mt-10) REVERT: J 72 ASP cc_start: 0.8516 (t0) cc_final: 0.7518 (t0) REVERT: J 75 ARG cc_start: 0.8706 (mtp85) cc_final: 0.8477 (mtp-110) REVERT: J 97 ARG cc_start: 0.7100 (mtt180) cc_final: 0.6644 (mtm110) REVERT: N 78 VAL cc_start: 0.9027 (p) cc_final: 0.8760 (m) REVERT: N 79 GLU cc_start: 0.8170 (mp0) cc_final: 0.7751 (mp0) REVERT: N 82 ASP cc_start: 0.8429 (m-30) cc_final: 0.7699 (m-30) REVERT: M 43 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7793 (ttp-110) REVERT: Q 79 GLU cc_start: 0.8716 (mp0) cc_final: 0.8250 (mp0) REVERT: Q 89 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: Q 103 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7293 (m-70) REVERT: P 43 ARG cc_start: 0.8649 (ptm160) cc_final: 0.8207 (ptm-80) REVERT: P 109 TYR cc_start: 0.8526 (t80) cc_final: 0.8305 (t80) REVERT: Y 24 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8005 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8589 (m-40) REVERT: X 43 ARG cc_start: 0.8454 (ttp80) cc_final: 0.7730 (ptm-80) REVERT: X 45 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7810 (mt-10) REVERT: X 72 ASP cc_start: 0.8074 (t0) cc_final: 0.7612 (t0) outliers start: 50 outliers final: 35 residues processed: 303 average time/residue: 0.1399 time to fit residues: 57.6144 Evaluate side-chains 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 chunk 94 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Y 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.071537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055905 restraints weight = 41999.838| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.85 r_work: 0.3005 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13565 Z= 0.125 Angle : 0.612 8.137 18455 Z= 0.316 Chirality : 0.045 0.359 1975 Planarity : 0.004 0.060 2350 Dihedral : 4.877 29.181 1860 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.76 % Allowed : 20.97 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.19), residues: 1675 helix: 0.39 (0.58), residues: 75 sheet: -2.23 (0.19), residues: 700 loop : -2.59 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 86 TYR 0.015 0.001 TYR X 99 PHE 0.012 0.001 PHE H 67 TRP 0.019 0.001 TRP P 46 HIS 0.012 0.002 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00292 (13545) covalent geometry : angle 0.61147 (18415) SS BOND : bond 0.00273 ( 20) SS BOND : angle 0.95139 ( 40) hydrogen bonds : bond 0.02525 ( 254) hydrogen bonds : angle 5.40656 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 0.508 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: B 41 GLU cc_start: 0.7882 (mp0) cc_final: 0.7563 (mp0) REVERT: C 61 ASN cc_start: 0.8583 (p0) cc_final: 0.8108 (p0) REVERT: C 84 GLU cc_start: 0.8770 (mp0) cc_final: 0.8501 (mp0) REVERT: D 36 ASP cc_start: 0.8880 (t0) cc_final: 0.8670 (t0) REVERT: D 61 ASN cc_start: 0.8551 (p0) cc_final: 0.8102 (p0) REVERT: E 28 ASP cc_start: 0.8268 (m-30) cc_final: 0.7913 (m-30) REVERT: E 36 ASP cc_start: 0.8882 (t0) cc_final: 0.8652 (t0) REVERT: L 24 ARG cc_start: 0.8904 (mmm160) cc_final: 0.8607 (mmm160) REVERT: L 70 ASP cc_start: 0.8856 (t0) cc_final: 0.8461 (p0) REVERT: L 103 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7802 (t70) REVERT: H 43 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8054 (tmm-80) REVERT: H 45 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8493 (mt-10) REVERT: H 72 ASP cc_start: 0.7793 (t0) cc_final: 0.7394 (t0) REVERT: H 86 ARG cc_start: 0.8512 (ptp90) cc_final: 0.8075 (ptp90) REVERT: H 99 TYR cc_start: 0.8608 (t80) cc_final: 0.8166 (t80) REVERT: H 108 ASP cc_start: 0.8281 (t0) cc_final: 0.8049 (t0) REVERT: K 2 ILE cc_start: 0.7923 (mt) cc_final: 0.7449 (mt) REVERT: K 24 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8347 (mmm160) REVERT: K 27 GLN cc_start: 0.8726 (mp10) cc_final: 0.8476 (mp10) REVERT: K 70 ASP cc_start: 0.8943 (t0) cc_final: 0.8660 (p0) REVERT: K 79 GLU cc_start: 0.8644 (mp0) cc_final: 0.8319 (mp0) REVERT: K 89 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: K 92 ASN cc_start: 0.8018 (m-40) cc_final: 0.7791 (m-40) REVERT: J 72 ASP cc_start: 0.8476 (t0) cc_final: 0.7445 (t0) REVERT: J 75 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8460 (mtp-110) REVERT: N 70 ASP cc_start: 0.8751 (t0) cc_final: 0.8495 (p0) REVERT: N 79 GLU cc_start: 0.8223 (mp0) cc_final: 0.7984 (mp0) REVERT: N 82 ASP cc_start: 0.8428 (m-30) cc_final: 0.8132 (m-30) REVERT: M 108 ASP cc_start: 0.7920 (m-30) cc_final: 0.7339 (m-30) REVERT: Q 24 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8321 (mmm160) REVERT: Q 79 GLU cc_start: 0.8766 (mp0) cc_final: 0.8352 (mp0) REVERT: Q 82 ASP cc_start: 0.8449 (m-30) cc_final: 0.8112 (m-30) REVERT: Q 89 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: Q 103 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7202 (m-70) REVERT: P 43 ARG cc_start: 0.8650 (ptm160) cc_final: 0.8280 (ptm-80) REVERT: P 64 LYS cc_start: 0.8814 (tppt) cc_final: 0.8326 (tppt) REVERT: P 109 TYR cc_start: 0.8524 (t80) cc_final: 0.8127 (t80) REVERT: Y 24 ARG cc_start: 0.8671 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: X 43 ARG cc_start: 0.8442 (ttp80) cc_final: 0.7858 (tmm-80) REVERT: X 45 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8172 (mt-10) REVERT: X 72 ASP cc_start: 0.8051 (t0) cc_final: 0.7592 (t0) REVERT: X 97 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8245 (ttp-170) REVERT: X 112 GLN cc_start: 0.8543 (pt0) cc_final: 0.8091 (pm20) outliers start: 40 outliers final: 27 residues processed: 315 average time/residue: 0.1516 time to fit residues: 63.6507 Evaluate side-chains 297 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 265 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 112 optimal weight: 0.3980 chunk 125 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN Y 89 GLN Y 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.069740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054018 restraints weight = 42397.975| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.83 r_work: 0.2968 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13565 Z= 0.228 Angle : 0.669 9.285 18455 Z= 0.348 Chirality : 0.045 0.241 1975 Planarity : 0.005 0.053 2350 Dihedral : 5.002 28.932 1860 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 3.10 % Allowed : 21.10 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.19), residues: 1675 helix: 0.45 (0.58), residues: 75 sheet: -2.12 (0.20), residues: 685 loop : -2.47 (0.18), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 86 TYR 0.013 0.001 TYR X 99 PHE 0.020 0.001 PHE J 26 TRP 0.016 0.001 TRP P 46 HIS 0.009 0.002 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00529 (13545) covalent geometry : angle 0.66781 (18415) SS BOND : bond 0.00394 ( 20) SS BOND : angle 0.95961 ( 40) hydrogen bonds : bond 0.02968 ( 254) hydrogen bonds : angle 5.43843 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.541 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: B 41 GLU cc_start: 0.8022 (mp0) cc_final: 0.7629 (mp0) REVERT: C 61 ASN cc_start: 0.8559 (p0) cc_final: 0.7815 (p0) REVERT: D 36 ASP cc_start: 0.8836 (t0) cc_final: 0.8575 (t0) REVERT: D 61 ASN cc_start: 0.8531 (p0) cc_final: 0.7977 (p0) REVERT: E 36 ASP cc_start: 0.8907 (t0) cc_final: 0.8643 (t0) REVERT: L 70 ASP cc_start: 0.8880 (t0) cc_final: 0.8416 (p0) REVERT: L 82 ASP cc_start: 0.8233 (m-30) cc_final: 0.7940 (m-30) REVERT: L 103 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7872 (t70) REVERT: H 43 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7756 (ttp80) REVERT: H 45 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8595 (mt-10) REVERT: H 72 ASP cc_start: 0.7798 (t0) cc_final: 0.7406 (t0) REVERT: H 86 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8234 (ptp90) REVERT: H 99 TYR cc_start: 0.8805 (t80) cc_final: 0.8379 (t80) REVERT: H 108 ASP cc_start: 0.8340 (t0) cc_final: 0.8062 (t0) REVERT: K 2 ILE cc_start: 0.7946 (mt) cc_final: 0.7618 (mt) REVERT: K 24 ARG cc_start: 0.8803 (mtp85) cc_final: 0.8445 (mmm160) REVERT: K 70 ASP cc_start: 0.8892 (t0) cc_final: 0.8658 (p0) REVERT: K 89 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: K 92 ASN cc_start: 0.8207 (m-40) cc_final: 0.7970 (m110) REVERT: J 43 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7896 (ptm-80) REVERT: J 45 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: J 72 ASP cc_start: 0.8368 (t0) cc_final: 0.7335 (t0) REVERT: J 75 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8473 (mtp-110) REVERT: N 24 ARG cc_start: 0.8827 (mtp85) cc_final: 0.8449 (ttm-80) REVERT: N 79 GLU cc_start: 0.8149 (mp0) cc_final: 0.7834 (mp0) REVERT: N 82 ASP cc_start: 0.8321 (m-30) cc_final: 0.7516 (m-30) REVERT: M 43 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.7273 (ttp-110) REVERT: M 45 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8080 (mt-10) REVERT: M 108 ASP cc_start: 0.7731 (m-30) cc_final: 0.7085 (m-30) REVERT: Q 24 ARG cc_start: 0.8645 (mmm160) cc_final: 0.8317 (mmm160) REVERT: Q 79 GLU cc_start: 0.8718 (mp0) cc_final: 0.8250 (mp0) REVERT: Q 82 ASP cc_start: 0.8499 (m-30) cc_final: 0.7952 (m-30) REVERT: Q 89 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: Q 103 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7358 (m-70) REVERT: P 43 ARG cc_start: 0.8634 (ptm160) cc_final: 0.8362 (ptm-80) REVERT: P 64 LYS cc_start: 0.8934 (tppt) cc_final: 0.8484 (tppt) REVERT: P 86 ARG cc_start: 0.8270 (mmp80) cc_final: 0.8067 (mmp80) REVERT: P 109 TYR cc_start: 0.8485 (t80) cc_final: 0.8193 (t80) REVERT: Y 24 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8564 (m-40) REVERT: X 31 TYR cc_start: 0.8500 (m-80) cc_final: 0.8196 (m-80) REVERT: X 43 ARG cc_start: 0.8470 (ttp80) cc_final: 0.7830 (tmm-80) REVERT: X 45 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8138 (mt-10) REVERT: X 72 ASP cc_start: 0.8076 (t0) cc_final: 0.7612 (t0) REVERT: X 86 ARG cc_start: 0.8020 (mtt-85) cc_final: 0.7779 (ptp-110) REVERT: X 97 ARG cc_start: 0.8412 (ttp80) cc_final: 0.7622 (ttp-170) outliers start: 45 outliers final: 32 residues processed: 288 average time/residue: 0.1521 time to fit residues: 58.8956 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 32 ASP Chi-restraints excluded: chain X residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 106 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 154 optimal weight: 0.2980 chunk 87 optimal weight: 0.0870 chunk 99 optimal weight: 0.9980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN Y 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.072055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056180 restraints weight = 41375.547| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.99 r_work: 0.3014 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13565 Z= 0.120 Angle : 0.639 7.711 18455 Z= 0.330 Chirality : 0.045 0.209 1975 Planarity : 0.004 0.055 2350 Dihedral : 4.741 26.513 1860 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.69 % Allowed : 21.59 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.19), residues: 1675 helix: 0.12 (0.57), residues: 80 sheet: -1.92 (0.20), residues: 685 loop : -2.33 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 86 TYR 0.016 0.001 TYR P 79 PHE 0.017 0.001 PHE J 26 TRP 0.021 0.001 TRP P 46 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00279 (13545) covalent geometry : angle 0.63838 (18415) SS BOND : bond 0.00249 ( 20) SS BOND : angle 0.85584 ( 40) hydrogen bonds : bond 0.02497 ( 254) hydrogen bonds : angle 5.18752 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.324 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 41 GLU cc_start: 0.7879 (mp0) cc_final: 0.7475 (mp0) REVERT: C 61 ASN cc_start: 0.8614 (p0) cc_final: 0.8142 (p0) REVERT: D 36 ASP cc_start: 0.8886 (t0) cc_final: 0.8609 (t0) REVERT: D 61 ASN cc_start: 0.8635 (p0) cc_final: 0.8141 (p0) REVERT: E 36 ASP cc_start: 0.8901 (t0) cc_final: 0.8599 (t0) REVERT: L 24 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8729 (mmm160) REVERT: L 70 ASP cc_start: 0.8896 (t0) cc_final: 0.8386 (p0) REVERT: L 82 ASP cc_start: 0.8103 (m-30) cc_final: 0.7803 (m-30) REVERT: L 103 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7827 (t70) REVERT: H 43 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7801 (tmm-80) REVERT: H 45 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8438 (mt-10) REVERT: H 72 ASP cc_start: 0.7771 (t0) cc_final: 0.7356 (t0) REVERT: H 86 ARG cc_start: 0.8572 (ptp90) cc_final: 0.8128 (ptp90) REVERT: H 99 TYR cc_start: 0.8625 (t80) cc_final: 0.8145 (t80) REVERT: H 108 ASP cc_start: 0.8302 (t0) cc_final: 0.7996 (t0) REVERT: K 24 ARG cc_start: 0.8801 (mtp85) cc_final: 0.8223 (mmp80) REVERT: K 70 ASP cc_start: 0.9018 (t0) cc_final: 0.8700 (p0) REVERT: K 79 GLU cc_start: 0.8724 (mp0) cc_final: 0.8458 (mp0) REVERT: K 82 ASP cc_start: 0.8544 (m-30) cc_final: 0.8280 (m-30) REVERT: K 89 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: J 72 ASP cc_start: 0.8296 (t0) cc_final: 0.7153 (t0) REVERT: J 75 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8407 (mtp-110) REVERT: J 79 TYR cc_start: 0.8863 (m-80) cc_final: 0.8640 (m-80) REVERT: N 24 ARG cc_start: 0.8878 (mtp85) cc_final: 0.8436 (ttm-80) REVERT: N 79 GLU cc_start: 0.8262 (mp0) cc_final: 0.7951 (mp0) REVERT: N 82 ASP cc_start: 0.8253 (m-30) cc_final: 0.7589 (m-30) REVERT: M 43 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.7105 (ptm-80) REVERT: M 45 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7791 (mp0) REVERT: M 108 ASP cc_start: 0.7753 (m-30) cc_final: 0.7127 (m-30) REVERT: Q 79 GLU cc_start: 0.8781 (mp0) cc_final: 0.8358 (mp0) REVERT: Q 82 ASP cc_start: 0.8471 (m-30) cc_final: 0.7992 (m-30) REVERT: Q 89 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8730 (tt0) REVERT: P 43 ARG cc_start: 0.8654 (ptm160) cc_final: 0.8298 (ptm-80) REVERT: P 64 LYS cc_start: 0.8938 (tppt) cc_final: 0.8469 (tppt) REVERT: P 109 TYR cc_start: 0.8469 (t80) cc_final: 0.8134 (t80) REVERT: Y 17 GLU cc_start: 0.9210 (tt0) cc_final: 0.8955 (pt0) REVERT: Y 24 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8030 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8211 (m-40) REVERT: X 43 ARG cc_start: 0.8529 (ttp80) cc_final: 0.7958 (ptm-80) REVERT: X 45 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7895 (mt-10) REVERT: X 72 ASP cc_start: 0.7948 (t0) cc_final: 0.7474 (t0) outliers start: 39 outliers final: 27 residues processed: 303 average time/residue: 0.1460 time to fit residues: 59.4893 Evaluate side-chains 289 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 21 optimal weight: 0.0070 chunk 153 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 49 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054280 restraints weight = 42048.200| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.05 r_work: 0.2958 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13565 Z= 0.205 Angle : 0.682 11.804 18455 Z= 0.352 Chirality : 0.045 0.212 1975 Planarity : 0.005 0.058 2350 Dihedral : 4.901 27.037 1860 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer: Outliers : 2.83 % Allowed : 22.00 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.20), residues: 1675 helix: 0.54 (0.60), residues: 75 sheet: -1.98 (0.20), residues: 710 loop : -2.26 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 86 TYR 0.011 0.001 TYR X 99 PHE 0.019 0.001 PHE J 26 TRP 0.016 0.001 TRP P 46 HIS 0.010 0.002 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00479 (13545) covalent geometry : angle 0.68110 (18415) SS BOND : bond 0.00376 ( 20) SS BOND : angle 0.96242 ( 40) hydrogen bonds : bond 0.02858 ( 254) hydrogen bonds : angle 5.24798 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.491 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: B 41 GLU cc_start: 0.8019 (mp0) cc_final: 0.7529 (mp0) REVERT: C 61 ASN cc_start: 0.8601 (p0) cc_final: 0.7877 (p0) REVERT: D 36 ASP cc_start: 0.8848 (t0) cc_final: 0.8536 (t0) REVERT: D 61 ASN cc_start: 0.8647 (p0) cc_final: 0.8052 (p0) REVERT: E 36 ASP cc_start: 0.8869 (t0) cc_final: 0.8554 (t0) REVERT: L 24 ARG cc_start: 0.8914 (mmm160) cc_final: 0.8650 (mmm160) REVERT: L 70 ASP cc_start: 0.8925 (t0) cc_final: 0.8443 (p0) REVERT: L 82 ASP cc_start: 0.8054 (m-30) cc_final: 0.7783 (m-30) REVERT: L 103 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7790 (t70) REVERT: H 43 ARG cc_start: 0.8298 (ttp80) cc_final: 0.7733 (tmm-80) REVERT: H 45 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8426 (mt-10) REVERT: H 72 ASP cc_start: 0.7820 (t0) cc_final: 0.7408 (t0) REVERT: H 86 ARG cc_start: 0.8449 (ptp90) cc_final: 0.8012 (ptp90) REVERT: H 99 TYR cc_start: 0.8749 (t80) cc_final: 0.8312 (t80) REVERT: K 70 ASP cc_start: 0.9019 (t0) cc_final: 0.8586 (p0) REVERT: K 79 GLU cc_start: 0.8571 (mp0) cc_final: 0.8341 (mp0) REVERT: K 89 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8709 (tt0) REVERT: J 72 ASP cc_start: 0.8303 (t0) cc_final: 0.7179 (t0) REVERT: J 75 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8436 (mtp-110) REVERT: J 79 TYR cc_start: 0.8901 (m-80) cc_final: 0.8674 (m-80) REVERT: N 24 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8453 (ttm-80) REVERT: N 79 GLU cc_start: 0.8152 (mp0) cc_final: 0.7752 (mp0) REVERT: N 82 ASP cc_start: 0.8161 (m-30) cc_final: 0.7276 (m-30) REVERT: M 43 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.6801 (ttp-110) REVERT: M 45 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7939 (mt-10) REVERT: M 108 ASP cc_start: 0.7710 (m-30) cc_final: 0.7034 (m-30) REVERT: Q 24 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8460 (mmm160) REVERT: Q 79 GLU cc_start: 0.8705 (mp0) cc_final: 0.8222 (mp0) REVERT: Q 82 ASP cc_start: 0.8399 (m-30) cc_final: 0.7770 (m-30) REVERT: Q 89 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8745 (tt0) REVERT: P 43 ARG cc_start: 0.8631 (ptm160) cc_final: 0.8140 (ptm-80) REVERT: P 45 GLU cc_start: 0.8538 (pt0) cc_final: 0.7969 (pt0) REVERT: P 109 TYR cc_start: 0.8519 (t80) cc_final: 0.8151 (t80) REVERT: Y 17 GLU cc_start: 0.9201 (tt0) cc_final: 0.8948 (pt0) REVERT: Y 24 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8031 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8407 (m-40) REVERT: X 43 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7783 (tmm-80) REVERT: X 45 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: X 72 ASP cc_start: 0.7991 (t0) cc_final: 0.7500 (t0) outliers start: 41 outliers final: 31 residues processed: 291 average time/residue: 0.1490 time to fit residues: 57.9883 Evaluate side-chains 291 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 48 optimal weight: 0.0970 chunk 131 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN Y 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055782 restraints weight = 41480.726| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.01 r_work: 0.3002 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13565 Z= 0.133 Angle : 0.667 10.640 18455 Z= 0.342 Chirality : 0.045 0.199 1975 Planarity : 0.004 0.061 2350 Dihedral : 4.794 26.212 1860 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 2.55 % Allowed : 22.62 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.20), residues: 1675 helix: 0.18 (0.59), residues: 80 sheet: -1.89 (0.20), residues: 710 loop : -2.23 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 86 TYR 0.020 0.001 TYR P 31 PHE 0.021 0.001 PHE J 26 TRP 0.019 0.001 TRP P 46 HIS 0.010 0.002 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00312 (13545) covalent geometry : angle 0.66654 (18415) SS BOND : bond 0.00277 ( 20) SS BOND : angle 0.85084 ( 40) hydrogen bonds : bond 0.02583 ( 254) hydrogen bonds : angle 5.17566 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.491 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: B 41 GLU cc_start: 0.7951 (mp0) cc_final: 0.7494 (mp0) REVERT: C 61 ASN cc_start: 0.8631 (p0) cc_final: 0.7908 (p0) REVERT: D 36 ASP cc_start: 0.8874 (t0) cc_final: 0.8582 (t0) REVERT: D 61 ASN cc_start: 0.8673 (p0) cc_final: 0.8084 (p0) REVERT: E 36 ASP cc_start: 0.8866 (t0) cc_final: 0.8562 (t0) REVERT: L 24 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8647 (mmm160) REVERT: L 70 ASP cc_start: 0.8940 (t0) cc_final: 0.8428 (p0) REVERT: L 103 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7795 (t70) REVERT: H 43 ARG cc_start: 0.8346 (ttp80) cc_final: 0.7773 (tmm-80) REVERT: H 45 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8435 (mt-10) REVERT: H 72 ASP cc_start: 0.7769 (t0) cc_final: 0.7019 (t0) REVERT: H 86 ARG cc_start: 0.8542 (ptp90) cc_final: 0.8141 (ptp90) REVERT: H 99 TYR cc_start: 0.8675 (t80) cc_final: 0.8216 (t80) REVERT: H 108 ASP cc_start: 0.8272 (t0) cc_final: 0.8041 (t0) REVERT: K 24 ARG cc_start: 0.8850 (mtp85) cc_final: 0.8543 (mmm160) REVERT: K 70 ASP cc_start: 0.8985 (t0) cc_final: 0.8553 (p0) REVERT: K 89 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8722 (tt0) REVERT: J 43 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7867 (ptm-80) REVERT: J 45 GLU cc_start: 0.8612 (pt0) cc_final: 0.8379 (pt0) REVERT: J 72 ASP cc_start: 0.8273 (t0) cc_final: 0.7108 (t0) REVERT: J 75 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8404 (mtp-110) REVERT: J 79 TYR cc_start: 0.8844 (m-80) cc_final: 0.8622 (m-80) REVERT: N 24 ARG cc_start: 0.8905 (mtp85) cc_final: 0.8476 (ttm-80) REVERT: N 79 GLU cc_start: 0.8247 (mp0) cc_final: 0.7838 (mp0) REVERT: N 82 ASP cc_start: 0.8144 (m-30) cc_final: 0.7228 (m-30) REVERT: M 43 ARG cc_start: 0.7164 (ttp-110) cc_final: 0.6660 (ttp-110) REVERT: M 108 ASP cc_start: 0.7752 (m-30) cc_final: 0.7053 (m-30) REVERT: Q 24 ARG cc_start: 0.8704 (mmm160) cc_final: 0.8339 (mmm160) REVERT: Q 79 GLU cc_start: 0.8752 (mp0) cc_final: 0.8310 (mp0) REVERT: Q 82 ASP cc_start: 0.8451 (m-30) cc_final: 0.7856 (m-30) REVERT: Q 89 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: P 17 LEU cc_start: 0.9072 (mt) cc_final: 0.8867 (tp) REVERT: P 43 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8175 (ptm-80) REVERT: P 45 GLU cc_start: 0.8459 (pt0) cc_final: 0.7933 (pt0) REVERT: P 75 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8587 (mmm-85) REVERT: P 109 TYR cc_start: 0.8596 (t80) cc_final: 0.8234 (t80) REVERT: Y 17 GLU cc_start: 0.9196 (tt0) cc_final: 0.8938 (pt0) REVERT: Y 24 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8064 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8318 (m-40) REVERT: X 43 ARG cc_start: 0.8490 (ttp80) cc_final: 0.7813 (tmm-80) REVERT: X 45 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: X 72 ASP cc_start: 0.7970 (t0) cc_final: 0.7502 (t0) outliers start: 37 outliers final: 27 residues processed: 289 average time/residue: 0.1521 time to fit residues: 58.8724 Evaluate side-chains 292 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 92 ASN Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 61 optimal weight: 0.4980 chunk 154 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 0.0170 chunk 124 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 HIS Y 92 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056713 restraints weight = 41526.262| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.04 r_work: 0.3021 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13565 Z= 0.120 Angle : 0.663 8.280 18455 Z= 0.341 Chirality : 0.045 0.181 1975 Planarity : 0.005 0.060 2350 Dihedral : 4.736 31.091 1860 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 2.34 % Allowed : 22.21 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.20), residues: 1675 helix: 0.12 (0.59), residues: 80 sheet: -1.80 (0.20), residues: 710 loop : -2.18 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG M 86 TYR 0.020 0.001 TYR P 31 PHE 0.017 0.001 PHE M 26 TRP 0.020 0.001 TRP P 46 HIS 0.009 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00281 (13545) covalent geometry : angle 0.66260 (18415) SS BOND : bond 0.00251 ( 20) SS BOND : angle 0.86892 ( 40) hydrogen bonds : bond 0.02479 ( 254) hydrogen bonds : angle 5.04432 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.01 seconds wall clock time: 56 minutes 16.19 seconds (3376.19 seconds total)