Starting phenix.real_space_refine on Thu Jul 31 01:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k7i_22700/07_2025/7k7i_22700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k7i_22700/07_2025/7k7i_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_22700/07_2025/7k7i_22700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k7i_22700/07_2025/7k7i_22700.map" model { file = "/net/cci-nas-00/data/ceres_data/7k7i_22700/07_2025/7k7i_22700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k7i_22700/07_2025/7k7i_22700.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.50, per 1000 atoms: 0.64 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: 2.72 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.57 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: 3.23 Time building geometry restraints manager: 3.32 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: 0.01 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: 4.520 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.280 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- 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 : 11.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP J 110 HIS 0.005 0.001 HIS C 43 PHE 0.008 0.001 PHE D 117 TYR 0.011 0.001 TYR X 99 ARG 0.003 0.000 ARG J 97 Details of bonding type rmsd hydrogen bonds : bond 0.31659 ( 254) hydrogen bonds : angle 12.84874 ( 660) SS BOND : bond 0.00283 ( 20) SS BOND : angle 0.79510 ( 40) covalent geometry : bond 0.00297 (13545) covalent geometry : angle 0.54951 (18415) *********************** 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 : 1.386 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: L 69 THR cc_start: 0.8725 (p) cc_final: 0.7088 (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: 0.7255 (t0) REVERT: N 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7714 (p0) 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: 0.6453 (m-30) REVERT: P 31 TYR cc_start: 0.7608 (m-80) cc_final: 0.7207 (m-80) REVERT: Y 75 ILE cc_start: 0.7703 (mt) cc_final: 0.7485 (mt) 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: 0.3113 time to fit residues: 162.6807 Evaluate side-chains 292 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 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 38 GLN M 98 GLN P 98 GLN Y 37 GLN Y 89 GLN X 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.054602 restraints weight = 42305.821| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.85 r_work: 0.2958 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 13565 Z= 0.322 Angle : 0.737 8.912 18455 Z= 0.387 Chirality : 0.047 0.149 1975 Planarity : 0.005 0.040 2350 Dihedral : 5.124 33.170 1860 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 1.86 % Allowed : 15.72 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.18), residues: 1675 helix: -1.45 (0.54), residues: 75 sheet: -3.39 (0.18), residues: 615 loop : -2.99 (0.17), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 46 HIS 0.008 0.002 HIS K 90 PHE 0.021 0.002 PHE H 67 TYR 0.034 0.002 TYR X 109 ARG 0.009 0.001 ARG M 75 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 254) hydrogen bonds : angle 7.13359 ( 660) SS BOND : bond 0.00468 ( 20) SS BOND : angle 1.15669 ( 40) covalent geometry : bond 0.00732 (13545) covalent geometry : angle 0.73632 (18415) *********************** 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 338 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 311 time to evaluate : 1.543 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: 0.7812 (mp0) cc_final: 0.7602 (mp0) REVERT: C 101 ILE cc_start: 0.9108 (mt) cc_final: 0.8889 (mt) REVERT: D 36 ASP cc_start: 0.8913 (t0) cc_final: 0.8625 (t0) REVERT: D 84 GLU cc_start: 0.8911 (mp0) cc_final: 0.8466 (mp0) REVERT: D 101 ILE cc_start: 0.9194 (mt) cc_final: 0.8981 (mt) REVERT: E 36 ASP cc_start: 0.8986 (t0) cc_final: 0.8759 (t0) REVERT: L 24 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7855 (mmm160) REVERT: L 27 GLN cc_start: 0.8859 (mp10) cc_final: 0.8647 (mp10) REVERT: L 82 ASP cc_start: 0.8208 (m-30) cc_final: 0.7942 (m-30) REVERT: L 85 ASP cc_start: 0.8474 (m-30) cc_final: 0.8100 (m-30) REVERT: H 43 ARG cc_start: 0.8332 (ttp80) cc_final: 0.8008 (ttp80) REVERT: H 45 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8555 (mt-10) REVERT: H 72 ASP cc_start: 0.7765 (t0) cc_final: 0.7305 (t0) REVERT: H 86 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8094 (mtm110) REVERT: H 99 TYR cc_start: 0.8746 (t80) cc_final: 0.8231 (t80) REVERT: H 108 ASP cc_start: 0.8302 (t0) cc_final: 0.8089 (t0) REVERT: K 27 GLN cc_start: 0.8842 (mp10) cc_final: 0.8254 (mp10) REVERT: J 72 ASP cc_start: 0.8482 (t0) cc_final: 0.7452 (t0) REVERT: N 24 ARG cc_start: 0.8722 (mtp85) cc_final: 0.8478 (mtp85) REVERT: N 27 GLN cc_start: 0.8893 (mp10) cc_final: 0.8666 (mp10) REVERT: N 79 GLU cc_start: 0.8254 (mp0) cc_final: 0.8018 (mp0) REVERT: N 82 ASP cc_start: 0.8453 (m-30) cc_final: 0.8049 (m-30) REVERT: M 43 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7924 (ptm-80) REVERT: M 79 TYR cc_start: 0.8237 (m-10) cc_final: 0.8028 (m-80) REVERT: M 97 ARG cc_start: 0.6994 (ptp-170) cc_final: 0.6655 (ptp-170) REVERT: Q 82 ASP cc_start: 0.8103 (m-30) cc_final: 0.7477 (m-30) REVERT: P 31 TYR cc_start: 0.8439 (m-80) cc_final: 0.7996 (m-80) REVERT: P 45 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8032 (pt0) REVERT: P 77 THR cc_start: 0.8547 (p) cc_final: 0.8141 (p) REVERT: P 85 LEU cc_start: 0.9532 (mp) cc_final: 0.9306 (mt) REVERT: P 97 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7693 (ptt90) REVERT: P 109 TYR cc_start: 0.8481 (t80) cc_final: 0.7942 (t80) REVERT: Y 17 GLU cc_start: 0.8928 (tt0) cc_final: 0.8722 (mt-10) REVERT: Y 24 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8899 (t0) cc_final: 0.8667 (m-40) REVERT: X 45 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8281 (mt-10) REVERT: X 72 ASP cc_start: 0.7914 (t0) cc_final: 0.7595 (t0) REVERT: X 108 ASP cc_start: 0.8582 (t0) cc_final: 0.8298 (m-30) outliers start: 27 outliers final: 16 residues processed: 323 average time/residue: 0.3047 time to fit residues: 133.6599 Evaluate side-chains 287 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 269 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 24 ARG Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 62 ILE 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 69 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 50 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 144 optimal weight: 0.0030 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 122 optimal weight: 0.0980 chunk 149 optimal weight: 0.0020 chunk 157 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN L 49 GLN L 92 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN M 38 GLN Q 37 GLN ** Y 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.074098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058367 restraints weight = 41878.602| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.89 r_work: 0.3056 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13565 Z= 0.114 Angle : 0.621 9.391 18455 Z= 0.320 Chirality : 0.044 0.164 1975 Planarity : 0.004 0.046 2350 Dihedral : 4.740 27.429 1860 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 2.14 % Allowed : 16.69 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.18), residues: 1675 helix: -1.27 (0.53), residues: 80 sheet: -2.80 (0.19), residues: 655 loop : -2.76 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 46 HIS 0.008 0.001 HIS L 90 PHE 0.014 0.001 PHE H 67 TYR 0.012 0.001 TYR X 99 ARG 0.010 0.001 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 254) hydrogen bonds : angle 6.08471 ( 660) SS BOND : bond 0.00226 ( 20) SS BOND : angle 0.73820 ( 40) covalent geometry : bond 0.00259 (13545) covalent geometry : angle 0.62053 (18415) *********************** 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 338 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8630 (tp) REVERT: C 101 ILE cc_start: 0.9049 (mt) cc_final: 0.8845 (mt) REVERT: D 36 ASP cc_start: 0.8859 (t0) cc_final: 0.8627 (t0) REVERT: D 61 ASN cc_start: 0.8555 (p0) cc_final: 0.8083 (p0) REVERT: D 77 ILE cc_start: 0.9019 (tp) cc_final: 0.8698 (mm) REVERT: D 101 ILE cc_start: 0.9158 (mt) cc_final: 0.8946 (mt) REVERT: E 36 ASP cc_start: 0.8937 (t0) cc_final: 0.8675 (t0) REVERT: L 61 ARG cc_start: 0.8549 (mtm110) cc_final: 0.8153 (mtm110) REVERT: L 79 GLU cc_start: 0.8571 (mp0) cc_final: 0.7467 (mp0) REVERT: L 82 ASP cc_start: 0.8317 (m-30) cc_final: 0.6952 (m-30) REVERT: L 103 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7817 (t70) REVERT: H 45 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8602 (mt-10) REVERT: H 72 ASP cc_start: 0.7767 (t0) cc_final: 0.7391 (t0) REVERT: H 99 TYR cc_start: 0.8603 (t80) cc_final: 0.7983 (t80) REVERT: H 108 ASP cc_start: 0.8229 (t0) cc_final: 0.7994 (t0) REVERT: H 112 GLN cc_start: 0.8588 (mp10) cc_final: 0.8243 (mp10) REVERT: K 26 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8870 (p) REVERT: K 70 ASP cc_start: 0.8851 (t0) cc_final: 0.8574 (p0) REVERT: K 89 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8670 (tt0) REVERT: J 26 PHE cc_start: 0.6949 (m-80) cc_final: 0.6582 (m-80) REVERT: J 72 ASP cc_start: 0.8453 (t0) cc_final: 0.7457 (t0) REVERT: J 75 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8422 (mtp-110) REVERT: J 97 ARG cc_start: 0.6887 (mtt-85) cc_final: 0.6609 (mtp-110) REVERT: J 109 TYR cc_start: 0.7773 (p90) cc_final: 0.7353 (p90) REVERT: N 24 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8150 (ttm-80) REVERT: N 79 GLU cc_start: 0.8248 (mp0) cc_final: 0.8012 (mp0) REVERT: N 82 ASP cc_start: 0.8413 (m-30) cc_final: 0.8044 (m-30) REVERT: M 43 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7754 (ptm-80) REVERT: M 109 TYR cc_start: 0.6730 (p90) cc_final: 0.6437 (p90) REVERT: M 112 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8288 (mm-40) REVERT: Q 24 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8504 (mmm160) REVERT: Q 103 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.7280 (m-70) REVERT: P 45 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7895 (pt0) REVERT: P 64 LYS cc_start: 0.8689 (tppt) cc_final: 0.8300 (tppt) REVERT: P 97 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8043 (ttt-90) REVERT: P 109 TYR cc_start: 0.8450 (t80) cc_final: 0.8220 (t80) REVERT: Y 24 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8036 (mtm-85) REVERT: X 72 ASP cc_start: 0.8043 (t0) cc_final: 0.7393 (t0) REVERT: X 75 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8527 (mtp85) REVERT: X 98 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8211 (mm-40) outliers start: 31 outliers final: 13 residues processed: 324 average time/residue: 0.3196 time to fit residues: 139.7084 Evaluate side-chains 296 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 277 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 77 ILE 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 26 SER 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 103 HIS Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain Y residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 72 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** N 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.069925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.054137 restraints weight = 42162.117| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.83 r_work: 0.2952 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13565 Z= 0.272 Angle : 0.683 7.353 18455 Z= 0.356 Chirality : 0.045 0.175 1975 Planarity : 0.005 0.071 2350 Dihedral : 5.000 29.768 1860 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 2.97 % Allowed : 17.86 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1675 helix: -0.87 (0.52), residues: 80 sheet: -2.67 (0.18), residues: 695 loop : -2.67 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 46 HIS 0.014 0.002 HIS L 90 PHE 0.016 0.002 PHE H 67 TYR 0.016 0.001 TYR M 100 ARG 0.008 0.001 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 254) hydrogen bonds : angle 5.94669 ( 660) SS BOND : bond 0.00445 ( 20) SS BOND : angle 0.97341 ( 40) covalent geometry : bond 0.00624 (13545) covalent geometry : angle 0.68248 (18415) *********************** 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 329 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.420 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: A 41 GLU cc_start: 0.8290 (mp0) cc_final: 0.8077 (mm-30) REVERT: C 61 ASN cc_start: 0.8401 (p0) cc_final: 0.8148 (p0) REVERT: D 36 ASP cc_start: 0.8872 (t0) cc_final: 0.8650 (t0) REVERT: D 61 ASN cc_start: 0.8576 (p0) cc_final: 0.7843 (p0) REVERT: E 36 ASP cc_start: 0.8928 (t0) cc_final: 0.8650 (t0) REVERT: L 2 ILE cc_start: 0.7425 (mt) cc_final: 0.7052 (mm) REVERT: L 24 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8161 (mmm160) REVERT: L 82 ASP cc_start: 0.8290 (m-30) cc_final: 0.7982 (m-30) REVERT: L 103 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7825 (t70) REVERT: H 43 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7623 (tmm-80) REVERT: H 45 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8366 (mt-10) REVERT: H 72 ASP cc_start: 0.7869 (t0) cc_final: 0.7412 (t0) REVERT: H 86 ARG cc_start: 0.8443 (ptp-110) cc_final: 0.8090 (mtm110) REVERT: H 99 TYR cc_start: 0.8800 (t80) cc_final: 0.8396 (t80) REVERT: K 26 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8730 (p) REVERT: K 70 ASP cc_start: 0.8838 (t0) cc_final: 0.8589 (p0) REVERT: K 82 ASP cc_start: 0.8484 (m-30) cc_final: 0.8137 (m-30) REVERT: K 89 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8761 (tt0) REVERT: J 72 ASP cc_start: 0.8477 (t0) cc_final: 0.7498 (t0) REVERT: J 75 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8458 (mtp-110) REVERT: J 109 TYR cc_start: 0.7981 (p90) cc_final: 0.7740 (p90) REVERT: N 24 ARG cc_start: 0.8751 (mtp85) cc_final: 0.8228 (ttm-80) REVERT: N 79 GLU cc_start: 0.8110 (mp0) cc_final: 0.7882 (mp0) REVERT: N 82 ASP cc_start: 0.8395 (m-30) cc_final: 0.7817 (m-30) REVERT: P 71 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7947 (mtm-85) REVERT: P 75 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8615 (mpp80) REVERT: P 97 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7953 (ttt-90) REVERT: P 109 TYR cc_start: 0.8500 (t80) cc_final: 0.8242 (t80) REVERT: Y 24 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8184 (mtm-85) REVERT: Y 79 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7867 (tm-30) REVERT: Y 92 ASN cc_start: 0.8937 (t0) cc_final: 0.8682 (m-40) REVERT: X 43 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7776 (tmm-80) REVERT: X 45 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8290 (mt-10) REVERT: X 72 ASP cc_start: 0.8073 (t0) cc_final: 0.7623 (t0) REVERT: X 107 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7279 (mmt) REVERT: X 108 ASP cc_start: 0.8476 (t0) cc_final: 0.8159 (m-30) outliers start: 43 outliers final: 28 residues processed: 308 average time/residue: 0.3289 time to fit residues: 136.3347 Evaluate side-chains 302 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 103 HIS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 26 SER 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 103 HIS Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 71 ARG 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 X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 100 TYR 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 84 optimal weight: 8.9990 chunk 157 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.071778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055927 restraints weight = 42379.958| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.90 r_work: 0.3005 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13565 Z= 0.145 Angle : 0.626 7.434 18455 Z= 0.323 Chirality : 0.044 0.203 1975 Planarity : 0.005 0.081 2350 Dihedral : 4.844 27.476 1860 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.76 % Allowed : 18.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.19), residues: 1675 helix: -0.34 (0.55), residues: 80 sheet: -2.41 (0.19), residues: 695 loop : -2.56 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 46 HIS 0.011 0.002 HIS N 90 PHE 0.014 0.001 PHE X 67 TYR 0.028 0.001 TYR X 31 ARG 0.011 0.001 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.02748 ( 254) hydrogen bonds : angle 5.56405 ( 660) SS BOND : bond 0.00299 ( 20) SS BOND : angle 0.73559 ( 40) covalent geometry : bond 0.00342 (13545) covalent geometry : angle 0.62555 (18415) *********************** 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 334 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 GLU cc_start: 0.8139 (mp0) cc_final: 0.7722 (mp0) REVERT: C 84 GLU cc_start: 0.8766 (mp0) cc_final: 0.8432 (mp0) REVERT: D 36 ASP cc_start: 0.8858 (t0) cc_final: 0.8658 (t0) REVERT: D 61 ASN cc_start: 0.8599 (p0) cc_final: 0.7902 (p0) REVERT: D 83 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8765 (ptmm) REVERT: E 36 ASP cc_start: 0.8894 (t0) cc_final: 0.8642 (t0) REVERT: L 26 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8684 (p) REVERT: L 82 ASP cc_start: 0.8277 (m-30) cc_final: 0.8010 (m-30) REVERT: L 103 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7827 (t70) REVERT: H 43 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7776 (tmm-80) REVERT: H 45 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8485 (mt-10) REVERT: H 72 ASP cc_start: 0.7861 (t0) cc_final: 0.7449 (t0) REVERT: H 86 ARG cc_start: 0.8535 (ptp-110) cc_final: 0.8201 (mtm110) REVERT: H 99 TYR cc_start: 0.8654 (t80) cc_final: 0.8168 (t80) REVERT: H 112 GLN cc_start: 0.8543 (mp10) cc_final: 0.8304 (mp10) REVERT: K 70 ASP cc_start: 0.8852 (t0) cc_final: 0.8579 (p0) REVERT: K 78 VAL cc_start: 0.8900 (m) cc_final: 0.8696 (p) REVERT: K 89 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8773 (tt0) REVERT: J 72 ASP cc_start: 0.8476 (t0) cc_final: 0.7483 (t0) REVERT: J 75 ARG cc_start: 0.8654 (mtp85) cc_final: 0.8401 (mtp-110) REVERT: J 112 GLN cc_start: 0.8270 (mm-40) cc_final: 0.8036 (mm-40) REVERT: N 24 ARG cc_start: 0.8722 (mtp85) cc_final: 0.8250 (ttm-80) REVERT: N 79 GLU cc_start: 0.8280 (mp0) cc_final: 0.8047 (mp0) REVERT: N 82 ASP cc_start: 0.8466 (m-30) cc_final: 0.7862 (m-30) REVERT: M 43 ARG cc_start: 0.7804 (ttp-110) cc_final: 0.7480 (ttp-110) REVERT: Q 79 GLU cc_start: 0.8633 (mp0) cc_final: 0.8352 (mp0) REVERT: Q 82 ASP cc_start: 0.8023 (m-30) cc_final: 0.7095 (m-30) REVERT: Q 103 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7293 (m-70) REVERT: P 45 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8083 (pt0) REVERT: P 64 LYS cc_start: 0.8849 (tppt) cc_final: 0.8647 (tppt) REVERT: P 109 TYR cc_start: 0.8463 (t80) cc_final: 0.8124 (t80) REVERT: Y 24 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: Y 79 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7900 (tm-30) REVERT: Y 82 ASP cc_start: 0.8423 (m-30) cc_final: 0.8218 (m-30) REVERT: Y 92 ASN cc_start: 0.8788 (t0) cc_final: 0.8540 (m-40) REVERT: X 43 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7848 (ttp80) REVERT: X 72 ASP cc_start: 0.8104 (t0) cc_final: 0.7668 (t0) REVERT: X 108 ASP cc_start: 0.8369 (t0) cc_final: 0.8038 (t0) outliers start: 40 outliers final: 25 residues processed: 314 average time/residue: 0.3302 time to fit residues: 139.3078 Evaluate side-chains 301 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 SER Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 26 SER 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 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 103 HIS Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 VAL Chi-restraints excluded: chain X residue 100 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 144 optimal weight: 0.2980 chunk 117 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.070510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054793 restraints weight = 42416.876| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.83 r_work: 0.2974 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13565 Z= 0.200 Angle : 0.640 9.225 18455 Z= 0.334 Chirality : 0.045 0.176 1975 Planarity : 0.004 0.054 2350 Dihedral : 4.890 26.589 1860 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 3.24 % Allowed : 18.90 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.19), residues: 1675 helix: 0.21 (0.57), residues: 75 sheet: -2.27 (0.19), residues: 695 loop : -2.50 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 46 HIS 0.013 0.002 HIS L 90 PHE 0.019 0.001 PHE X 67 TYR 0.011 0.001 TYR X 109 ARG 0.011 0.001 ARG M 43 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 254) hydrogen bonds : angle 5.46957 ( 660) SS BOND : bond 0.00385 ( 20) SS BOND : angle 0.76184 ( 40) covalent geometry : bond 0.00464 (13545) covalent geometry : angle 0.63949 (18415) *********************** 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 318 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 1.517 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: 0.8216 (mp0) cc_final: 0.7759 (mp0) REVERT: C 61 ASN cc_start: 0.8569 (p0) cc_final: 0.7916 (p0) REVERT: D 36 ASP cc_start: 0.8855 (t0) cc_final: 0.8641 (t0) REVERT: D 61 ASN cc_start: 0.8574 (p0) cc_final: 0.7853 (p0) REVERT: E 36 ASP cc_start: 0.8886 (t0) cc_final: 0.8613 (t0) REVERT: L 24 ARG cc_start: 0.8837 (mmm160) cc_final: 0.8566 (mmm160) REVERT: L 26 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8627 (p) REVERT: L 82 ASP cc_start: 0.8306 (m-30) cc_final: 0.8045 (m-30) REVERT: L 103 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7853 (t70) REVERT: H 43 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7785 (tmm-80) REVERT: H 45 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8461 (mt-10) REVERT: H 72 ASP cc_start: 0.7834 (t0) cc_final: 0.7436 (t0) REVERT: H 86 ARG cc_start: 0.8549 (ptp-110) cc_final: 0.8220 (ptp90) REVERT: H 99 TYR cc_start: 0.8698 (t80) cc_final: 0.8177 (t80) REVERT: K 70 ASP cc_start: 0.8835 (t0) cc_final: 0.8560 (p0) REVERT: K 89 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8851 (tt0) REVERT: J 72 ASP cc_start: 0.8488 (t0) cc_final: 0.7479 (t0) REVERT: J 75 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8432 (mtp-110) REVERT: N 24 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8370 (ttm-80) REVERT: N 79 GLU cc_start: 0.8226 (mp0) cc_final: 0.7799 (mp0) REVERT: N 82 ASP cc_start: 0.8440 (m-30) cc_final: 0.7587 (m-30) REVERT: M 43 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7367 (ptm-80) REVERT: M 45 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: Q 79 GLU cc_start: 0.8686 (mp0) cc_final: 0.8484 (mp0) REVERT: Q 82 ASP cc_start: 0.8152 (m-30) cc_final: 0.7869 (m-30) REVERT: Q 89 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: Q 103 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7313 (m-70) REVERT: P 64 LYS cc_start: 0.8914 (tppt) cc_final: 0.8562 (tppt) REVERT: P 109 TYR cc_start: 0.8414 (t80) cc_final: 0.8144 (t80) REVERT: Y 24 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8093 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8847 (t0) cc_final: 0.8593 (m-40) REVERT: X 43 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8020 (ttp80) REVERT: X 72 ASP cc_start: 0.8094 (t0) cc_final: 0.7632 (t0) outliers start: 47 outliers final: 29 residues processed: 297 average time/residue: 0.3457 time to fit residues: 139.2685 Evaluate side-chains 299 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain L residue 26 SER 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 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 M residue 82 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 78 VAL 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 62 ILE Chi-restraints excluded: chain P residue 77 THR 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 Chi-restraints excluded: chain X residue 100 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 134 optimal weight: 0.0870 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN 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 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.072562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056257 restraints weight = 41478.126| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.06 r_work: 0.3005 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13565 Z= 0.132 Angle : 0.627 8.069 18455 Z= 0.325 Chirality : 0.045 0.199 1975 Planarity : 0.004 0.054 2350 Dihedral : 4.771 26.374 1860 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.62 % Allowed : 20.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.19), residues: 1675 helix: 0.14 (0.58), residues: 80 sheet: -2.12 (0.19), residues: 715 loop : -2.33 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 46 HIS 0.012 0.002 HIS L 90 PHE 0.017 0.001 PHE J 26 TYR 0.013 0.001 TYR X 109 ARG 0.013 0.001 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 254) hydrogen bonds : angle 5.27121 ( 660) SS BOND : bond 0.00290 ( 20) SS BOND : angle 0.64640 ( 40) covalent geometry : bond 0.00310 (13545) covalent geometry : angle 0.62679 (18415) *********************** 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 324 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 GLU cc_start: 0.8133 (mp0) cc_final: 0.7641 (mp0) REVERT: C 61 ASN cc_start: 0.8663 (p0) cc_final: 0.8014 (p0) REVERT: D 36 ASP cc_start: 0.8867 (t0) cc_final: 0.8642 (t0) REVERT: D 61 ASN cc_start: 0.8605 (p0) cc_final: 0.7976 (p0) REVERT: E 36 ASP cc_start: 0.8869 (t0) cc_final: 0.8578 (t0) REVERT: E 41 GLU cc_start: 0.8210 (mp0) cc_final: 0.8002 (mp0) REVERT: L 24 ARG cc_start: 0.8899 (mmm160) cc_final: 0.8632 (mmm160) REVERT: L 70 ASP cc_start: 0.8788 (t0) cc_final: 0.8499 (p0) REVERT: L 103 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7839 (t70) REVERT: H 43 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7702 (tmm-80) REVERT: H 45 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8350 (mt-10) REVERT: H 72 ASP cc_start: 0.7865 (t0) cc_final: 0.7480 (t0) REVERT: H 86 ARG cc_start: 0.8593 (ptp-110) cc_final: 0.8331 (ptp90) REVERT: H 99 TYR cc_start: 0.8598 (t80) cc_final: 0.8091 (t80) REVERT: H 112 GLN cc_start: 0.8625 (mp10) cc_final: 0.8356 (mp10) REVERT: K 70 ASP cc_start: 0.8905 (t0) cc_final: 0.8546 (p0) REVERT: K 89 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: J 72 ASP cc_start: 0.8456 (t0) cc_final: 0.7421 (t0) REVERT: J 75 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8420 (mtp-110) REVERT: N 24 ARG cc_start: 0.8822 (mtp85) cc_final: 0.8431 (ttm-80) REVERT: N 79 GLU cc_start: 0.8410 (mp0) cc_final: 0.8169 (mp0) REVERT: N 82 ASP cc_start: 0.8366 (m-30) cc_final: 0.7703 (m-30) REVERT: M 108 ASP cc_start: 0.7736 (m-30) cc_final: 0.7193 (m-30) REVERT: Q 24 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8400 (mmm160) REVERT: Q 70 ASP cc_start: 0.8730 (t0) cc_final: 0.8407 (p0) REVERT: Q 79 GLU cc_start: 0.8753 (mp0) cc_final: 0.8539 (mp0) REVERT: Q 82 ASP cc_start: 0.8159 (m-30) cc_final: 0.7808 (m-30) REVERT: Q 89 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8690 (tt0) REVERT: Q 103 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7249 (m-70) REVERT: P 72 ASP cc_start: 0.8141 (m-30) cc_final: 0.7588 (p0) REVERT: P 77 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8528 (p) REVERT: P 79 TYR cc_start: 0.8357 (m-80) cc_final: 0.8070 (m-10) REVERT: P 96 VAL cc_start: 0.9164 (t) cc_final: 0.8805 (p) REVERT: P 109 TYR cc_start: 0.8432 (t80) cc_final: 0.8130 (t80) REVERT: Y 17 GLU cc_start: 0.9110 (tt0) cc_final: 0.8827 (pt0) REVERT: Y 24 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8138 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8838 (t0) cc_final: 0.8546 (m-40) REVERT: X 43 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8052 (ttp80) REVERT: X 72 ASP cc_start: 0.8034 (t0) cc_final: 0.7568 (t0) REVERT: X 108 ASP cc_start: 0.8466 (t0) cc_final: 0.8166 (m-30) outliers start: 38 outliers final: 23 residues processed: 307 average time/residue: 0.3178 time to fit residues: 132.2964 Evaluate side-chains 301 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 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 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 97 ARG Chi-restraints excluded: chain Q residue 89 GLN 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 77 THR Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 100 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 0.0060 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.073741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057425 restraints weight = 41583.293| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.11 r_work: 0.3035 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13565 Z= 0.115 Angle : 0.620 6.787 18455 Z= 0.322 Chirality : 0.044 0.177 1975 Planarity : 0.004 0.052 2350 Dihedral : 4.609 23.813 1860 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 2.21 % Allowed : 20.69 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.19), residues: 1675 helix: 0.07 (0.58), residues: 80 sheet: -1.86 (0.20), residues: 690 loop : -2.29 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 46 HIS 0.016 0.002 HIS L 90 PHE 0.017 0.001 PHE J 26 TYR 0.016 0.001 TYR P 31 ARG 0.013 0.001 ARG J 86 Details of bonding type rmsd hydrogen bonds : bond 0.02396 ( 254) hydrogen bonds : angle 5.07117 ( 660) SS BOND : bond 0.00253 ( 20) SS BOND : angle 0.61331 ( 40) covalent geometry : bond 0.00269 (13545) covalent geometry : angle 0.62006 (18415) *********************** 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 324 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.498 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 28 ASP cc_start: 0.7957 (m-30) cc_final: 0.7535 (m-30) REVERT: B 41 GLU cc_start: 0.8116 (mp0) cc_final: 0.7624 (mp0) REVERT: C 61 ASN cc_start: 0.8681 (p0) cc_final: 0.8045 (p0) REVERT: C 101 ILE cc_start: 0.9139 (mt) cc_final: 0.8938 (mt) REVERT: D 36 ASP cc_start: 0.8870 (t0) cc_final: 0.8637 (t0) REVERT: D 61 ASN cc_start: 0.8599 (p0) cc_final: 0.7938 (p0) REVERT: E 36 ASP cc_start: 0.8869 (t0) cc_final: 0.8598 (t0) REVERT: L 24 ARG cc_start: 0.8904 (mmm160) cc_final: 0.8621 (mmm160) REVERT: L 70 ASP cc_start: 0.8820 (t0) cc_final: 0.8416 (p0) REVERT: L 79 GLU cc_start: 0.8736 (mp0) cc_final: 0.8343 (mp0) REVERT: L 82 ASP cc_start: 0.8221 (m-30) cc_final: 0.7631 (m-30) REVERT: L 103 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7797 (t70) REVERT: H 43 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7774 (tmm-80) REVERT: H 45 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8362 (mt-10) REVERT: H 72 ASP cc_start: 0.7870 (t0) cc_final: 0.7509 (t0) REVERT: H 86 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.8259 (ptp90) REVERT: H 108 ASP cc_start: 0.8196 (t0) cc_final: 0.7342 (p0) REVERT: K 70 ASP cc_start: 0.8904 (t0) cc_final: 0.8545 (p0) REVERT: J 43 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8129 (ptm-80) REVERT: J 72 ASP cc_start: 0.8387 (t0) cc_final: 0.7345 (t0) REVERT: J 75 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8405 (mtp-110) REVERT: J 96 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8464 (m) REVERT: N 24 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8476 (ttm-80) REVERT: N 79 GLU cc_start: 0.8448 (mp0) cc_final: 0.8176 (mp0) REVERT: N 82 ASP cc_start: 0.8297 (m-30) cc_final: 0.7637 (m-30) REVERT: M 43 ARG cc_start: 0.7664 (ttp-110) cc_final: 0.7264 (ttp-110) REVERT: M 108 ASP cc_start: 0.7836 (m-30) cc_final: 0.7243 (m-30) REVERT: Q 24 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8255 (tpp-160) REVERT: Q 70 ASP cc_start: 0.8787 (t0) cc_final: 0.8490 (p0) REVERT: Q 79 GLU cc_start: 0.8837 (mp0) cc_final: 0.8609 (mp0) REVERT: Q 82 ASP cc_start: 0.8082 (m-30) cc_final: 0.7185 (m-30) REVERT: Q 89 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8761 (tt0) REVERT: P 64 LYS cc_start: 0.8830 (tppt) cc_final: 0.8367 (tppt) REVERT: P 72 ASP cc_start: 0.8035 (m-30) cc_final: 0.6840 (p0) REVERT: P 75 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8273 (mpp80) REVERT: P 77 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8549 (p) REVERT: P 79 TYR cc_start: 0.8319 (m-80) cc_final: 0.8038 (m-10) REVERT: P 96 VAL cc_start: 0.9200 (t) cc_final: 0.8872 (p) REVERT: P 109 TYR cc_start: 0.8436 (t80) cc_final: 0.8085 (t80) REVERT: Y 17 GLU cc_start: 0.9102 (tt0) cc_final: 0.8820 (pt0) REVERT: Y 24 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: Y 92 ASN cc_start: 0.8812 (t0) cc_final: 0.8574 (m-40) REVERT: X 43 ARG cc_start: 0.8551 (ttp80) cc_final: 0.7938 (ttp80) REVERT: X 45 GLU cc_start: 0.8533 (pt0) cc_final: 0.8205 (pm20) REVERT: X 72 ASP cc_start: 0.7990 (t0) cc_final: 0.7624 (t0) REVERT: X 96 VAL cc_start: 0.9567 (m) cc_final: 0.9335 (p) REVERT: X 108 ASP cc_start: 0.8406 (t0) cc_final: 0.8100 (m-30) outliers start: 32 outliers final: 22 residues processed: 309 average time/residue: 0.3235 time to fit residues: 135.0280 Evaluate side-chains 303 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 126 SER Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain E residue 126 SER 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 103 HIS 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 M residue 97 ARG Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 ASN L 49 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Q 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.070509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054110 restraints weight = 40978.076| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.98 r_work: 0.2934 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13565 Z= 0.292 Angle : 0.735 8.844 18455 Z= 0.383 Chirality : 0.047 0.189 1975 Planarity : 0.005 0.067 2350 Dihedral : 5.168 28.193 1860 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 2.41 % Allowed : 21.24 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.20), residues: 1675 helix: 0.45 (0.57), residues: 75 sheet: -1.82 (0.21), residues: 645 loop : -2.31 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 110 HIS 0.013 0.002 HIS L 90 PHE 0.019 0.002 PHE X 67 TYR 0.023 0.002 TYR H 99 ARG 0.016 0.001 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.03140 ( 254) hydrogen bonds : angle 5.46180 ( 660) SS BOND : bond 0.00493 ( 20) SS BOND : angle 0.85654 ( 40) covalent geometry : bond 0.00674 (13545) covalent geometry : angle 0.73477 (18415) *********************** 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: 35 poor density : 270 time to evaluate : 1.436 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: A 61 ASN cc_start: 0.8269 (p0) cc_final: 0.7854 (p0) REVERT: B 41 GLU cc_start: 0.8226 (mp0) cc_final: 0.7677 (mp0) REVERT: C 61 ASN cc_start: 0.8641 (p0) cc_final: 0.7794 (p0) REVERT: D 36 ASP cc_start: 0.8835 (t0) cc_final: 0.8582 (t0) REVERT: D 61 ASN cc_start: 0.8568 (p0) cc_final: 0.7753 (p0) REVERT: E 36 ASP cc_start: 0.8868 (t0) cc_final: 0.8577 (t0) REVERT: L 24 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8606 (mmm160) REVERT: L 103 HIS cc_start: 0.8155 (OUTLIER) cc_final: 0.7807 (t70) REVERT: H 43 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7565 (tmm-80) REVERT: H 45 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8327 (mt-10) REVERT: H 72 ASP cc_start: 0.7903 (t0) cc_final: 0.7525 (t0) REVERT: H 86 ARG cc_start: 0.8550 (ptp-110) cc_final: 0.8288 (ptp90) REVERT: H 99 TYR cc_start: 0.8761 (t80) cc_final: 0.8430 (t80) REVERT: H 112 GLN cc_start: 0.8565 (mp10) cc_final: 0.8279 (mp10) REVERT: K 70 ASP cc_start: 0.8861 (t0) cc_final: 0.8514 (p0) REVERT: K 89 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8818 (tt0) REVERT: J 43 ARG cc_start: 0.8360 (ptm-80) cc_final: 0.8053 (ptm-80) REVERT: J 72 ASP cc_start: 0.8481 (t0) cc_final: 0.7463 (t0) REVERT: J 75 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8454 (mtp-110) REVERT: N 24 ARG cc_start: 0.8896 (mtp85) cc_final: 0.7591 (ttm110) REVERT: N 79 GLU cc_start: 0.8310 (mp0) cc_final: 0.7953 (mp0) REVERT: N 82 ASP cc_start: 0.8267 (m-30) cc_final: 0.7499 (m-30) REVERT: M 108 ASP cc_start: 0.7684 (m-30) cc_final: 0.7038 (m-30) REVERT: Q 18 ARG cc_start: 0.8950 (tpp-160) cc_final: 0.8382 (mmm160) REVERT: Q 24 ARG cc_start: 0.8696 (mmm160) cc_final: 0.8192 (mmp80) REVERT: Q 79 GLU cc_start: 0.8854 (mp0) cc_final: 0.8380 (mp0) REVERT: Q 82 ASP cc_start: 0.8329 (m-30) cc_final: 0.8046 (m-30) REVERT: Q 89 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8749 (tt0) REVERT: P 31 TYR cc_start: 0.8115 (m-80) cc_final: 0.7719 (t80) REVERT: P 64 LYS cc_start: 0.8950 (tppt) cc_final: 0.8521 (tppt) REVERT: P 75 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8672 (mmm-85) REVERT: P 109 TYR cc_start: 0.8484 (t80) cc_final: 0.8068 (t80) REVERT: Y 17 GLU cc_start: 0.9066 (tt0) cc_final: 0.8802 (pt0) REVERT: Y 24 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8205 (mtm-85) REVERT: Y 78 VAL cc_start: 0.9068 (m) cc_final: 0.8790 (p) REVERT: Y 92 ASN cc_start: 0.8899 (t0) cc_final: 0.8575 (m-40) REVERT: X 72 ASP cc_start: 0.8149 (t0) cc_final: 0.7694 (t0) REVERT: X 108 ASP cc_start: 0.8460 (t0) cc_final: 0.8167 (m-30) outliers start: 35 outliers final: 31 residues processed: 290 average time/residue: 0.3198 time to fit residues: 124.0274 Evaluate side-chains 290 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 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 82 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 37 optimal weight: 0.0040 chunk 105 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 132 optimal weight: 0.0070 chunk 113 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 overall best weight: 0.2210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Y 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.078197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060611 restraints weight = 37926.835| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.32 r_work: 0.3046 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13565 Z= 0.123 Angle : 0.681 8.876 18455 Z= 0.350 Chirality : 0.045 0.195 1975 Planarity : 0.004 0.058 2350 Dihedral : 4.749 23.315 1860 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.93 % Allowed : 22.41 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.19), residues: 1675 helix: 0.15 (0.57), residues: 80 sheet: -1.59 (0.21), residues: 650 loop : -2.31 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 46 HIS 0.010 0.002 HIS L 90 PHE 0.016 0.001 PHE J 26 TYR 0.018 0.001 TYR H 99 ARG 0.015 0.001 ARG J 86 Details of bonding type rmsd hydrogen bonds : bond 0.02523 ( 254) hydrogen bonds : angle 5.15897 ( 660) SS BOND : bond 0.00229 ( 20) SS BOND : angle 0.60184 ( 40) covalent geometry : bond 0.00283 (13545) covalent geometry : angle 0.68139 (18415) ********************** 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 313 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 285 time to evaluate : 1.889 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: 0.8052 (mp0) cc_final: 0.7583 (mp0) REVERT: C 61 ASN cc_start: 0.8699 (p0) cc_final: 0.8092 (p0) REVERT: D 36 ASP cc_start: 0.8852 (t0) cc_final: 0.8636 (t0) REVERT: D 61 ASN cc_start: 0.8614 (p0) cc_final: 0.7912 (p0) REVERT: D 83 LYS cc_start: 0.8901 (ptmm) cc_final: 0.8616 (ptmm) REVERT: E 36 ASP cc_start: 0.8884 (t0) cc_final: 0.8599 (t0) REVERT: L 24 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8559 (mmm160) REVERT: L 69 THR cc_start: 0.9428 (p) cc_final: 0.9088 (m) REVERT: L 79 GLU cc_start: 0.8788 (mp0) cc_final: 0.8430 (mp0) REVERT: L 82 ASP cc_start: 0.8106 (m-30) cc_final: 0.7531 (m-30) REVERT: L 85 ASP cc_start: 0.8009 (m-30) cc_final: 0.7131 (p0) REVERT: L 103 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7793 (t70) REVERT: H 43 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7812 (tmm-80) REVERT: H 45 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8399 (mt-10) REVERT: H 72 ASP cc_start: 0.7855 (t0) cc_final: 0.7196 (t0) REVERT: H 82 MET cc_start: 0.8850 (ptp) cc_final: 0.8437 (mtp) REVERT: H 86 ARG cc_start: 0.8533 (ptp-110) cc_final: 0.8289 (ptp90) REVERT: H 108 ASP cc_start: 0.8229 (t0) cc_final: 0.7421 (p0) REVERT: K 70 ASP cc_start: 0.8839 (t0) cc_final: 0.8506 (p0) REVERT: J 43 ARG cc_start: 0.8312 (ptm-80) cc_final: 0.7963 (ptm-80) REVERT: J 72 ASP cc_start: 0.8445 (t0) cc_final: 0.7408 (t0) REVERT: J 75 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8403 (mtp-110) REVERT: N 79 GLU cc_start: 0.8471 (mp0) cc_final: 0.8217 (mp0) REVERT: N 82 ASP cc_start: 0.8282 (m-30) cc_final: 0.7632 (m-30) REVERT: M 43 ARG cc_start: 0.7625 (ttp-110) cc_final: 0.6905 (ptm-80) REVERT: M 45 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: M 108 ASP cc_start: 0.7931 (m-30) cc_final: 0.7386 (m-30) REVERT: Q 24 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8449 (mmm160) REVERT: Q 79 GLU cc_start: 0.8939 (mp0) cc_final: 0.8662 (mp0) REVERT: Q 82 ASP cc_start: 0.8195 (m-30) cc_final: 0.7351 (m-30) REVERT: Q 89 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8781 (tt0) REVERT: P 64 LYS cc_start: 0.8773 (tppt) cc_final: 0.8284 (tppt) REVERT: P 72 ASP cc_start: 0.7941 (m-30) cc_final: 0.7550 (p0) REVERT: P 75 ARG cc_start: 0.8893 (ttm110) cc_final: 0.8513 (mmm-85) REVERT: P 96 VAL cc_start: 0.9173 (t) cc_final: 0.8789 (p) REVERT: P 98 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8005 (mt0) REVERT: P 109 TYR cc_start: 0.8437 (t80) cc_final: 0.8089 (t80) REVERT: Y 17 GLU cc_start: 0.9063 (tt0) cc_final: 0.8758 (pt0) REVERT: Y 24 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8163 (mtm-85) REVERT: X 43 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7996 (ptm-80) REVERT: X 72 ASP cc_start: 0.8113 (t0) cc_final: 0.7640 (t0) REVERT: X 96 VAL cc_start: 0.9608 (m) cc_final: 0.9364 (p) REVERT: X 108 ASP cc_start: 0.8374 (t0) cc_final: 0.8111 (m-30) outliers start: 28 outliers final: 19 residues processed: 301 average time/residue: 0.3188 time to fit residues: 130.8660 Evaluate side-chains 287 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 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 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 45 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain P residue 17 LEU Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 0.0970 chunk 129 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN ** 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 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.069740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054062 restraints weight = 42823.517| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.94 r_work: 0.2957 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13565 Z= 0.236 Angle : 0.715 8.468 18455 Z= 0.372 Chirality : 0.046 0.202 1975 Planarity : 0.005 0.070 2350 Dihedral : 5.019 26.405 1860 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.86 % Allowed : 22.21 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.20), residues: 1675 helix: 0.30 (0.58), residues: 80 sheet: -1.43 (0.20), residues: 710 loop : -2.41 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 46 HIS 0.011 0.002 HIS L 90 PHE 0.013 0.001 PHE J 26 TYR 0.030 0.001 TYR H 99 ARG 0.014 0.001 ARG M 86 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 254) hydrogen bonds : angle 5.24383 ( 660) SS BOND : bond 0.00433 ( 20) SS BOND : angle 0.80349 ( 40) covalent geometry : bond 0.00549 (13545) covalent geometry : angle 0.71469 (18415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6870.53 seconds wall clock time: 120 minutes 3.57 seconds (7203.57 seconds total)