Starting phenix.real_space_refine on Mon Aug 25 20:42:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8keg_37155/08_2025/8keg_37155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8keg_37155/08_2025/8keg_37155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8keg_37155/08_2025/8keg_37155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8keg_37155/08_2025/8keg_37155.map" model { file = "/net/cci-nas-00/data/ceres_data/8keg_37155/08_2025/8keg_37155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8keg_37155/08_2025/8keg_37155_neut.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 19620 2.51 5 N 5070 2.21 5 O 6165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30930 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "B" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "C" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "D" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "E" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "F" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "G" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "H" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "J" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "K" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "L" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "M" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "N" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "O" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "a" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "b" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "c" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "e" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "f" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "g" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "h" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "i" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "j" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "k" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "l" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "m" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "n" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "o" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Time building chain proxies: 7.97, per 1000 atoms: 0.26 Number of scatterers: 30930 At special positions: 0 Unit cell: (218.28, 209.72, 82.39, 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 75 16.00 O 6165 8.00 N 5070 7.00 C 19620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7380 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 52 sheets defined 41.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.974A pdb=" N PHE A 19 " --> pdb=" O TYR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.910A pdb=" N ILE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 119 Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 57 through 84 removed outlier: 3.673A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'C' and resid 10 through 19 removed outlier: 4.070A pdb=" N PHE C 19 " --> pdb=" O TYR C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.779A pdb=" N ALA C 52 " --> pdb=" O ASN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 82 removed outlier: 3.849A pdb=" N ILE C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 118 Processing helix chain 'D' and resid 10 through 18 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.242A pdb=" N ALA D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 82 removed outlier: 3.819A pdb=" N ILE D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 118 removed outlier: 3.542A pdb=" N LEU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 3.808A pdb=" N GLN E 18 " --> pdb=" O SER E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 57 through 84 removed outlier: 3.780A pdb=" N LYS E 79 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 119 Processing helix chain 'F' and resid 10 through 18 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 57 through 82 removed outlier: 3.927A pdb=" N ILE F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 118 removed outlier: 3.507A pdb=" N LEU F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.872A pdb=" N PHE G 19 " --> pdb=" O TYR G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 41 Processing helix chain 'G' and resid 46 through 54 removed outlier: 4.142A pdb=" N ALA G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 82 removed outlier: 3.876A pdb=" N ILE G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 118 Processing helix chain 'H' and resid 10 through 17 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 57 through 82 Processing helix chain 'H' and resid 98 through 118 Processing helix chain 'I' and resid 10 through 18 Processing helix chain 'I' and resid 29 through 41 Processing helix chain 'I' and resid 46 through 54 Processing helix chain 'I' and resid 57 through 83 removed outlier: 3.588A pdb=" N LYS I 79 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE I 82 " --> pdb=" O ASN I 78 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU I 83 " --> pdb=" O LYS I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 118 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.805A pdb=" N PHE J 19 " --> pdb=" O TYR J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 41 Processing helix chain 'J' and resid 46 through 54 removed outlier: 4.199A pdb=" N ALA J 52 " --> pdb=" O ASN J 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 82 removed outlier: 3.591A pdb=" N ILE J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 118 Processing helix chain 'K' and resid 10 through 17 Processing helix chain 'K' and resid 29 through 40 Processing helix chain 'K' and resid 46 through 54 Processing helix chain 'K' and resid 57 through 82 removed outlier: 3.559A pdb=" N LYS K 79 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 118 Processing helix chain 'L' and resid 10 through 18 Processing helix chain 'L' and resid 29 through 41 Processing helix chain 'L' and resid 46 through 54 Processing helix chain 'L' and resid 57 through 82 removed outlier: 3.912A pdb=" N ILE L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 118 Processing helix chain 'M' and resid 10 through 18 Processing helix chain 'M' and resid 29 through 41 Processing helix chain 'M' and resid 48 through 55 Processing helix chain 'M' and resid 57 through 82 removed outlier: 3.667A pdb=" N ILE M 82 " --> pdb=" O ASN M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 118 Processing helix chain 'N' and resid 10 through 17 Processing helix chain 'N' and resid 29 through 41 Processing helix chain 'N' and resid 46 through 54 removed outlier: 3.729A pdb=" N ALA N 52 " --> pdb=" O ASN N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 82 removed outlier: 3.553A pdb=" N LYS N 79 " --> pdb=" O ASP N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 119 Processing helix chain 'O' and resid 10 through 18 Processing helix chain 'O' and resid 29 through 41 Processing helix chain 'O' and resid 46 through 54 Processing helix chain 'O' and resid 57 through 82 removed outlier: 4.004A pdb=" N ILE O 82 " --> pdb=" O ASN O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 118 Processing helix chain 'a' and resid 88 through 95 removed outlier: 3.626A pdb=" N VAL a 92 " --> pdb=" O GLU a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 125 Processing helix chain 'b' and resid 89 through 94 Processing helix chain 'b' and resid 101 through 106 removed outlier: 4.117A pdb=" N ASN b 106 " --> pdb=" O GLU b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 124 removed outlier: 4.776A pdb=" N ASP b 113 " --> pdb=" O ASN b 109 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN b 121 " --> pdb=" O ASP b 117 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN b 123 " --> pdb=" O ILE b 119 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA b 124 " --> pdb=" O ALA b 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 96 Processing helix chain 'c' and resid 97 through 99 No H-bonds generated for 'chain 'c' and resid 97 through 99' Processing helix chain 'c' and resid 106 through 123 Processing helix chain 'd' and resid 88 through 95 removed outlier: 3.600A pdb=" N VAL d 92 " --> pdb=" O GLU d 88 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA d 95 " --> pdb=" O VAL d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 125 Processing helix chain 'e' and resid 89 through 96 Processing helix chain 'e' and resid 110 through 123 Processing helix chain 'f' and resid 89 through 96 Processing helix chain 'f' and resid 97 through 99 No H-bonds generated for 'chain 'f' and resid 97 through 99' Processing helix chain 'f' and resid 104 through 125 removed outlier: 4.247A pdb=" N LEU f 108 " --> pdb=" O TYR f 104 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER f 125 " --> pdb=" O ASN f 121 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 95 removed outlier: 4.070A pdb=" N VAL g 92 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA g 95 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 105 through 123 removed outlier: 4.299A pdb=" N GLN g 123 " --> pdb=" O ILE g 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 89 through 94 Processing helix chain 'h' and resid 107 through 125 removed outlier: 4.074A pdb=" N SER h 125 " --> pdb=" O ASN h 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 96 Processing helix chain 'i' and resid 97 through 99 No H-bonds generated for 'chain 'i' and resid 97 through 99' Processing helix chain 'i' and resid 104 through 125 Processing helix chain 'j' and resid 88 through 95 removed outlier: 3.908A pdb=" N VAL j 92 " --> pdb=" O GLU j 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 125 Processing helix chain 'k' and resid 89 through 94 Processing helix chain 'k' and resid 104 through 125 removed outlier: 4.011A pdb=" N LEU k 108 " --> pdb=" O TYR k 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER k 125 " --> pdb=" O ASN k 121 " (cutoff:3.500A) Processing helix chain 'l' and resid 89 through 96 Processing helix chain 'l' and resid 105 through 124 Processing helix chain 'm' and resid 88 through 95 removed outlier: 3.782A pdb=" N VAL m 92 " --> pdb=" O GLU m 88 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA m 95 " --> pdb=" O VAL m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 104 through 124 Processing helix chain 'n' and resid 89 through 93 Processing helix chain 'n' and resid 104 through 124 Processing helix chain 'o' and resid 89 through 96 Processing helix chain 'o' and resid 97 through 100 removed outlier: 3.579A pdb=" N THR o 100 " --> pdb=" O ILE o 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 100' Processing helix chain 'o' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AA3, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'L' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'M' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'a' and resid 2 through 3 Processing sheet with id=AA9, first strand: chain 'a' and resid 40 through 44 Processing sheet with id=AB1, first strand: chain 'a' and resid 29 through 30 Processing sheet with id=AB2, first strand: chain 'b' and resid 50 through 55 removed outlier: 5.624A pdb=" N ARG b 3 " --> pdb=" O ILE b 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 40 through 44 Processing sheet with id=AB4, first strand: chain 'b' and resid 29 through 30 Processing sheet with id=AB5, first strand: chain 'c' and resid 50 through 54 Processing sheet with id=AB6, first strand: chain 'c' and resid 40 through 44 Processing sheet with id=AB7, first strand: chain 'c' and resid 29 through 30 Processing sheet with id=AB8, first strand: chain 'd' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'd' and resid 6 through 7 Processing sheet with id=AC1, first strand: chain 'd' and resid 40 through 44 Processing sheet with id=AC2, first strand: chain 'd' and resid 29 through 30 Processing sheet with id=AC3, first strand: chain 'e' and resid 50 through 55 removed outlier: 5.901A pdb=" N ARG e 3 " --> pdb=" O ILE e 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 40 through 44 Processing sheet with id=AC5, first strand: chain 'e' and resid 29 through 30 Processing sheet with id=AC6, first strand: chain 'f' and resid 50 through 55 Processing sheet with id=AC7, first strand: chain 'f' and resid 40 through 44 Processing sheet with id=AC8, first strand: chain 'f' and resid 29 through 30 Processing sheet with id=AC9, first strand: chain 'g' and resid 6 through 7 Processing sheet with id=AD1, first strand: chain 'g' and resid 40 through 44 Processing sheet with id=AD2, first strand: chain 'g' and resid 29 through 30 Processing sheet with id=AD3, first strand: chain 'h' and resid 50 through 55 Processing sheet with id=AD4, first strand: chain 'h' and resid 40 through 44 removed outlier: 3.644A pdb=" N PHE h 22 " --> pdb=" O THR h 69 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR h 65 " --> pdb=" O ILE h 26 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'h' and resid 29 through 30 Processing sheet with id=AD6, first strand: chain 'i' and resid 50 through 55 Processing sheet with id=AD7, first strand: chain 'i' and resid 40 through 44 Processing sheet with id=AD8, first strand: chain 'i' and resid 29 through 31 Processing sheet with id=AD9, first strand: chain 'j' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'j' and resid 29 through 31 removed outlier: 3.582A pdb=" N ASN j 34 " --> pdb=" O ASN j 31 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'k' and resid 50 through 54 removed outlier: 5.821A pdb=" N ARG k 3 " --> pdb=" O ILE k 87 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'k' and resid 40 through 44 Processing sheet with id=AE4, first strand: chain 'k' and resid 29 through 31 removed outlier: 3.791A pdb=" N ASN k 34 " --> pdb=" O ASN k 31 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'l' and resid 50 through 54 removed outlier: 6.207A pdb=" N ARG l 3 " --> pdb=" O ILE l 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'l' and resid 40 through 44 removed outlier: 3.516A pdb=" N TYR l 66 " --> pdb=" O PHE l 78 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'l' and resid 29 through 31 Processing sheet with id=AE8, first strand: chain 'm' and resid 6 through 7 Processing sheet with id=AE9, first strand: chain 'm' and resid 40 through 44 Processing sheet with id=AF1, first strand: chain 'm' and resid 29 through 30 Processing sheet with id=AF2, first strand: chain 'n' and resid 50 through 55 Processing sheet with id=AF3, first strand: chain 'n' and resid 40 through 44 Processing sheet with id=AF4, first strand: chain 'n' and resid 29 through 30 Processing sheet with id=AF5, first strand: chain 'o' and resid 50 through 55 Processing sheet with id=AF6, first strand: chain 'o' and resid 40 through 44 Processing sheet with id=AF7, first strand: chain 'o' and resid 29 through 30 1420 hydrogen bonds defined for protein. 4086 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: 5.80 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10316 1.34 - 1.46: 4700 1.46 - 1.57: 16319 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 31470 Sorted by residual: bond pdb=" CB GLU g 103 " pdb=" CG GLU g 103 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.08e+00 bond pdb=" N ARG F 136 " pdb=" CA ARG F 136 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" C ASP k 101 " pdb=" N PRO k 102 " ideal model delta sigma weight residual 1.331 1.344 -0.013 7.90e-03 1.60e+04 2.68e+00 bond pdb=" CA ILE F 93 " pdb=" CB ILE F 93 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.05e-02 9.07e+03 2.10e+00 bond pdb=" CA ASP f 101 " pdb=" C ASP f 101 " ideal model delta sigma weight residual 1.534 1.521 0.013 9.50e-03 1.11e+04 2.02e+00 ... (remaining 31465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 42628 4.32 - 8.63: 91 8.63 - 12.95: 7 12.95 - 17.26: 42 17.26 - 21.58: 12 Bond angle restraints: 42780 Sorted by residual: angle pdb=" C ARG n 93 " pdb=" N GLU n 94 " pdb=" CA GLU n 94 " ideal model delta sigma weight residual 121.14 141.60 -20.46 1.75e+00 3.27e-01 1.37e+02 angle pdb=" C PRO o 57 " pdb=" N ASN o 58 " pdb=" CA ASN o 58 " ideal model delta sigma weight residual 120.60 139.21 -18.61 1.60e+00 3.91e-01 1.35e+02 angle pdb=" C ASP H 124 " pdb=" N ASN H 125 " pdb=" CA ASN H 125 " ideal model delta sigma weight residual 122.11 139.75 -17.64 1.59e+00 3.96e-01 1.23e+02 angle pdb=" C GLU L 134 " pdb=" N GLY L 135 " pdb=" CA GLY L 135 " ideal model delta sigma weight residual 121.41 142.99 -21.58 1.96e+00 2.60e-01 1.21e+02 angle pdb=" C ALA d 95 " pdb=" N GLY d 96 " pdb=" CA GLY d 96 " ideal model delta sigma weight residual 121.41 142.30 -20.89 1.96e+00 2.60e-01 1.14e+02 ... (remaining 42775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17464 17.97 - 35.93: 1295 35.93 - 53.90: 237 53.90 - 71.87: 63 71.87 - 89.83: 21 Dihedral angle restraints: 19080 sinusoidal: 7695 harmonic: 11385 Sorted by residual: dihedral pdb=" CA PRO i 57 " pdb=" C PRO i 57 " pdb=" N ASN i 58 " pdb=" CA ASN i 58 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASP l 101 " pdb=" C ASP l 101 " pdb=" N PRO l 102 " pdb=" CA PRO l 102 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" C LYS M 89 " pdb=" N LYS M 89 " pdb=" CA LYS M 89 " pdb=" CB LYS M 89 " ideal model delta harmonic sigma weight residual -122.60 -134.52 11.92 0 2.50e+00 1.60e-01 2.27e+01 ... (remaining 19077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 4897 0.348 - 0.697: 70 0.697 - 1.045: 0 1.045 - 1.394: 1 1.394 - 1.742: 27 Chirality restraints: 4995 Sorted by residual: chirality pdb=" CB ILE M 93 " pdb=" CA ILE M 93 " pdb=" CG1 ILE M 93 " pdb=" CG2 ILE M 93 " both_signs ideal model delta sigma weight residual False 2.64 0.90 1.74 2.00e-01 2.50e+01 7.59e+01 chirality pdb=" CB ILE D 93 " pdb=" CA ILE D 93 " pdb=" CG1 ILE D 93 " pdb=" CG2 ILE D 93 " both_signs ideal model delta sigma weight residual False 2.64 0.92 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CB ILE J 93 " pdb=" CA ILE J 93 " pdb=" CG1 ILE J 93 " pdb=" CG2 ILE J 93 " both_signs ideal model delta sigma weight residual False 2.64 0.93 1.71 2.00e-01 2.50e+01 7.34e+01 ... (remaining 4992 not shown) Planarity restraints: 5565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 42 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 43 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP a 101 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO a 102 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO a 102 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO a 102 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 23 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO E 24 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 24 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 24 " 0.023 5.00e-02 4.00e+02 ... (remaining 5562 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 682 2.52 - 3.11: 29675 3.11 - 3.71: 52709 3.71 - 4.30: 71241 4.30 - 4.90: 113028 Nonbonded interactions: 267335 Sorted by model distance: nonbonded pdb=" OG1 THR g 70 " pdb=" OD1 ASP g 72 " model vdw 1.923 3.040 nonbonded pdb=" O ILE c 97 " pdb=" OG1 THR c 100 " model vdw 1.947 3.040 nonbonded pdb=" OG1 THR e 70 " pdb=" OD1 ASP e 72 " model vdw 1.948 3.040 nonbonded pdb=" O THR H 88 " pdb=" OG1 THR I 94 " model vdw 1.964 3.040 nonbonded pdb=" O ILE i 97 " pdb=" OG1 THR i 100 " model vdw 1.972 3.040 ... (remaining 267330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.690 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 0.053 31470 Z= 0.159 Angle : 0.887 21.577 42780 Z= 0.486 Chirality : 0.135 1.742 4995 Planarity : 0.004 0.054 5565 Dihedral : 13.566 89.833 11700 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.83 % Favored : 91.04 % Rotamer: Outliers : 4.91 % Allowed : 13.08 % Favored : 82.01 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 3795 helix: 1.31 (0.13), residues: 1489 sheet: -1.24 (0.21), residues: 569 loop : -2.26 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 65 TYR 0.012 0.001 TYR n 104 PHE 0.009 0.001 PHE I 42 TRP 0.011 0.001 TRP o 16 HIS 0.006 0.001 HIS o 10 Details of bonding type rmsd covalent geometry : bond 0.00316 (31470) covalent geometry : angle 0.88681 (42780) hydrogen bonds : bond 0.13310 ( 1420) hydrogen bonds : angle 6.33352 ( 4086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1282 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 35 PHE cc_start: 0.9614 (t80) cc_final: 0.9030 (t80) REVERT: A 38 MET cc_start: 0.8923 (tmm) cc_final: 0.8406 (tmm) REVERT: A 39 CYS cc_start: 0.8889 (p) cc_final: 0.8670 (p) REVERT: A 92 ASP cc_start: 0.8125 (p0) cc_final: 0.7619 (p0) REVERT: A 95 MET cc_start: 0.8632 (mtp) cc_final: 0.8376 (mtm) REVERT: A 102 ASP cc_start: 0.9160 (m-30) cc_final: 0.8805 (m-30) REVERT: A 106 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 122 VAL cc_start: 0.9061 (t) cc_final: 0.8746 (p) REVERT: B 49 PHE cc_start: 0.9700 (t80) cc_final: 0.9348 (t80) REVERT: B 63 THR cc_start: 0.9665 (m) cc_final: 0.9443 (p) REVERT: B 86 GLN cc_start: 0.9120 (mm-40) cc_final: 0.8470 (tm-30) REVERT: B 131 ASP cc_start: 0.8632 (t0) cc_final: 0.8386 (t0) REVERT: C 13 GLU cc_start: 0.8468 (tp30) cc_final: 0.7788 (tp30) REVERT: C 17 ASN cc_start: 0.9155 (m-40) cc_final: 0.8374 (m-40) REVERT: C 19 PHE cc_start: 0.8654 (m-80) cc_final: 0.8447 (m-80) REVERT: C 39 CYS cc_start: 0.9149 (p) cc_final: 0.8713 (p) REVERT: C 70 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8536 (mm-30) REVERT: C 92 ASP cc_start: 0.7616 (p0) cc_final: 0.6912 (p0) REVERT: C 105 ASP cc_start: 0.9342 (m-30) cc_final: 0.9107 (m-30) REVERT: C 124 ASP cc_start: 0.7955 (t0) cc_final: 0.6499 (t70) REVERT: C 134 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.6058 (tp30) REVERT: D 76 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8679 (mmtm) REVERT: E 49 PHE cc_start: 0.9602 (t80) cc_final: 0.9392 (t80) REVERT: E 89 LYS cc_start: 0.8675 (ptmm) cc_final: 0.7792 (ptmm) REVERT: E 105 ASP cc_start: 0.9223 (m-30) cc_final: 0.9018 (m-30) REVERT: F 38 MET cc_start: 0.8573 (tmm) cc_final: 0.8342 (tmm) REVERT: F 39 CYS cc_start: 0.9241 (p) cc_final: 0.8849 (p) REVERT: F 60 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8651 (mt-10) REVERT: F 70 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8447 (mm-30) REVERT: F 86 GLN cc_start: 0.9011 (mm110) cc_final: 0.8698 (tp40) REVERT: F 92 ASP cc_start: 0.7255 (t70) cc_final: 0.6598 (t70) REVERT: F 105 ASP cc_start: 0.9338 (m-30) cc_final: 0.9084 (m-30) REVERT: F 110 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8181 (mm-30) REVERT: F 116 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8146 (mmm160) REVERT: G 89 LYS cc_start: 0.9030 (ptmm) cc_final: 0.8776 (ptmm) REVERT: G 110 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8997 (mm-30) REVERT: G 113 LYS cc_start: 0.9455 (mttt) cc_final: 0.9062 (mtmt) REVERT: G 132 ASP cc_start: 0.7431 (m-30) cc_final: 0.7130 (m-30) REVERT: H 38 MET cc_start: 0.9298 (ttp) cc_final: 0.8973 (ttm) REVERT: H 44 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8248 (ptm160) REVERT: H 49 PHE cc_start: 0.9739 (t80) cc_final: 0.9487 (t80) REVERT: H 89 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8011 (ttmm) REVERT: H 92 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7702 (p0) REVERT: H 98 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8818 (p0) REVERT: H 119 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9277 (mmtm) REVERT: H 124 ASP cc_start: 0.8743 (t0) cc_final: 0.8460 (t0) REVERT: I 17 ASN cc_start: 0.9556 (m-40) cc_final: 0.9278 (m-40) REVERT: I 38 MET cc_start: 0.8829 (tmm) cc_final: 0.8492 (tmm) REVERT: I 39 CYS cc_start: 0.9169 (p) cc_final: 0.8563 (p) REVERT: I 83 GLU cc_start: 0.7512 (mp0) cc_final: 0.7308 (mp0) REVERT: I 86 GLN cc_start: 0.8710 (tp40) cc_final: 0.8481 (tp40) REVERT: I 102 ASP cc_start: 0.8914 (m-30) cc_final: 0.8657 (m-30) REVERT: I 106 GLU cc_start: 0.9129 (tp30) cc_final: 0.8866 (mm-30) REVERT: J 13 GLU cc_start: 0.8249 (tp30) cc_final: 0.7999 (tp30) REVERT: J 25 THR cc_start: 0.8230 (p) cc_final: 0.7659 (t) REVERT: J 60 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8364 (mt-10) REVERT: J 70 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8317 (mm-30) REVERT: J 76 LYS cc_start: 0.9440 (tttt) cc_final: 0.9064 (ptmm) REVERT: J 80 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7753 (mt-10) REVERT: J 83 GLU cc_start: 0.7839 (pp20) cc_final: 0.7635 (tm-30) REVERT: J 92 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8372 (p0) REVERT: K 15 TYR cc_start: 0.9002 (t80) cc_final: 0.8674 (t80) REVERT: K 27 GLU cc_start: 0.7915 (pm20) cc_final: 0.7685 (pm20) REVERT: K 29 GLU cc_start: 0.8266 (mp0) cc_final: 0.8045 (mp0) REVERT: K 43 PRO cc_start: 0.9437 (Cg_exo) cc_final: 0.8860 (Cg_endo) REVERT: K 69 LYS cc_start: 0.9715 (tttp) cc_final: 0.9334 (ttmm) REVERT: K 89 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8567 (ptmm) REVERT: K 90 VAL cc_start: 0.8678 (t) cc_final: 0.8467 (t) REVERT: K 116 ARG cc_start: 0.9198 (mmt-90) cc_final: 0.8911 (tpp80) REVERT: L 21 ASP cc_start: 0.7427 (p0) cc_final: 0.6933 (p0) REVERT: L 38 MET cc_start: 0.8776 (tmm) cc_final: 0.8501 (tmm) REVERT: L 39 CYS cc_start: 0.9043 (p) cc_final: 0.8525 (p) REVERT: L 60 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8760 (mt-10) REVERT: L 83 GLU cc_start: 0.8212 (mp0) cc_final: 0.7990 (mp0) REVERT: L 86 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8791 (tp40) REVERT: L 106 GLU cc_start: 0.9131 (tp30) cc_final: 0.8902 (mm-30) REVERT: L 107 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9366 (mp) REVERT: M 15 TYR cc_start: 0.8729 (t80) cc_final: 0.8446 (t80) REVERT: M 70 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8671 (mm-30) REVERT: M 75 ASP cc_start: 0.8602 (p0) cc_final: 0.8393 (p0) REVERT: M 105 ASP cc_start: 0.9074 (m-30) cc_final: 0.8869 (m-30) REVERT: M 131 ASP cc_start: 0.8616 (t0) cc_final: 0.8309 (t0) REVERT: N 15 TYR cc_start: 0.9192 (t80) cc_final: 0.8963 (t80) REVERT: O 13 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8798 (mt-10) REVERT: O 21 ASP cc_start: 0.7556 (p0) cc_final: 0.7191 (p0) REVERT: O 38 MET cc_start: 0.8605 (tmm) cc_final: 0.8373 (tmm) REVERT: O 39 CYS cc_start: 0.9168 (p) cc_final: 0.8904 (p) REVERT: O 60 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8360 (mt-10) REVERT: O 69 LYS cc_start: 0.9539 (ttmt) cc_final: 0.9239 (ttmm) REVERT: O 83 GLU cc_start: 0.7770 (mp0) cc_final: 0.7534 (mp0) REVERT: O 91 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: O 112 LYS cc_start: 0.9488 (ptpp) cc_final: 0.9275 (ptpp) REVERT: O 129 SER cc_start: 0.8657 (p) cc_final: 0.7602 (p) REVERT: O 130 TYR cc_start: 0.7086 (p90) cc_final: 0.6822 (p90) REVERT: a 48 ASN cc_start: 0.9068 (t0) cc_final: 0.8564 (t0) REVERT: a 50 GLU cc_start: 0.8096 (mp0) cc_final: 0.7687 (mp0) REVERT: a 113 ASP cc_start: 0.9100 (t70) cc_final: 0.8899 (t0) REVERT: a 117 ASP cc_start: 0.9289 (m-30) cc_final: 0.9051 (m-30) REVERT: d 18 ASN cc_start: 0.8945 (t0) cc_final: 0.8658 (t0) REVERT: d 48 ASN cc_start: 0.9041 (t0) cc_final: 0.8743 (t0) REVERT: d 82 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: e 14 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: e 16 TRP cc_start: 0.7478 (OUTLIER) cc_final: 0.4707 (m100) REVERT: e 23 LEU cc_start: 0.8021 (tp) cc_final: 0.7820 (tp) REVERT: e 30 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7686 (p90) REVERT: e 36 TYR cc_start: 0.8190 (m-80) cc_final: 0.7974 (m-10) REVERT: e 90 SER cc_start: 0.8610 (t) cc_final: 0.7981 (p) REVERT: e 103 GLU cc_start: -0.2715 (OUTLIER) cc_final: -0.3653 (pt0) REVERT: e 107 VAL cc_start: 0.7132 (t) cc_final: 0.6745 (t) REVERT: e 108 LEU cc_start: 0.8965 (mt) cc_final: 0.8660 (mt) REVERT: f 5 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7429 (mtmm) REVERT: f 17 ILE cc_start: 0.7397 (mp) cc_final: 0.7058 (mm) REVERT: f 27 ASN cc_start: 0.8303 (m-40) cc_final: 0.7595 (m-40) REVERT: f 58 ASN cc_start: 0.5949 (OUTLIER) cc_final: 0.5540 (m110) REVERT: f 64 SER cc_start: 0.6176 (OUTLIER) cc_final: 0.5574 (t) REVERT: f 91 VAL cc_start: 0.9526 (t) cc_final: 0.9194 (m) REVERT: f 109 ASN cc_start: 0.8873 (m-40) cc_final: 0.8512 (m110) REVERT: f 110 TYR cc_start: 0.9138 (t80) cc_final: 0.8837 (t80) REVERT: g 48 ASN cc_start: 0.9035 (t0) cc_final: 0.8791 (t0) REVERT: g 50 GLU cc_start: 0.7993 (mp0) cc_final: 0.7743 (mp0) REVERT: g 68 LEU cc_start: 0.9376 (tt) cc_final: 0.9168 (tt) REVERT: g 91 VAL cc_start: 0.8721 (m) cc_final: 0.8487 (p) REVERT: h 1 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5573 (tmm) REVERT: h 27 ASN cc_start: 0.6243 (t0) cc_final: 0.5895 (t0) REVERT: h 36 TYR cc_start: 0.8519 (m-80) cc_final: 0.8223 (m-80) REVERT: j 12 ASP cc_start: 0.8395 (p0) cc_final: 0.7372 (p0) REVERT: j 48 ASN cc_start: 0.9001 (t0) cc_final: 0.8691 (t0) REVERT: j 50 GLU cc_start: 0.7859 (pm20) cc_final: 0.7336 (pm20) REVERT: j 54 ASN cc_start: 0.7088 (t0) cc_final: 0.6648 (t0) REVERT: j 111 LEU cc_start: 0.9543 (mt) cc_final: 0.9293 (mt) REVERT: j 117 ASP cc_start: 0.8703 (p0) cc_final: 0.8487 (p0) REVERT: k 5 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: k 25 LEU cc_start: 0.8556 (tp) cc_final: 0.8337 (tp) REVERT: k 58 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.6263 (m-40) REVERT: k 116 ASP cc_start: 0.9462 (m-30) cc_final: 0.9221 (m-30) REVERT: l 77 SER cc_start: 0.9288 (p) cc_final: 0.9076 (t) REVERT: l 94 GLU cc_start: 0.8359 (tp30) cc_final: 0.7884 (tp30) REVERT: l 110 TYR cc_start: 0.8995 (t80) cc_final: 0.8723 (t80) REVERT: m 48 ASN cc_start: 0.8556 (t0) cc_final: 0.8308 (t0) REVERT: m 50 GLU cc_start: 0.7848 (pm20) cc_final: 0.7271 (pm20) REVERT: n 42 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8090 (t70) REVERT: n 59 VAL cc_start: 0.8768 (m) cc_final: 0.8454 (m) REVERT: n 111 LEU cc_start: 0.9388 (mm) cc_final: 0.8868 (pp) outliers start: 173 outliers final: 95 residues processed: 1391 average time/residue: 0.2181 time to fit residues: 473.6433 Evaluate side-chains 1136 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1024 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 55 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 130 TYR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 93 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 125 ASN Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain a residue 23 LEU Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 65 TYR Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 86 ASP Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 58 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 82 ASP Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 14 GLN Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 103 GLU Chi-restraints excluded: chain f residue 58 ASN Chi-restraints excluded: chain f residue 64 SER Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 11 LEU Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 72 ASP Chi-restraints excluded: chain h residue 112 GLU Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain k residue 5 LYS Chi-restraints excluded: chain k residue 14 GLN Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 58 ASN Chi-restraints excluded: chain k residue 70 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 100 THR Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 69 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 86 GLN A 98 ASN C 86 GLN F 51 ASN F 86 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 ASN N 140 ASN O 17 ASN O 78 ASN a 10 HIS a 18 ASN a 58 ASN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 73 ASN ** f 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 73 ASN g 42 HIS g 109 ASN g 121 ASN h 31 ASN ** h 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 ASN ** i 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 35 GLN j 73 ASN k 18 ASN l 27 ASN m 18 ASN ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 121 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058071 restraints weight = 148986.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059672 restraints weight = 93517.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060813 restraints weight = 66609.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.061619 restraints weight = 51783.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062096 restraints weight = 42799.890| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31470 Z= 0.212 Angle : 0.781 9.340 42780 Z= 0.412 Chirality : 0.048 0.246 4995 Planarity : 0.005 0.070 5565 Dihedral : 8.946 96.705 4390 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.64 % Favored : 91.23 % Rotamer: Outliers : 5.79 % Allowed : 17.84 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.13), residues: 3795 helix: 0.78 (0.13), residues: 1604 sheet: -0.88 (0.20), residues: 603 loop : -2.26 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG l 9 TYR 0.028 0.002 TYR f 36 PHE 0.025 0.002 PHE I 19 TRP 0.017 0.002 TRP o 16 HIS 0.020 0.002 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00472 (31470) covalent geometry : angle 0.78141 (42780) hydrogen bonds : bond 0.04594 ( 1420) hydrogen bonds : angle 5.56661 ( 4086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1170 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8953 (tp30) cc_final: 0.8525 (tp30) REVERT: A 16 TYR cc_start: 0.9450 (m-10) cc_final: 0.9240 (m-10) REVERT: A 17 ASN cc_start: 0.8900 (m110) cc_final: 0.8206 (m110) REVERT: A 38 MET cc_start: 0.9228 (tmm) cc_final: 0.8625 (tmm) REVERT: A 39 CYS cc_start: 0.8934 (p) cc_final: 0.8732 (p) REVERT: A 92 ASP cc_start: 0.8342 (p0) cc_final: 0.7973 (p0) REVERT: A 112 LYS cc_start: 0.9434 (mttm) cc_final: 0.9201 (mmtm) REVERT: A 116 ARG cc_start: 0.8248 (tpp80) cc_final: 0.8026 (tpp80) REVERT: A 122 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8631 (m) REVERT: B 42 PHE cc_start: 0.9487 (m-80) cc_final: 0.9163 (m-80) REVERT: B 49 PHE cc_start: 0.9770 (t80) cc_final: 0.9388 (t80) REVERT: B 86 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8916 (tp-100) REVERT: B 131 ASP cc_start: 0.9212 (t0) cc_final: 0.8808 (t0) REVERT: C 13 GLU cc_start: 0.8857 (tp30) cc_final: 0.7733 (tp30) REVERT: C 17 ASN cc_start: 0.9337 (m-40) cc_final: 0.7958 (m-40) REVERT: C 19 PHE cc_start: 0.8765 (m-80) cc_final: 0.8471 (m-80) REVERT: C 30 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: C 38 MET cc_start: 0.8973 (tmm) cc_final: 0.8701 (tmm) REVERT: C 39 CYS cc_start: 0.9300 (p) cc_final: 0.8927 (p) REVERT: C 60 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8726 (mt-10) REVERT: C 89 LYS cc_start: 0.9286 (ptmm) cc_final: 0.9032 (ttpp) REVERT: C 92 ASP cc_start: 0.7966 (p0) cc_final: 0.7172 (p0) REVERT: C 102 ASP cc_start: 0.9086 (m-30) cc_final: 0.8710 (m-30) REVERT: C 105 ASP cc_start: 0.9415 (m-30) cc_final: 0.9139 (m-30) REVERT: D 29 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 44 ARG cc_start: 0.8869 (ptm160) cc_final: 0.8417 (ptm160) REVERT: D 60 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8905 (mm-30) REVERT: D 92 ASP cc_start: 0.8688 (p0) cc_final: 0.8364 (p0) REVERT: D 106 GLU cc_start: 0.8889 (tp30) cc_final: 0.8657 (tp30) REVERT: D 116 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8448 (tpp80) REVERT: D 132 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7567 (t0) REVERT: E 46 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8519 (tm-30) REVERT: E 49 PHE cc_start: 0.9687 (t80) cc_final: 0.9189 (t80) REVERT: E 75 ASP cc_start: 0.8846 (t0) cc_final: 0.8606 (t0) REVERT: E 105 ASP cc_start: 0.9249 (m-30) cc_final: 0.9018 (m-30) REVERT: F 38 MET cc_start: 0.9039 (tmm) cc_final: 0.8801 (tmm) REVERT: F 39 CYS cc_start: 0.9310 (p) cc_final: 0.8944 (p) REVERT: F 60 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8766 (mt-10) REVERT: F 92 ASP cc_start: 0.7531 (t70) cc_final: 0.7321 (t0) REVERT: F 105 ASP cc_start: 0.9396 (m-30) cc_final: 0.9175 (m-30) REVERT: F 106 GLU cc_start: 0.9391 (tp30) cc_final: 0.9084 (mm-30) REVERT: F 110 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8183 (mm-30) REVERT: G 70 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8004 (tp30) REVERT: G 73 ARG cc_start: 0.9064 (ttp-170) cc_final: 0.8572 (ttp80) REVERT: G 92 ASP cc_start: 0.8674 (p0) cc_final: 0.8416 (p0) REVERT: G 110 GLU cc_start: 0.9331 (mm-30) cc_final: 0.9052 (mm-30) REVERT: G 132 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: H 21 ASP cc_start: 0.7508 (p0) cc_final: 0.7115 (p0) REVERT: H 38 MET cc_start: 0.9397 (ttp) cc_final: 0.9173 (ttm) REVERT: H 42 PHE cc_start: 0.9392 (m-80) cc_final: 0.9140 (m-80) REVERT: H 44 ARG cc_start: 0.8761 (ptm-80) cc_final: 0.7890 (ttt180) REVERT: H 46 GLN cc_start: 0.7652 (mt0) cc_final: 0.7218 (mt0) REVERT: H 89 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8402 (ttmm) REVERT: H 92 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7456 (p0) REVERT: H 95 MET cc_start: 0.9009 (mmm) cc_final: 0.8796 (mmm) REVERT: H 105 ASP cc_start: 0.9096 (m-30) cc_final: 0.8862 (m-30) REVERT: H 124 ASP cc_start: 0.9000 (t0) cc_final: 0.8698 (t0) REVERT: I 17 ASN cc_start: 0.9644 (m-40) cc_final: 0.9373 (m-40) REVERT: I 21 ASP cc_start: 0.8206 (p0) cc_final: 0.7871 (p0) REVERT: I 38 MET cc_start: 0.9173 (tmm) cc_final: 0.8898 (tmm) REVERT: I 39 CYS cc_start: 0.9293 (p) cc_final: 0.8776 (p) REVERT: I 86 GLN cc_start: 0.8814 (tp40) cc_final: 0.8598 (tp40) REVERT: I 89 LYS cc_start: 0.9548 (ttpp) cc_final: 0.9201 (ttpp) REVERT: I 91 GLU cc_start: 0.8502 (pp20) cc_final: 0.8233 (pp20) REVERT: I 95 MET cc_start: 0.8828 (mmm) cc_final: 0.8556 (mmm) REVERT: I 102 ASP cc_start: 0.8903 (m-30) cc_final: 0.8679 (m-30) REVERT: I 106 GLU cc_start: 0.9265 (tp30) cc_final: 0.9007 (mm-30) REVERT: I 116 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8093 (mmm160) REVERT: J 13 GLU cc_start: 0.8776 (tp30) cc_final: 0.8238 (tp30) REVERT: J 17 ASN cc_start: 0.8768 (m110) cc_final: 0.7932 (m110) REVERT: J 21 ASP cc_start: 0.8557 (p0) cc_final: 0.8239 (p0) REVERT: J 27 GLU cc_start: 0.7185 (mp0) cc_final: 0.6960 (mp0) REVERT: J 60 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8596 (mt-10) REVERT: J 83 GLU cc_start: 0.7971 (pp20) cc_final: 0.7761 (tm-30) REVERT: J 92 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8577 (p0) REVERT: K 42 PHE cc_start: 0.9500 (m-80) cc_final: 0.9198 (m-80) REVERT: K 69 LYS cc_start: 0.9756 (tttp) cc_final: 0.9484 (ttmm) REVERT: K 79 LYS cc_start: 0.9094 (mppt) cc_final: 0.8545 (mmtm) REVERT: K 86 GLN cc_start: 0.9099 (tp40) cc_final: 0.8800 (tp-100) REVERT: K 89 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8825 (ptmm) REVERT: K 116 ARG cc_start: 0.9264 (mmt-90) cc_final: 0.8855 (tpp80) REVERT: L 17 ASN cc_start: 0.9455 (m110) cc_final: 0.9173 (m-40) REVERT: L 21 ASP cc_start: 0.7483 (p0) cc_final: 0.7250 (p0) REVERT: L 38 MET cc_start: 0.9036 (tmm) cc_final: 0.8731 (tmm) REVERT: L 39 CYS cc_start: 0.9225 (p) cc_final: 0.8680 (p) REVERT: L 75 ASP cc_start: 0.8941 (t0) cc_final: 0.8250 (t0) REVERT: L 76 LYS cc_start: 0.9394 (mmmm) cc_final: 0.9148 (mmtt) REVERT: L 83 GLU cc_start: 0.8376 (mp0) cc_final: 0.8022 (mp0) REVERT: L 86 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8880 (tp40) REVERT: L 89 LYS cc_start: 0.8592 (ptmm) cc_final: 0.8122 (ptmm) REVERT: L 102 ASP cc_start: 0.9102 (m-30) cc_final: 0.8829 (m-30) REVERT: M 34 GLU cc_start: 0.9016 (tt0) cc_final: 0.8729 (tt0) REVERT: M 46 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6164 (tm-30) REVERT: M 83 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7574 (pp20) REVERT: M 102 ASP cc_start: 0.9282 (m-30) cc_final: 0.8881 (m-30) REVERT: M 105 ASP cc_start: 0.9069 (m-30) cc_final: 0.8856 (m-30) REVERT: M 106 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8606 (mp0) REVERT: M 116 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8569 (tpp80) REVERT: M 131 ASP cc_start: 0.8821 (t0) cc_final: 0.8535 (t0) REVERT: N 15 TYR cc_start: 0.9120 (t80) cc_final: 0.8819 (t80) REVERT: N 89 LYS cc_start: 0.8130 (ptmm) cc_final: 0.7557 (ptmm) REVERT: N 90 VAL cc_start: 0.9039 (m) cc_final: 0.8674 (p) REVERT: N 92 ASP cc_start: 0.8065 (p0) cc_final: 0.7340 (p0) REVERT: N 105 ASP cc_start: 0.9193 (m-30) cc_final: 0.8913 (m-30) REVERT: O 21 ASP cc_start: 0.7550 (p0) cc_final: 0.7226 (p0) REVERT: O 35 PHE cc_start: 0.9534 (t80) cc_final: 0.8987 (t80) REVERT: O 38 MET cc_start: 0.8824 (tmm) cc_final: 0.8563 (tmm) REVERT: O 39 CYS cc_start: 0.9176 (p) cc_final: 0.8846 (p) REVERT: O 91 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: O 92 ASP cc_start: 0.6698 (t70) cc_final: 0.6357 (t0) REVERT: O 94 THR cc_start: 0.9165 (m) cc_final: 0.8719 (p) REVERT: O 95 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8198 (mtm) REVERT: O 98 ASN cc_start: 0.9163 (m-40) cc_final: 0.8947 (m-40) REVERT: O 99 TYR cc_start: 0.8682 (t80) cc_final: 0.8394 (t80) REVERT: O 102 ASP cc_start: 0.9056 (m-30) cc_final: 0.8645 (m-30) REVERT: a 48 ASN cc_start: 0.9343 (t0) cc_final: 0.8761 (t0) REVERT: a 50 GLU cc_start: 0.8433 (mp0) cc_final: 0.7870 (mp0) REVERT: a 68 LEU cc_start: 0.9691 (tt) cc_final: 0.9329 (tt) REVERT: a 113 ASP cc_start: 0.9079 (t70) cc_final: 0.8840 (t0) REVERT: a 117 ASP cc_start: 0.9375 (m-30) cc_final: 0.9129 (m-30) REVERT: b 1 MET cc_start: 0.7761 (tpt) cc_final: 0.6577 (tpt) REVERT: c 5 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7243 (mtmm) REVERT: d 17 ILE cc_start: 0.8988 (pt) cc_final: 0.8699 (mm) REVERT: d 29 THR cc_start: 0.8535 (m) cc_final: 0.8221 (p) REVERT: d 50 GLU cc_start: 0.7167 (tp30) cc_final: 0.6749 (tp30) REVERT: e 16 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.5018 (m100) REVERT: e 30 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7314 (p90) REVERT: e 108 LEU cc_start: 0.9113 (mt) cc_final: 0.8890 (mt) REVERT: f 3 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7863 (ttp80) REVERT: f 17 ILE cc_start: 0.8074 (mp) cc_final: 0.7657 (mm) REVERT: f 27 ASN cc_start: 0.8359 (m-40) cc_final: 0.7833 (m-40) REVERT: f 54 ASN cc_start: 0.7317 (p0) cc_final: 0.7016 (t0) REVERT: f 59 VAL cc_start: 0.7344 (p) cc_final: 0.6763 (p) REVERT: f 82 ASP cc_start: 0.8094 (t0) cc_final: 0.7577 (m-30) REVERT: f 86 ASP cc_start: 0.8298 (p0) cc_final: 0.7133 (p0) REVERT: f 91 VAL cc_start: 0.9588 (t) cc_final: 0.9312 (m) REVERT: f 109 ASN cc_start: 0.8866 (m-40) cc_final: 0.8371 (m110) REVERT: g 14 GLN cc_start: 0.9154 (mp10) cc_final: 0.8865 (mm-40) REVERT: g 48 ASN cc_start: 0.9319 (t0) cc_final: 0.8792 (t0) REVERT: g 50 GLU cc_start: 0.8445 (mp0) cc_final: 0.7845 (mp0) REVERT: g 68 LEU cc_start: 0.9552 (tt) cc_final: 0.9328 (tt) REVERT: h 1 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.5495 (tmm) REVERT: h 36 TYR cc_start: 0.8777 (m-80) cc_final: 0.8231 (m-10) REVERT: i 69 THR cc_start: 0.8693 (p) cc_final: 0.8490 (t) REVERT: j 12 ASP cc_start: 0.8529 (p0) cc_final: 0.7388 (p0) REVERT: j 48 ASN cc_start: 0.9147 (t0) cc_final: 0.8848 (t0) REVERT: j 50 GLU cc_start: 0.8389 (pm20) cc_final: 0.7583 (pm20) REVERT: k 58 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6555 (m-40) REVERT: l 14 GLN cc_start: 0.9119 (mp10) cc_final: 0.8774 (mp10) REVERT: l 110 TYR cc_start: 0.9158 (t80) cc_final: 0.8918 (t80) REVERT: m 48 ASN cc_start: 0.8850 (t0) cc_final: 0.8412 (t0) REVERT: m 50 GLU cc_start: 0.8148 (pm20) cc_final: 0.7265 (pm20) REVERT: n 42 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8194 (t70) REVERT: n 62 ASP cc_start: 0.9187 (t70) cc_final: 0.8851 (t0) REVERT: n 111 LEU cc_start: 0.9478 (mm) cc_final: 0.9070 (pp) outliers start: 204 outliers final: 119 residues processed: 1277 average time/residue: 0.2195 time to fit residues: 436.7569 Evaluate side-chains 1159 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1027 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 130 TYR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 13 GLU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 36 TYR Chi-restraints excluded: chain k residue 58 ASN Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 30 PHE Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 103 GLU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 34 ASN Chi-restraints excluded: chain o residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 222 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 203 optimal weight: 20.0000 chunk 348 optimal weight: 30.0000 chunk 185 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN F 10 HIS F 51 ASN G 17 ASN G 47 ASN J 46 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN L 78 ASN ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 78 ASN a 58 ASN ** a 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 ASN ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 ASN g 42 HIS ** i 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 ASN ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 58 ASN m 58 ASN ** m 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.056443 restraints weight = 149175.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.058050 restraints weight = 93902.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.059179 restraints weight = 66238.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059970 restraints weight = 51270.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060555 restraints weight = 42373.449| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31470 Z= 0.198 Angle : 0.761 12.300 42780 Z= 0.401 Chirality : 0.046 0.185 4995 Planarity : 0.005 0.073 5565 Dihedral : 7.852 83.195 4271 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.17 % Favored : 91.70 % Rotamer: Outliers : 6.18 % Allowed : 21.05 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.13), residues: 3795 helix: 0.58 (0.13), residues: 1621 sheet: -0.97 (0.20), residues: 615 loop : -2.22 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG l 9 TYR 0.040 0.002 TYR h 114 PHE 0.032 0.002 PHE I 19 TRP 0.016 0.001 TRP o 16 HIS 0.017 0.002 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00437 (31470) covalent geometry : angle 0.76144 (42780) hydrogen bonds : bond 0.04255 ( 1420) hydrogen bonds : angle 5.38958 ( 4086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 1140 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8912 (tp30) cc_final: 0.8400 (tp30) REVERT: A 17 ASN cc_start: 0.8996 (m110) cc_final: 0.8284 (m110) REVERT: A 38 MET cc_start: 0.9251 (tmm) cc_final: 0.8579 (tmm) REVERT: A 70 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8563 (tp30) REVERT: A 92 ASP cc_start: 0.8551 (p0) cc_final: 0.8129 (p0) REVERT: A 106 GLU cc_start: 0.8257 (tp30) cc_final: 0.7732 (tp30) REVERT: A 112 LYS cc_start: 0.9466 (mttm) cc_final: 0.9230 (mmtm) REVERT: B 49 PHE cc_start: 0.9744 (t80) cc_final: 0.9485 (t80) REVERT: B 51 ASN cc_start: 0.9356 (m110) cc_final: 0.9054 (p0) REVERT: B 86 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8821 (tp-100) REVERT: B 105 ASP cc_start: 0.9248 (m-30) cc_final: 0.8950 (m-30) REVERT: B 106 GLU cc_start: 0.9277 (tp30) cc_final: 0.9043 (tp30) REVERT: B 131 ASP cc_start: 0.9247 (t0) cc_final: 0.8813 (t0) REVERT: C 13 GLU cc_start: 0.8859 (tp30) cc_final: 0.7717 (tp30) REVERT: C 17 ASN cc_start: 0.9371 (m-40) cc_final: 0.8215 (m-40) REVERT: C 19 PHE cc_start: 0.8786 (m-80) cc_final: 0.8474 (m-80) REVERT: C 30 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: C 38 MET cc_start: 0.9040 (tmm) cc_final: 0.8701 (tmm) REVERT: C 39 CYS cc_start: 0.9289 (p) cc_final: 0.8874 (p) REVERT: C 60 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8730 (mt-10) REVERT: C 70 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8848 (mm-30) REVERT: C 86 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8634 (tp40) REVERT: C 102 ASP cc_start: 0.9100 (m-30) cc_final: 0.8881 (m-30) REVERT: C 105 ASP cc_start: 0.9417 (m-30) cc_final: 0.9149 (m-30) REVERT: C 124 ASP cc_start: 0.7710 (t0) cc_final: 0.7508 (t0) REVERT: D 34 GLU cc_start: 0.8988 (tt0) cc_final: 0.8660 (tt0) REVERT: D 44 ARG cc_start: 0.8831 (ptm160) cc_final: 0.8297 (ptm160) REVERT: D 46 GLN cc_start: 0.8079 (pt0) cc_final: 0.7265 (pt0) REVERT: D 90 VAL cc_start: 0.8794 (m) cc_final: 0.8165 (m) REVERT: D 92 ASP cc_start: 0.8948 (p0) cc_final: 0.8640 (p0) REVERT: D 113 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9196 (mtmt) REVERT: D 116 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8379 (tpp80) REVERT: E 75 ASP cc_start: 0.8795 (t0) cc_final: 0.8540 (t0) REVERT: E 92 ASP cc_start: 0.7922 (p0) cc_final: 0.7324 (p0) REVERT: F 38 MET cc_start: 0.9136 (tmm) cc_final: 0.8882 (tmm) REVERT: F 60 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8796 (mt-10) REVERT: F 70 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8584 (mt-10) REVERT: F 86 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8566 (tp40) REVERT: F 102 ASP cc_start: 0.9020 (m-30) cc_final: 0.8819 (m-30) REVERT: F 105 ASP cc_start: 0.9405 (m-30) cc_final: 0.9174 (m-30) REVERT: F 110 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8285 (mm-30) REVERT: G 29 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8581 (tm-30) REVERT: G 34 GLU cc_start: 0.8738 (tt0) cc_final: 0.8277 (tt0) REVERT: G 70 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8143 (tp30) REVERT: G 73 ARG cc_start: 0.9055 (ttp-170) cc_final: 0.8720 (tmm160) REVERT: G 79 LYS cc_start: 0.9451 (mppt) cc_final: 0.9118 (mtmm) REVERT: G 92 ASP cc_start: 0.8756 (p0) cc_final: 0.8447 (p0) REVERT: G 132 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: H 21 ASP cc_start: 0.7517 (p0) cc_final: 0.7161 (p0) REVERT: H 44 ARG cc_start: 0.8872 (ptm-80) cc_final: 0.8267 (ttt180) REVERT: H 49 PHE cc_start: 0.9757 (t80) cc_final: 0.9489 (t80) REVERT: H 53 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9113 (mm) REVERT: H 59 ILE cc_start: 0.9620 (OUTLIER) cc_final: 0.9292 (pt) REVERT: H 89 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8408 (ttmm) REVERT: H 105 ASP cc_start: 0.9099 (m-30) cc_final: 0.8860 (m-30) REVERT: H 124 ASP cc_start: 0.8893 (t0) cc_final: 0.8551 (t0) REVERT: I 13 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8856 (mt-10) REVERT: I 17 ASN cc_start: 0.9641 (m-40) cc_final: 0.9365 (m-40) REVERT: I 21 ASP cc_start: 0.8409 (p0) cc_final: 0.8101 (p0) REVERT: I 27 GLU cc_start: 0.7717 (mp0) cc_final: 0.7512 (mp0) REVERT: I 38 MET cc_start: 0.9198 (tmm) cc_final: 0.8900 (tmm) REVERT: I 39 CYS cc_start: 0.9307 (p) cc_final: 0.8809 (p) REVERT: I 60 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8699 (mt-10) REVERT: I 89 LYS cc_start: 0.9497 (ttpp) cc_final: 0.9199 (ttpp) REVERT: I 95 MET cc_start: 0.8830 (mmm) cc_final: 0.8625 (mmm) REVERT: I 102 ASP cc_start: 0.8869 (m-30) cc_final: 0.8653 (m-30) REVERT: I 106 GLU cc_start: 0.9345 (tp30) cc_final: 0.9066 (mm-30) REVERT: I 116 ARG cc_start: 0.8682 (mmm160) cc_final: 0.7946 (mmm160) REVERT: J 13 GLU cc_start: 0.8742 (tp30) cc_final: 0.8158 (tp30) REVERT: J 17 ASN cc_start: 0.8725 (m110) cc_final: 0.7905 (m110) REVERT: J 21 ASP cc_start: 0.8613 (p0) cc_final: 0.8267 (p0) REVERT: J 27 GLU cc_start: 0.7165 (mp0) cc_final: 0.6941 (mp0) REVERT: J 60 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8623 (mt-10) REVERT: J 92 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8773 (p0) REVERT: J 110 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8605 (mm-30) REVERT: K 51 ASN cc_start: 0.9392 (m110) cc_final: 0.9142 (p0) REVERT: K 69 LYS cc_start: 0.9767 (tttp) cc_final: 0.9461 (ttmm) REVERT: K 86 GLN cc_start: 0.9168 (tp40) cc_final: 0.8747 (tp-100) REVERT: K 89 LYS cc_start: 0.9182 (ptmm) cc_final: 0.8948 (ptmm) REVERT: K 105 ASP cc_start: 0.9319 (m-30) cc_final: 0.9011 (m-30) REVERT: L 17 ASN cc_start: 0.9534 (m-40) cc_final: 0.9190 (m-40) REVERT: L 21 ASP cc_start: 0.7595 (p0) cc_final: 0.7302 (p0) REVERT: L 38 MET cc_start: 0.9105 (tmm) cc_final: 0.8842 (tmm) REVERT: L 39 CYS cc_start: 0.9198 (p) cc_final: 0.8598 (p) REVERT: L 83 GLU cc_start: 0.8261 (mp0) cc_final: 0.7771 (mp0) REVERT: L 86 GLN cc_start: 0.9326 (mm-40) cc_final: 0.8847 (tp40) REVERT: L 124 ASP cc_start: 0.8678 (t0) cc_final: 0.7952 (t0) REVERT: M 34 GLU cc_start: 0.9067 (tt0) cc_final: 0.8740 (tt0) REVERT: M 70 GLU cc_start: 0.9107 (tp30) cc_final: 0.8302 (tp30) REVERT: M 73 ARG cc_start: 0.9389 (tmm-80) cc_final: 0.8888 (ttp80) REVERT: M 75 ASP cc_start: 0.8888 (p0) cc_final: 0.8349 (p0) REVERT: M 76 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8910 (mmtp) REVERT: M 83 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7514 (pp20) REVERT: M 86 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8526 (mm110) REVERT: M 102 ASP cc_start: 0.9260 (m-30) cc_final: 0.8920 (m-30) REVERT: M 106 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8586 (mp0) REVERT: M 116 ARG cc_start: 0.8860 (tpp80) cc_final: 0.8489 (tpp80) REVERT: M 131 ASP cc_start: 0.8876 (t0) cc_final: 0.8565 (t0) REVERT: N 44 ARG cc_start: 0.8612 (ttt90) cc_final: 0.8358 (ttt180) REVERT: N 89 LYS cc_start: 0.8312 (ptmm) cc_final: 0.7587 (ptmm) REVERT: N 90 VAL cc_start: 0.8947 (m) cc_final: 0.8521 (p) REVERT: N 92 ASP cc_start: 0.8005 (p0) cc_final: 0.7261 (p0) REVERT: N 105 ASP cc_start: 0.9202 (m-30) cc_final: 0.8913 (m-30) REVERT: N 124 ASP cc_start: 0.8972 (t0) cc_final: 0.8250 (t0) REVERT: O 21 ASP cc_start: 0.7530 (p0) cc_final: 0.7227 (p0) REVERT: O 35 PHE cc_start: 0.9568 (t80) cc_final: 0.9054 (t80) REVERT: O 38 MET cc_start: 0.8874 (tmm) cc_final: 0.8607 (tmm) REVERT: O 39 CYS cc_start: 0.9155 (p) cc_final: 0.8803 (p) REVERT: O 86 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8844 (tp40) REVERT: O 91 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: O 92 ASP cc_start: 0.6781 (t70) cc_final: 0.6311 (t0) REVERT: O 94 THR cc_start: 0.9219 (m) cc_final: 0.8805 (p) REVERT: O 95 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8126 (mtm) REVERT: O 98 ASN cc_start: 0.9196 (m-40) cc_final: 0.8985 (m-40) REVERT: O 102 ASP cc_start: 0.9075 (m-30) cc_final: 0.8808 (m-30) REVERT: a 48 ASN cc_start: 0.9323 (t0) cc_final: 0.8647 (t0) REVERT: a 50 GLU cc_start: 0.8335 (mp0) cc_final: 0.7720 (mp0) REVERT: a 62 ASP cc_start: 0.7609 (t0) cc_final: 0.7392 (t0) REVERT: a 112 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8685 (mm-30) REVERT: a 113 ASP cc_start: 0.9088 (t70) cc_final: 0.8718 (t0) REVERT: a 117 ASP cc_start: 0.9406 (m-30) cc_final: 0.9115 (m-30) REVERT: b 1 MET cc_start: 0.7968 (tpt) cc_final: 0.6696 (tpt) REVERT: b 55 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8268 (t) REVERT: b 91 VAL cc_start: 0.9609 (t) cc_final: 0.9373 (p) REVERT: c 5 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7527 (mtmm) REVERT: c 82 ASP cc_start: 0.7642 (t0) cc_final: 0.7392 (m-30) REVERT: c 103 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8751 (mm-30) REVERT: c 114 TYR cc_start: 0.9086 (t80) cc_final: 0.8853 (t80) REVERT: d 17 ILE cc_start: 0.9153 (pt) cc_final: 0.8868 (mm) REVERT: d 29 THR cc_start: 0.8696 (m) cc_final: 0.8324 (p) REVERT: d 50 GLU cc_start: 0.7286 (tp30) cc_final: 0.6983 (tp30) REVERT: d 58 ASN cc_start: 0.7025 (t0) cc_final: 0.6807 (t0) REVERT: e 5 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8334 (mtmm) REVERT: e 30 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7167 (p90) REVERT: f 5 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7337 (mtmm) REVERT: f 17 ILE cc_start: 0.8654 (mp) cc_final: 0.8262 (mm) REVERT: f 27 ASN cc_start: 0.8588 (m-40) cc_final: 0.8098 (m-40) REVERT: f 59 VAL cc_start: 0.7608 (p) cc_final: 0.7013 (p) REVERT: f 82 ASP cc_start: 0.8165 (t0) cc_final: 0.7756 (m-30) REVERT: f 109 ASN cc_start: 0.8925 (m-40) cc_final: 0.8613 (m110) REVERT: g 1 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7033 (tmm) REVERT: g 14 GLN cc_start: 0.9167 (mp10) cc_final: 0.8917 (mm-40) REVERT: g 48 ASN cc_start: 0.9371 (t0) cc_final: 0.8789 (t0) REVERT: g 50 GLU cc_start: 0.8427 (mp0) cc_final: 0.7756 (mp0) REVERT: g 58 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.6791 (m-40) REVERT: g 68 LEU cc_start: 0.9594 (tt) cc_final: 0.9384 (tt) REVERT: h 1 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.5743 (ttp) REVERT: h 21 LEU cc_start: 0.9564 (mt) cc_final: 0.9334 (mt) REVERT: h 36 TYR cc_start: 0.8771 (m-80) cc_final: 0.8209 (m-10) REVERT: j 14 GLN cc_start: 0.8732 (mp10) cc_final: 0.8434 (mp10) REVERT: j 48 ASN cc_start: 0.9089 (t0) cc_final: 0.8723 (t0) REVERT: j 50 GLU cc_start: 0.8470 (pm20) cc_final: 0.7585 (pm20) REVERT: k 58 ASN cc_start: 0.6736 (OUTLIER) cc_final: 0.6210 (m-40) REVERT: l 14 GLN cc_start: 0.9243 (mp10) cc_final: 0.8880 (mp10) REVERT: l 27 ASN cc_start: 0.8699 (m-40) cc_final: 0.8399 (m-40) REVERT: l 47 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8234 (mm-40) REVERT: m 29 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7426 (p) REVERT: m 48 ASN cc_start: 0.8978 (t0) cc_final: 0.8625 (t0) REVERT: m 54 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.6889 (p0) REVERT: n 42 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8371 (t70) REVERT: n 111 LEU cc_start: 0.9470 (mm) cc_final: 0.9081 (pp) REVERT: o 1 MET cc_start: 0.7520 (ttm) cc_final: 0.7306 (ttp) REVERT: o 14 GLN cc_start: 0.9415 (mp10) cc_final: 0.9117 (mp10) REVERT: o 54 ASN cc_start: 0.7756 (p0) cc_final: 0.7408 (p0) outliers start: 218 outliers final: 130 residues processed: 1264 average time/residue: 0.2187 time to fit residues: 431.3777 Evaluate side-chains 1175 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1027 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 129 SER Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 78 ASN Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 91 VAL Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 32 SER Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 58 ASN Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 65 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 323 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 chunk 201 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN E 51 ASN I 78 ASN K 18 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN a 35 GLN a 58 ASN a 73 ASN c 10 HIS ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** i 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 109 ASN n 58 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 48 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.056295 restraints weight = 149822.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.057869 restraints weight = 94024.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058994 restraints weight = 67409.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.059795 restraints weight = 52811.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.060340 restraints weight = 43953.550| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31470 Z= 0.154 Angle : 0.753 10.240 42780 Z= 0.392 Chirality : 0.046 0.208 4995 Planarity : 0.005 0.057 5565 Dihedral : 7.602 82.731 4255 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.06 % Favored : 91.81 % Rotamer: Outliers : 6.24 % Allowed : 22.24 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.13), residues: 3795 helix: 0.59 (0.13), residues: 1617 sheet: -0.77 (0.20), residues: 627 loop : -2.17 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG d 9 TYR 0.037 0.002 TYR i 104 PHE 0.032 0.002 PHE J 49 TRP 0.011 0.001 TRP o 16 HIS 0.011 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00339 (31470) covalent geometry : angle 0.75325 (42780) hydrogen bonds : bond 0.03950 ( 1420) hydrogen bonds : angle 5.19023 ( 4086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1163 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8827 (tp30) cc_final: 0.8255 (tp30) REVERT: A 17 ASN cc_start: 0.8924 (m110) cc_final: 0.8031 (m110) REVERT: A 38 MET cc_start: 0.9214 (tmm) cc_final: 0.8480 (tmm) REVERT: A 69 LYS cc_start: 0.9686 (tptm) cc_final: 0.9456 (tptm) REVERT: A 70 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8395 (tp30) REVERT: A 92 ASP cc_start: 0.8637 (p0) cc_final: 0.8312 (p0) REVERT: A 112 LYS cc_start: 0.9467 (mttm) cc_final: 0.9252 (mmtm) REVERT: B 49 PHE cc_start: 0.9728 (t80) cc_final: 0.9523 (t80) REVERT: B 51 ASN cc_start: 0.9365 (m110) cc_final: 0.9070 (p0) REVERT: B 86 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8779 (tp-100) REVERT: B 89 LYS cc_start: 0.8708 (tppt) cc_final: 0.8503 (tppt) REVERT: B 106 GLU cc_start: 0.9291 (tp30) cc_final: 0.8954 (tp30) REVERT: B 131 ASP cc_start: 0.9242 (t0) cc_final: 0.9018 (t0) REVERT: C 13 GLU cc_start: 0.8864 (tp30) cc_final: 0.7717 (tp30) REVERT: C 17 ASN cc_start: 0.9393 (m-40) cc_final: 0.8184 (m-40) REVERT: C 19 PHE cc_start: 0.8831 (m-80) cc_final: 0.8549 (m-80) REVERT: C 30 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: C 38 MET cc_start: 0.9045 (tmm) cc_final: 0.8651 (tmm) REVERT: C 39 CYS cc_start: 0.9252 (p) cc_final: 0.8850 (p) REVERT: C 60 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8773 (mt-10) REVERT: C 86 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8448 (tp40) REVERT: C 102 ASP cc_start: 0.9097 (m-30) cc_final: 0.8868 (m-30) REVERT: C 105 ASP cc_start: 0.9412 (m-30) cc_final: 0.9183 (m-30) REVERT: C 128 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8917 (p) REVERT: D 15 TYR cc_start: 0.9025 (t80) cc_final: 0.8799 (t80) REVERT: D 34 GLU cc_start: 0.8958 (tt0) cc_final: 0.8746 (tt0) REVERT: D 44 ARG cc_start: 0.8823 (ptm160) cc_final: 0.8332 (ptm160) REVERT: D 60 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8917 (mm-30) REVERT: D 69 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9347 (ttpp) REVERT: D 70 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8524 (tp30) REVERT: D 92 ASP cc_start: 0.9016 (p0) cc_final: 0.8689 (p0) REVERT: D 106 GLU cc_start: 0.8946 (tp30) cc_final: 0.8510 (tp30) REVERT: D 113 LYS cc_start: 0.9448 (mtpt) cc_final: 0.9248 (mtmt) REVERT: D 116 ARG cc_start: 0.8603 (tpp80) cc_final: 0.8355 (tpp80) REVERT: E 75 ASP cc_start: 0.8805 (t0) cc_final: 0.8562 (t0) REVERT: E 90 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8867 (m) REVERT: E 92 ASP cc_start: 0.7716 (p0) cc_final: 0.7437 (p0) REVERT: E 105 ASP cc_start: 0.9234 (m-30) cc_final: 0.9009 (m-30) REVERT: E 132 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: F 27 GLU cc_start: 0.8332 (mp0) cc_final: 0.8116 (pm20) REVERT: F 34 GLU cc_start: 0.9217 (tt0) cc_final: 0.8911 (tt0) REVERT: F 38 MET cc_start: 0.9084 (tmm) cc_final: 0.8804 (tmm) REVERT: F 60 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8803 (mt-10) REVERT: F 70 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8656 (mt-10) REVERT: F 86 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8509 (tp40) REVERT: F 102 ASP cc_start: 0.9011 (m-30) cc_final: 0.8794 (m-30) REVERT: F 110 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8296 (mm-30) REVERT: G 29 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8595 (tm-30) REVERT: G 34 GLU cc_start: 0.8759 (tt0) cc_final: 0.8325 (tt0) REVERT: G 70 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8166 (tp30) REVERT: G 73 ARG cc_start: 0.9033 (ttp-170) cc_final: 0.8735 (tmm160) REVERT: G 92 ASP cc_start: 0.8846 (p0) cc_final: 0.8542 (p0) REVERT: G 117 ILE cc_start: 0.9573 (mt) cc_final: 0.9346 (tt) REVERT: H 17 ASN cc_start: 0.8884 (m110) cc_final: 0.8588 (m110) REVERT: H 21 ASP cc_start: 0.7515 (p0) cc_final: 0.7163 (p0) REVERT: H 44 ARG cc_start: 0.8926 (ptm-80) cc_final: 0.8602 (ttt180) REVERT: H 82 ILE cc_start: 0.9291 (tp) cc_final: 0.9018 (mt) REVERT: H 86 GLN cc_start: 0.9069 (tp40) cc_final: 0.8711 (tp40) REVERT: H 105 ASP cc_start: 0.9100 (m-30) cc_final: 0.8862 (m-30) REVERT: H 124 ASP cc_start: 0.8846 (t0) cc_final: 0.8632 (t0) REVERT: I 13 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8861 (mt-10) REVERT: I 17 ASN cc_start: 0.9637 (m-40) cc_final: 0.9368 (m-40) REVERT: I 38 MET cc_start: 0.9209 (tmm) cc_final: 0.8890 (tmm) REVERT: I 39 CYS cc_start: 0.9283 (p) cc_final: 0.8698 (p) REVERT: I 60 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8795 (mt-10) REVERT: I 92 ASP cc_start: 0.8257 (t0) cc_final: 0.8006 (t0) REVERT: I 99 TYR cc_start: 0.8354 (t80) cc_final: 0.7976 (t80) REVERT: I 102 ASP cc_start: 0.8876 (m-30) cc_final: 0.8669 (m-30) REVERT: I 116 ARG cc_start: 0.8704 (mmm160) cc_final: 0.7947 (mmm160) REVERT: J 13 GLU cc_start: 0.8720 (tp30) cc_final: 0.8086 (tp30) REVERT: J 17 ASN cc_start: 0.8718 (m110) cc_final: 0.7834 (m110) REVERT: J 21 ASP cc_start: 0.8627 (p0) cc_final: 0.8367 (p0) REVERT: J 27 GLU cc_start: 0.7094 (mp0) cc_final: 0.6874 (mp0) REVERT: J 60 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8636 (mt-10) REVERT: J 79 LYS cc_start: 0.9216 (mtmm) cc_final: 0.8965 (mtmm) REVERT: J 83 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7801 (pp20) REVERT: K 69 LYS cc_start: 0.9764 (tttp) cc_final: 0.9459 (ttmm) REVERT: K 86 GLN cc_start: 0.9179 (tp40) cc_final: 0.8748 (tp-100) REVERT: K 89 LYS cc_start: 0.9253 (ptmm) cc_final: 0.8998 (ptmm) REVERT: K 90 VAL cc_start: 0.9048 (t) cc_final: 0.8814 (p) REVERT: K 105 ASP cc_start: 0.9279 (m-30) cc_final: 0.9029 (m-30) REVERT: K 116 ARG cc_start: 0.9091 (mmt-90) cc_final: 0.8731 (tpp80) REVERT: L 13 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8762 (mt-10) REVERT: L 17 ASN cc_start: 0.9574 (m-40) cc_final: 0.9240 (m-40) REVERT: L 38 MET cc_start: 0.9156 (tmm) cc_final: 0.8884 (tmm) REVERT: L 39 CYS cc_start: 0.9203 (p) cc_final: 0.8602 (p) REVERT: L 83 GLU cc_start: 0.8204 (mp0) cc_final: 0.7566 (mp0) REVERT: L 86 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8828 (tp40) REVERT: L 124 ASP cc_start: 0.8691 (t0) cc_final: 0.8052 (t0) REVERT: M 17 ASN cc_start: 0.9481 (m-40) cc_final: 0.9268 (m110) REVERT: M 34 GLU cc_start: 0.9087 (tt0) cc_final: 0.8716 (tt0) REVERT: M 44 ARG cc_start: 0.8203 (ttt180) cc_final: 0.7492 (tpt170) REVERT: M 70 GLU cc_start: 0.9042 (tp30) cc_final: 0.8726 (tp30) REVERT: M 73 ARG cc_start: 0.9378 (tmm-80) cc_final: 0.8800 (ttp80) REVERT: M 83 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7472 (pp20) REVERT: M 102 ASP cc_start: 0.9175 (m-30) cc_final: 0.8945 (m-30) REVERT: M 106 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8579 (mp0) REVERT: M 116 ARG cc_start: 0.8808 (tpp80) cc_final: 0.8458 (tpp80) REVERT: M 131 ASP cc_start: 0.8912 (t0) cc_final: 0.8572 (t0) REVERT: N 79 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8755 (mmtm) REVERT: N 89 LYS cc_start: 0.8406 (ptmm) cc_final: 0.7639 (ptmm) REVERT: N 90 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8582 (p) REVERT: N 92 ASP cc_start: 0.7992 (p0) cc_final: 0.7703 (p0) REVERT: N 105 ASP cc_start: 0.9217 (m-30) cc_final: 0.8908 (m-30) REVERT: O 13 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8903 (mt-10) REVERT: O 21 ASP cc_start: 0.7469 (p0) cc_final: 0.7155 (p0) REVERT: O 38 MET cc_start: 0.8862 (tmm) cc_final: 0.8543 (tmm) REVERT: O 39 CYS cc_start: 0.9148 (p) cc_final: 0.8751 (p) REVERT: O 70 GLU cc_start: 0.8820 (mm-30) cc_final: 0.7982 (mm-30) REVERT: O 86 GLN cc_start: 0.8993 (mm-40) cc_final: 0.8786 (tp40) REVERT: O 91 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: O 92 ASP cc_start: 0.6982 (t70) cc_final: 0.6530 (t0) REVERT: O 94 THR cc_start: 0.9236 (m) cc_final: 0.8876 (p) REVERT: O 98 ASN cc_start: 0.9208 (m-40) cc_final: 0.8924 (m-40) REVERT: O 99 TYR cc_start: 0.8467 (t80) cc_final: 0.8001 (t80) REVERT: O 102 ASP cc_start: 0.9022 (m-30) cc_final: 0.8585 (m-30) REVERT: a 62 ASP cc_start: 0.7694 (t0) cc_final: 0.7278 (t0) REVERT: a 101 ASP cc_start: 0.8997 (p0) cc_final: 0.8734 (p0) REVERT: a 112 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8946 (mm-30) REVERT: a 113 ASP cc_start: 0.9154 (t70) cc_final: 0.8796 (t0) REVERT: a 117 ASP cc_start: 0.9435 (m-30) cc_final: 0.9144 (m-30) REVERT: b 1 MET cc_start: 0.8049 (tpt) cc_final: 0.6898 (tpt) REVERT: b 55 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8383 (t) REVERT: b 91 VAL cc_start: 0.9583 (t) cc_final: 0.9327 (p) REVERT: c 5 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7598 (ptpp) REVERT: c 79 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8186 (t) REVERT: c 88 GLU cc_start: 0.7615 (tp30) cc_final: 0.7275 (tp30) REVERT: c 93 ARG cc_start: 0.7531 (ttm170) cc_final: 0.6800 (ttm110) REVERT: d 14 GLN cc_start: 0.8981 (mp10) cc_final: 0.8742 (mp10) REVERT: d 17 ILE cc_start: 0.9239 (pt) cc_final: 0.8930 (mm) REVERT: d 29 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8303 (p) REVERT: d 50 GLU cc_start: 0.7357 (tp30) cc_final: 0.7028 (tp30) REVERT: e 1 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7465 (tpp) REVERT: e 5 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8306 (mtmm) REVERT: e 30 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.6851 (p90) REVERT: f 3 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.7812 (ttp-110) REVERT: f 27 ASN cc_start: 0.8641 (m-40) cc_final: 0.8255 (m-40) REVERT: f 59 VAL cc_start: 0.7742 (p) cc_final: 0.7145 (p) REVERT: f 82 ASP cc_start: 0.8155 (t0) cc_final: 0.7793 (m-30) REVERT: f 86 ASP cc_start: 0.8432 (p0) cc_final: 0.7843 (p0) REVERT: f 91 VAL cc_start: 0.9696 (t) cc_final: 0.9340 (p) REVERT: f 109 ASN cc_start: 0.8936 (m-40) cc_final: 0.8630 (m110) REVERT: g 14 GLN cc_start: 0.9130 (mp10) cc_final: 0.8888 (mm-40) REVERT: g 24 THR cc_start: 0.9308 (m) cc_final: 0.9026 (p) REVERT: g 48 ASN cc_start: 0.9360 (t0) cc_final: 0.8841 (t0) REVERT: g 50 GLU cc_start: 0.8384 (mp0) cc_final: 0.7681 (mp0) REVERT: g 68 LEU cc_start: 0.9623 (tt) cc_final: 0.9398 (tt) REVERT: h 1 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.5555 (tmm) REVERT: h 21 LEU cc_start: 0.9545 (mt) cc_final: 0.9309 (mt) REVERT: h 36 TYR cc_start: 0.8794 (m-80) cc_final: 0.8416 (m-10) REVERT: l 14 GLN cc_start: 0.9237 (mp10) cc_final: 0.8903 (mp10) REVERT: l 27 ASN cc_start: 0.8652 (m-40) cc_final: 0.8300 (m-40) REVERT: m 29 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7391 (p) REVERT: m 36 TYR cc_start: 0.8117 (m-80) cc_final: 0.7792 (m-80) REVERT: m 48 ASN cc_start: 0.8995 (t0) cc_final: 0.8623 (t0) REVERT: n 42 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8442 (t70) REVERT: n 111 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9146 (pp) REVERT: o 14 GLN cc_start: 0.9423 (mp10) cc_final: 0.9100 (mp10) REVERT: o 54 ASN cc_start: 0.7762 (p0) cc_final: 0.7179 (p0) REVERT: o 65 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.5443 (t80) REVERT: o 77 SER cc_start: 0.9438 (p) cc_final: 0.9005 (p) outliers start: 220 outliers final: 133 residues processed: 1288 average time/residue: 0.2158 time to fit residues: 435.3954 Evaluate side-chains 1202 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1050 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 112 GLU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 72 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 79 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 90 SER Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain d residue 110 TYR Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 91 VAL Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 100 THR Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 34 ASN Chi-restraints excluded: chain o residue 52 VAL Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 261 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 341 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 10 HIS E 17 ASN E 18 GLN G 46 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 58 ASN ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 48 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.069325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054877 restraints weight = 150265.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056452 restraints weight = 94832.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057540 restraints weight = 67719.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058297 restraints weight = 53247.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058869 restraints weight = 44716.837| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31470 Z= 0.172 Angle : 0.758 10.260 42780 Z= 0.396 Chirality : 0.046 0.190 4995 Planarity : 0.005 0.101 5565 Dihedral : 7.372 81.476 4238 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.04 % Favored : 91.83 % Rotamer: Outliers : 6.61 % Allowed : 23.18 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 3795 helix: 0.44 (0.12), residues: 1669 sheet: -0.69 (0.20), residues: 624 loop : -2.36 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 44 TYR 0.041 0.002 TYR h 114 PHE 0.029 0.002 PHE c 89 TRP 0.013 0.001 TRP o 16 HIS 0.010 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00377 (31470) covalent geometry : angle 0.75813 (42780) hydrogen bonds : bond 0.03975 ( 1420) hydrogen bonds : angle 5.12548 ( 4086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 1141 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8832 (tp30) cc_final: 0.8279 (tp30) REVERT: A 17 ASN cc_start: 0.8942 (m110) cc_final: 0.8054 (m110) REVERT: A 29 GLU cc_start: 0.9062 (tp30) cc_final: 0.8738 (tp30) REVERT: A 38 MET cc_start: 0.9253 (tmm) cc_final: 0.8667 (tmm) REVERT: A 46 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8749 (pt0) REVERT: A 92 ASP cc_start: 0.8745 (p0) cc_final: 0.8483 (p0) REVERT: A 124 ASP cc_start: 0.9217 (t0) cc_final: 0.8899 (t0) REVERT: B 49 PHE cc_start: 0.9738 (t80) cc_final: 0.9531 (t80) REVERT: B 86 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8785 (tp-100) REVERT: B 105 ASP cc_start: 0.9242 (m-30) cc_final: 0.9010 (m-30) REVERT: B 106 GLU cc_start: 0.9307 (tp30) cc_final: 0.8971 (tp30) REVERT: B 116 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8761 (tpp80) REVERT: B 124 ASP cc_start: 0.8695 (t0) cc_final: 0.8147 (t0) REVERT: B 131 ASP cc_start: 0.9403 (t0) cc_final: 0.8820 (t0) REVERT: C 13 GLU cc_start: 0.8907 (tp30) cc_final: 0.7802 (tp30) REVERT: C 17 ASN cc_start: 0.9408 (m-40) cc_final: 0.8286 (m-40) REVERT: C 19 PHE cc_start: 0.8856 (m-80) cc_final: 0.8536 (m-80) REVERT: C 30 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: C 38 MET cc_start: 0.9068 (tmm) cc_final: 0.8630 (tmm) REVERT: C 39 CYS cc_start: 0.9277 (p) cc_final: 0.8889 (p) REVERT: C 60 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8670 (mt-10) REVERT: C 86 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8430 (tp40) REVERT: C 90 VAL cc_start: 0.9200 (t) cc_final: 0.8965 (p) REVERT: C 102 ASP cc_start: 0.9145 (m-30) cc_final: 0.8862 (m-30) REVERT: C 105 ASP cc_start: 0.9426 (m-30) cc_final: 0.9201 (m-30) REVERT: C 116 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8208 (mmm160) REVERT: D 34 GLU cc_start: 0.8965 (tt0) cc_final: 0.8657 (tt0) REVERT: D 60 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8941 (mm-30) REVERT: D 69 LYS cc_start: 0.9668 (OUTLIER) cc_final: 0.9362 (ttpp) REVERT: D 70 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8467 (tp30) REVERT: D 75 ASP cc_start: 0.8153 (p0) cc_final: 0.7907 (p0) REVERT: D 92 ASP cc_start: 0.8966 (p0) cc_final: 0.8606 (p0) REVERT: D 106 GLU cc_start: 0.8964 (tp30) cc_final: 0.8456 (tp30) REVERT: D 113 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9248 (mtmt) REVERT: D 116 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8417 (tpp80) REVERT: D 132 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7384 (t0) REVERT: E 17 ASN cc_start: 0.9505 (m-40) cc_final: 0.9240 (m-40) REVERT: E 92 ASP cc_start: 0.7814 (p0) cc_final: 0.7286 (p0) REVERT: E 105 ASP cc_start: 0.9254 (m-30) cc_final: 0.9020 (m-30) REVERT: E 132 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: F 38 MET cc_start: 0.9113 (tmm) cc_final: 0.8791 (tmm) REVERT: F 60 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8970 (mt-10) REVERT: F 86 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8568 (tp40) REVERT: F 110 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8417 (mm-30) REVERT: F 116 ARG cc_start: 0.8348 (mmm160) cc_final: 0.7920 (mmm160) REVERT: G 29 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8490 (tm-30) REVERT: G 34 GLU cc_start: 0.8755 (tt0) cc_final: 0.8375 (tt0) REVERT: G 60 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8911 (mt-10) REVERT: G 70 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8158 (tp30) REVERT: G 73 ARG cc_start: 0.9047 (ttp-170) cc_final: 0.8836 (tmm160) REVERT: G 92 ASP cc_start: 0.8887 (p0) cc_final: 0.8579 (p0) REVERT: G 132 ASP cc_start: 0.8593 (m-30) cc_final: 0.8344 (t70) REVERT: H 21 ASP cc_start: 0.7565 (p0) cc_final: 0.7179 (p0) REVERT: H 44 ARG cc_start: 0.9034 (ptm-80) cc_final: 0.8375 (ttt180) REVERT: H 105 ASP cc_start: 0.9134 (m-30) cc_final: 0.8875 (m-30) REVERT: I 13 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8869 (mt-10) REVERT: I 17 ASN cc_start: 0.9642 (m-40) cc_final: 0.9392 (m-40) REVERT: I 21 ASP cc_start: 0.8258 (p0) cc_final: 0.7976 (p0) REVERT: I 35 PHE cc_start: 0.9622 (t80) cc_final: 0.8955 (t80) REVERT: I 38 MET cc_start: 0.9227 (tmm) cc_final: 0.8906 (tmm) REVERT: I 39 CYS cc_start: 0.9313 (p) cc_final: 0.8731 (p) REVERT: I 60 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8817 (mt-10) REVERT: I 90 VAL cc_start: 0.9077 (t) cc_final: 0.8672 (t) REVERT: I 99 TYR cc_start: 0.8510 (t80) cc_final: 0.8117 (t80) REVERT: I 116 ARG cc_start: 0.8713 (mmm160) cc_final: 0.7905 (mmm160) REVERT: J 13 GLU cc_start: 0.8748 (tp30) cc_final: 0.8130 (tp30) REVERT: J 17 ASN cc_start: 0.8776 (m110) cc_final: 0.7858 (m110) REVERT: J 21 ASP cc_start: 0.8649 (p0) cc_final: 0.8128 (p0) REVERT: J 27 GLU cc_start: 0.7158 (mp0) cc_final: 0.6939 (mp0) REVERT: J 60 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8683 (mt-10) REVERT: J 70 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8377 (mm-30) REVERT: J 74 LEU cc_start: 0.9809 (OUTLIER) cc_final: 0.9310 (mt) REVERT: J 83 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7869 (tm-30) REVERT: J 92 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8579 (p0) REVERT: J 110 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8779 (mm-30) REVERT: K 69 LYS cc_start: 0.9768 (tttp) cc_final: 0.9449 (ttmm) REVERT: K 76 LYS cc_start: 0.9492 (tppt) cc_final: 0.9273 (mttt) REVERT: K 86 GLN cc_start: 0.9206 (tp40) cc_final: 0.8794 (tp-100) REVERT: K 90 VAL cc_start: 0.9073 (t) cc_final: 0.8862 (p) REVERT: K 105 ASP cc_start: 0.9280 (m-30) cc_final: 0.9077 (m-30) REVERT: L 21 ASP cc_start: 0.7671 (p0) cc_final: 0.7302 (p0) REVERT: L 38 MET cc_start: 0.9194 (tmm) cc_final: 0.8888 (tmm) REVERT: L 39 CYS cc_start: 0.9199 (p) cc_final: 0.8618 (p) REVERT: L 83 GLU cc_start: 0.8215 (mp0) cc_final: 0.7935 (mp0) REVERT: L 86 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8845 (tp40) REVERT: L 110 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8843 (tp30) REVERT: L 124 ASP cc_start: 0.8655 (t0) cc_final: 0.8132 (t0) REVERT: M 17 ASN cc_start: 0.9513 (m-40) cc_final: 0.9290 (m110) REVERT: M 46 GLN cc_start: 0.6447 (tm-30) cc_final: 0.6212 (tm-30) REVERT: M 70 GLU cc_start: 0.9026 (tp30) cc_final: 0.8152 (tp30) REVERT: M 73 ARG cc_start: 0.9371 (tmm-80) cc_final: 0.9094 (tmm-80) REVERT: M 83 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7455 (pp20) REVERT: M 102 ASP cc_start: 0.9202 (m-30) cc_final: 0.8977 (m-30) REVERT: M 106 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8621 (mp0) REVERT: M 116 ARG cc_start: 0.8796 (tpp80) cc_final: 0.8466 (tpp80) REVERT: M 131 ASP cc_start: 0.8961 (t0) cc_final: 0.8635 (t0) REVERT: N 44 ARG cc_start: 0.8596 (tpp80) cc_final: 0.8118 (tpt170) REVERT: N 79 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8591 (mmtp) REVERT: N 86 GLN cc_start: 0.8072 (mp10) cc_final: 0.7627 (mp10) REVERT: N 89 LYS cc_start: 0.8436 (ptmm) cc_final: 0.7565 (ptmm) REVERT: N 90 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8489 (m) REVERT: N 92 ASP cc_start: 0.7843 (p0) cc_final: 0.7453 (p0) REVERT: N 105 ASP cc_start: 0.9202 (m-30) cc_final: 0.8908 (m-30) REVERT: O 13 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8932 (mt-10) REVERT: O 21 ASP cc_start: 0.7492 (p0) cc_final: 0.7193 (p0) REVERT: O 38 MET cc_start: 0.8880 (tmm) cc_final: 0.8434 (ppp) REVERT: O 39 CYS cc_start: 0.9152 (p) cc_final: 0.8802 (p) REVERT: O 86 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8762 (tp40) REVERT: O 92 ASP cc_start: 0.7024 (t70) cc_final: 0.6568 (t0) REVERT: O 97 MET cc_start: 0.9180 (mmm) cc_final: 0.8858 (mmm) REVERT: O 98 ASN cc_start: 0.9274 (m-40) cc_final: 0.9029 (m-40) REVERT: O 99 TYR cc_start: 0.8540 (t80) cc_final: 0.8225 (t80) REVERT: O 102 ASP cc_start: 0.9032 (m-30) cc_final: 0.8780 (m-30) REVERT: a 62 ASP cc_start: 0.7874 (t0) cc_final: 0.7581 (t0) REVERT: a 108 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8907 (mm) REVERT: a 112 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8873 (mm-30) REVERT: a 113 ASP cc_start: 0.9169 (t70) cc_final: 0.8799 (t0) REVERT: a 117 ASP cc_start: 0.9444 (m-30) cc_final: 0.9158 (m-30) REVERT: b 1 MET cc_start: 0.8185 (tpt) cc_final: 0.7279 (tpt) REVERT: b 55 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8432 (t) REVERT: b 91 VAL cc_start: 0.9619 (t) cc_final: 0.9382 (p) REVERT: c 3 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7809 (tmm-80) REVERT: c 5 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7527 (mtmm) REVERT: c 50 GLU cc_start: 0.7641 (tp30) cc_final: 0.7319 (tp30) REVERT: c 82 ASP cc_start: 0.8122 (t0) cc_final: 0.7880 (m-30) REVERT: c 86 ASP cc_start: 0.8285 (p0) cc_final: 0.7750 (p0) REVERT: c 88 GLU cc_start: 0.7700 (tp30) cc_final: 0.7328 (tp30) REVERT: d 14 GLN cc_start: 0.8937 (mp10) cc_final: 0.8639 (mp10) REVERT: d 17 ILE cc_start: 0.9355 (pt) cc_final: 0.9050 (mm) REVERT: d 29 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8446 (p) REVERT: d 50 GLU cc_start: 0.7378 (tp30) cc_final: 0.7066 (tp30) REVERT: e 1 MET cc_start: 0.7868 (tpt) cc_final: 0.7515 (tpp) REVERT: e 5 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8315 (mtmm) REVERT: e 14 GLN cc_start: 0.8861 (mp10) cc_final: 0.8466 (mm-40) REVERT: e 30 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.6858 (p90) REVERT: e 108 LEU cc_start: 0.9099 (mt) cc_final: 0.8861 (mt) REVERT: f 3 ARG cc_start: 0.8459 (mtp-110) cc_final: 0.7970 (ttp-110) REVERT: f 27 ASN cc_start: 0.8718 (m-40) cc_final: 0.8235 (m-40) REVERT: f 59 VAL cc_start: 0.7882 (p) cc_final: 0.7367 (p) REVERT: f 82 ASP cc_start: 0.8192 (t0) cc_final: 0.7875 (m-30) REVERT: f 86 ASP cc_start: 0.8425 (p0) cc_final: 0.8092 (p0) REVERT: f 109 ASN cc_start: 0.8922 (m-40) cc_final: 0.8621 (m110) REVERT: g 5 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8118 (tppt) REVERT: g 48 ASN cc_start: 0.9391 (t0) cc_final: 0.8939 (t0) REVERT: g 50 GLU cc_start: 0.8403 (mp0) cc_final: 0.7756 (pm20) REVERT: g 68 LEU cc_start: 0.9606 (tt) cc_final: 0.9377 (tt) REVERT: h 1 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.5512 (tmm) REVERT: h 21 LEU cc_start: 0.9528 (mt) cc_final: 0.9315 (mt) REVERT: h 36 TYR cc_start: 0.8784 (m-80) cc_final: 0.8481 (m-10) REVERT: h 74 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8952 (mmmm) REVERT: i 73 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8615 (t0) REVERT: i 74 LYS cc_start: 0.7865 (tmtt) cc_final: 0.7648 (tptp) REVERT: j 14 GLN cc_start: 0.8989 (mp10) cc_final: 0.8624 (mp10) REVERT: j 48 ASN cc_start: 0.8956 (t0) cc_final: 0.8528 (t0) REVERT: j 50 GLU cc_start: 0.8405 (pm20) cc_final: 0.8033 (pm20) REVERT: k 17 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9383 (mm) REVERT: k 67 ILE cc_start: 0.8205 (mp) cc_final: 0.7868 (mp) REVERT: l 14 GLN cc_start: 0.9293 (mp10) cc_final: 0.9051 (mm-40) REVERT: l 27 ASN cc_start: 0.8694 (m-40) cc_final: 0.8452 (m-40) REVERT: m 29 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7519 (p) REVERT: m 48 ASN cc_start: 0.9050 (t0) cc_final: 0.8601 (t0) REVERT: n 111 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9180 (pp) REVERT: o 1 MET cc_start: 0.7806 (ttp) cc_final: 0.6898 (tmm) REVERT: o 14 GLN cc_start: 0.9458 (mp10) cc_final: 0.9116 (mp10) REVERT: o 50 GLU cc_start: 0.7801 (tp30) cc_final: 0.7437 (tp30) REVERT: o 54 ASN cc_start: 0.7766 (p0) cc_final: 0.7388 (p0) REVERT: o 65 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.5409 (t80) REVERT: o 77 SER cc_start: 0.9464 (p) cc_final: 0.8990 (p) REVERT: o 93 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8335 (tmt-80) outliers start: 233 outliers final: 146 residues processed: 1272 average time/residue: 0.2188 time to fit residues: 434.2257 Evaluate side-chains 1196 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1029 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 81 SER Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 74 LEU Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 3 ARG Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 90 SER Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain i residue 73 ASN Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 347 optimal weight: 30.0000 chunk 44 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 354 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 51 ASN E 51 ASN F 51 ASN ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN l 123 GLN m 58 ASN n 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.067477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053973 restraints weight = 148432.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055512 restraints weight = 92076.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056589 restraints weight = 65179.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057259 restraints weight = 50496.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057864 restraints weight = 42445.082| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31470 Z= 0.191 Angle : 0.789 11.390 42780 Z= 0.416 Chirality : 0.047 0.250 4995 Planarity : 0.005 0.085 5565 Dihedral : 7.184 59.876 4224 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.67 % Favored : 91.17 % Rotamer: Outliers : 6.89 % Allowed : 24.09 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.13), residues: 3795 helix: 0.40 (0.12), residues: 1620 sheet: -0.62 (0.20), residues: 623 loop : -2.19 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG n 3 TYR 0.047 0.002 TYR m 110 PHE 0.036 0.002 PHE A 49 TRP 0.013 0.001 TRP o 16 HIS 0.010 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00420 (31470) covalent geometry : angle 0.78881 (42780) hydrogen bonds : bond 0.04079 ( 1420) hydrogen bonds : angle 5.22707 ( 4086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1112 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8841 (tp30) cc_final: 0.8346 (tp30) REVERT: A 29 GLU cc_start: 0.8975 (tp30) cc_final: 0.8397 (tp30) REVERT: A 30 GLU cc_start: 0.8736 (pm20) cc_final: 0.8013 (pm20) REVERT: A 38 MET cc_start: 0.9235 (tmm) cc_final: 0.8674 (tmm) REVERT: A 53 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8890 (mt) REVERT: A 76 LYS cc_start: 0.9442 (tppt) cc_final: 0.9127 (tppt) REVERT: A 92 ASP cc_start: 0.8859 (p0) cc_final: 0.8580 (p0) REVERT: A 112 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9122 (mtmm) REVERT: A 124 ASP cc_start: 0.9255 (t0) cc_final: 0.8866 (t0) REVERT: A 132 ASP cc_start: 0.8515 (m-30) cc_final: 0.8123 (m-30) REVERT: B 86 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8855 (tp-100) REVERT: B 105 ASP cc_start: 0.9222 (m-30) cc_final: 0.9004 (m-30) REVERT: B 106 GLU cc_start: 0.9336 (tp30) cc_final: 0.8950 (tp30) REVERT: B 116 ARG cc_start: 0.9141 (tpp80) cc_final: 0.8707 (tpp80) REVERT: B 131 ASP cc_start: 0.9259 (t0) cc_final: 0.8852 (t0) REVERT: C 13 GLU cc_start: 0.8899 (tp30) cc_final: 0.7818 (tp30) REVERT: C 17 ASN cc_start: 0.9452 (m-40) cc_final: 0.8559 (m-40) REVERT: C 19 PHE cc_start: 0.8781 (m-80) cc_final: 0.8455 (m-80) REVERT: C 30 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: C 38 MET cc_start: 0.9108 (tmm) cc_final: 0.8697 (tmm) REVERT: C 39 CYS cc_start: 0.9223 (p) cc_final: 0.8782 (p) REVERT: C 60 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8619 (mt-10) REVERT: C 83 GLU cc_start: 0.7933 (mp0) cc_final: 0.7611 (mp0) REVERT: C 86 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8322 (tp40) REVERT: C 90 VAL cc_start: 0.9192 (t) cc_final: 0.8963 (p) REVERT: C 102 ASP cc_start: 0.9077 (m-30) cc_final: 0.8829 (m-30) REVERT: C 105 ASP cc_start: 0.9408 (m-30) cc_final: 0.9172 (m-30) REVERT: C 124 ASP cc_start: 0.7788 (t0) cc_final: 0.7557 (t0) REVERT: D 21 ASP cc_start: 0.7582 (p0) cc_final: 0.7325 (p0) REVERT: D 34 GLU cc_start: 0.8960 (tt0) cc_final: 0.8687 (tt0) REVERT: D 44 ARG cc_start: 0.8793 (ptm160) cc_final: 0.8299 (ptm160) REVERT: D 60 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8910 (mm-30) REVERT: D 69 LYS cc_start: 0.9679 (OUTLIER) cc_final: 0.9422 (ttpp) REVERT: D 70 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8467 (tp30) REVERT: D 75 ASP cc_start: 0.8098 (p0) cc_final: 0.7767 (p0) REVERT: D 92 ASP cc_start: 0.9031 (p0) cc_final: 0.8705 (p0) REVERT: D 106 GLU cc_start: 0.8956 (tp30) cc_final: 0.8350 (tp30) REVERT: D 116 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8440 (tpp80) REVERT: D 132 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7406 (t0) REVERT: E 17 ASN cc_start: 0.9489 (m-40) cc_final: 0.9177 (m110) REVERT: E 92 ASP cc_start: 0.7731 (p0) cc_final: 0.7179 (p0) REVERT: E 105 ASP cc_start: 0.9214 (m-30) cc_final: 0.8987 (m-30) REVERT: F 13 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8858 (pt0) REVERT: F 38 MET cc_start: 0.9157 (tmm) cc_final: 0.8788 (tmm) REVERT: F 70 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8549 (mt-10) REVERT: F 86 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8553 (tp40) REVERT: F 110 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8524 (mm-30) REVERT: G 34 GLU cc_start: 0.8764 (tt0) cc_final: 0.8236 (tt0) REVERT: G 60 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8871 (mt-10) REVERT: G 70 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8437 (tp30) REVERT: G 92 ASP cc_start: 0.8932 (p0) cc_final: 0.8597 (p0) REVERT: G 132 ASP cc_start: 0.8570 (m-30) cc_final: 0.8358 (t70) REVERT: H 21 ASP cc_start: 0.7601 (p0) cc_final: 0.7229 (p0) REVERT: H 44 ARG cc_start: 0.9070 (ptm-80) cc_final: 0.8547 (ttt180) REVERT: H 59 ILE cc_start: 0.9652 (OUTLIER) cc_final: 0.9285 (pt) REVERT: H 90 VAL cc_start: 0.9191 (t) cc_final: 0.8961 (p) REVERT: H 105 ASP cc_start: 0.9176 (m-30) cc_final: 0.8903 (m-30) REVERT: H 116 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8557 (tpp80) REVERT: I 13 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8833 (mt-10) REVERT: I 17 ASN cc_start: 0.9634 (m-40) cc_final: 0.9371 (m-40) REVERT: I 21 ASP cc_start: 0.8277 (p0) cc_final: 0.7891 (p0) REVERT: I 35 PHE cc_start: 0.9635 (t80) cc_final: 0.8986 (t80) REVERT: I 38 MET cc_start: 0.9223 (tmm) cc_final: 0.8932 (tmm) REVERT: I 39 CYS cc_start: 0.9356 (p) cc_final: 0.8711 (p) REVERT: I 60 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8802 (mt-10) REVERT: I 90 VAL cc_start: 0.9071 (t) cc_final: 0.8655 (t) REVERT: I 116 ARG cc_start: 0.8681 (mmm160) cc_final: 0.8443 (mmp80) REVERT: J 13 GLU cc_start: 0.8777 (tp30) cc_final: 0.8152 (tp30) REVERT: J 17 ASN cc_start: 0.8731 (m110) cc_final: 0.7761 (m110) REVERT: J 21 ASP cc_start: 0.8653 (p0) cc_final: 0.8270 (p0) REVERT: J 27 GLU cc_start: 0.7185 (mp0) cc_final: 0.6887 (mp0) REVERT: J 60 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8720 (mt-10) REVERT: J 70 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8285 (mm-30) REVERT: J 74 LEU cc_start: 0.9789 (OUTLIER) cc_final: 0.9066 (mt) REVERT: J 83 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7891 (tm-30) REVERT: J 92 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8616 (p0) REVERT: K 69 LYS cc_start: 0.9765 (tttp) cc_final: 0.9448 (ttmm) REVERT: K 86 GLN cc_start: 0.9157 (tp40) cc_final: 0.8736 (tp-100) REVERT: L 38 MET cc_start: 0.9213 (tmm) cc_final: 0.8913 (tmm) REVERT: L 39 CYS cc_start: 0.9236 (p) cc_final: 0.8655 (p) REVERT: L 76 LYS cc_start: 0.9364 (mmmm) cc_final: 0.9030 (mmmm) REVERT: L 83 GLU cc_start: 0.8218 (mp0) cc_final: 0.7959 (mp0) REVERT: L 86 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8934 (tp40) REVERT: L 110 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8837 (tp30) REVERT: M 17 ASN cc_start: 0.9529 (m-40) cc_final: 0.9301 (m110) REVERT: M 34 GLU cc_start: 0.8922 (tt0) cc_final: 0.8673 (tt0) REVERT: M 51 ASN cc_start: 0.9559 (OUTLIER) cc_final: 0.9192 (p0) REVERT: M 70 GLU cc_start: 0.9031 (tp30) cc_final: 0.8191 (tp30) REVERT: M 73 ARG cc_start: 0.9377 (tmm-80) cc_final: 0.9075 (tmm-80) REVERT: M 83 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7557 (pp20) REVERT: M 102 ASP cc_start: 0.9210 (m-30) cc_final: 0.8998 (m-30) REVERT: M 106 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8606 (mp0) REVERT: M 131 ASP cc_start: 0.8984 (t0) cc_final: 0.8596 (t0) REVERT: M 132 ASP cc_start: 0.8824 (m-30) cc_final: 0.8230 (m-30) REVERT: N 44 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8001 (tpp-160) REVERT: N 89 LYS cc_start: 0.8653 (ptmm) cc_final: 0.7923 (ptmm) REVERT: N 90 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8269 (m) REVERT: N 92 ASP cc_start: 0.7755 (p0) cc_final: 0.7253 (p0) REVERT: N 105 ASP cc_start: 0.9186 (m-30) cc_final: 0.8890 (m-30) REVERT: O 21 ASP cc_start: 0.7542 (p0) cc_final: 0.7166 (p0) REVERT: O 38 MET cc_start: 0.8918 (tmm) cc_final: 0.8575 (tmm) REVERT: O 39 CYS cc_start: 0.9145 (p) cc_final: 0.8784 (p) REVERT: O 69 LYS cc_start: 0.9413 (ttpp) cc_final: 0.9094 (ttmm) REVERT: O 86 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8824 (tp40) REVERT: O 92 ASP cc_start: 0.7241 (t70) cc_final: 0.6796 (t0) REVERT: O 94 THR cc_start: 0.9267 (m) cc_final: 0.8929 (p) REVERT: O 97 MET cc_start: 0.9108 (mmm) cc_final: 0.8816 (mmm) REVERT: O 102 ASP cc_start: 0.9048 (m-30) cc_final: 0.8781 (m-30) REVERT: O 112 LYS cc_start: 0.9606 (mttp) cc_final: 0.9180 (mtmm) REVERT: a 62 ASP cc_start: 0.7886 (t0) cc_final: 0.7581 (t0) REVERT: a 108 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9059 (mm) REVERT: a 112 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8726 (mm-30) REVERT: a 113 ASP cc_start: 0.9150 (t70) cc_final: 0.8757 (t0) REVERT: a 117 ASP cc_start: 0.9427 (m-30) cc_final: 0.9130 (m-30) REVERT: b 1 MET cc_start: 0.8420 (tpt) cc_final: 0.7956 (tpt) REVERT: b 18 ASN cc_start: 0.9288 (t0) cc_final: 0.9028 (t0) REVERT: b 55 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8658 (t) REVERT: b 91 VAL cc_start: 0.9620 (t) cc_final: 0.9377 (p) REVERT: c 3 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8026 (ttp80) REVERT: c 103 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8744 (mm-30) REVERT: c 114 TYR cc_start: 0.9192 (t80) cc_final: 0.8951 (t80) REVERT: d 1 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8369 (tpp) REVERT: d 14 GLN cc_start: 0.8970 (mp10) cc_final: 0.8680 (mp10) REVERT: d 17 ILE cc_start: 0.9406 (pt) cc_final: 0.9156 (mm) REVERT: d 29 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8509 (p) REVERT: d 50 GLU cc_start: 0.7449 (tp30) cc_final: 0.7186 (tp30) REVERT: e 5 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8310 (mtmm) REVERT: e 14 GLN cc_start: 0.8909 (mp10) cc_final: 0.8451 (mm-40) REVERT: e 30 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.6868 (p90) REVERT: f 3 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.7784 (tmm-80) REVERT: f 27 ASN cc_start: 0.8747 (m-40) cc_final: 0.8408 (m-40) REVERT: f 50 GLU cc_start: 0.7934 (tp30) cc_final: 0.7647 (tp30) REVERT: f 86 ASP cc_start: 0.8404 (p0) cc_final: 0.8167 (p0) REVERT: f 109 ASN cc_start: 0.8897 (m-40) cc_final: 0.8563 (m110) REVERT: g 14 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8631 (mm-40) REVERT: g 50 GLU cc_start: 0.8400 (mp0) cc_final: 0.8090 (pm20) REVERT: g 68 LEU cc_start: 0.9637 (tt) cc_final: 0.9400 (tt) REVERT: h 1 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.5501 (tmm) REVERT: h 36 TYR cc_start: 0.8739 (m-80) cc_final: 0.8493 (m-10) REVERT: h 50 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7725 (mm-30) REVERT: h 74 LYS cc_start: 0.9394 (mmtp) cc_final: 0.9116 (mmmm) REVERT: j 14 GLN cc_start: 0.8984 (mp10) cc_final: 0.8745 (mp10) REVERT: j 48 ASN cc_start: 0.8878 (t0) cc_final: 0.8330 (t0) REVERT: j 50 GLU cc_start: 0.8175 (pm20) cc_final: 0.7761 (pm20) REVERT: k 67 ILE cc_start: 0.8640 (mp) cc_final: 0.8237 (mp) REVERT: l 14 GLN cc_start: 0.9300 (mp10) cc_final: 0.9004 (mm-40) REVERT: l 27 ASN cc_start: 0.8818 (m-40) cc_final: 0.8551 (m-40) REVERT: m 12 ASP cc_start: 0.7447 (p0) cc_final: 0.6823 (p0) REVERT: m 13 ASP cc_start: 0.8105 (m-30) cc_final: 0.7768 (m-30) REVERT: m 29 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7710 (p) REVERT: m 48 ASN cc_start: 0.9077 (t0) cc_final: 0.8613 (t0) REVERT: n 107 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7991 (m) REVERT: n 111 LEU cc_start: 0.9482 (mm) cc_final: 0.9145 (pp) REVERT: o 1 MET cc_start: 0.7966 (ttp) cc_final: 0.7085 (tmm) REVERT: o 50 GLU cc_start: 0.7871 (tp30) cc_final: 0.7377 (tp30) REVERT: o 54 ASN cc_start: 0.7678 (p0) cc_final: 0.7379 (p0) REVERT: o 65 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5680 (t80) REVERT: o 77 SER cc_start: 0.9459 (p) cc_final: 0.8880 (p) REVERT: o 93 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8346 (tmt-80) outliers start: 243 outliers final: 166 residues processed: 1256 average time/residue: 0.2184 time to fit residues: 429.7592 Evaluate side-chains 1221 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1034 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 3 ARG Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 70 THR Chi-restraints excluded: chain d residue 90 SER Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 94 GLU Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 110 TYR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 52 VAL Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Chi-restraints excluded: chain o residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 116 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 369 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN c 54 ASN ** e 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 42 HIS ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN o 109 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052225 restraints weight = 150999.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053765 restraints weight = 93315.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054800 restraints weight = 66232.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055567 restraints weight = 51850.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056079 restraints weight = 43246.513| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31470 Z= 0.194 Angle : 0.823 15.553 42780 Z= 0.429 Chirality : 0.047 0.229 4995 Planarity : 0.005 0.087 5565 Dihedral : 7.187 59.985 4220 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.72 % Favored : 91.17 % Rotamer: Outliers : 6.35 % Allowed : 26.30 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.13), residues: 3795 helix: 0.39 (0.12), residues: 1620 sheet: -0.48 (0.20), residues: 621 loop : -2.19 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 136 TYR 0.043 0.002 TYR h 114 PHE 0.027 0.002 PHE A 49 TRP 0.012 0.001 TRP o 16 HIS 0.009 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00434 (31470) covalent geometry : angle 0.82331 (42780) hydrogen bonds : bond 0.04048 ( 1420) hydrogen bonds : angle 5.20185 ( 4086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1113 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8840 (tp30) cc_final: 0.8337 (tp30) REVERT: A 29 GLU cc_start: 0.8914 (tp30) cc_final: 0.8143 (tp30) REVERT: A 30 GLU cc_start: 0.8812 (pm20) cc_final: 0.8130 (pm20) REVERT: A 35 PHE cc_start: 0.9676 (t80) cc_final: 0.9358 (t80) REVERT: A 38 MET cc_start: 0.9250 (tmm) cc_final: 0.8617 (tmm) REVERT: A 53 LEU cc_start: 0.9320 (mm) cc_final: 0.8901 (mt) REVERT: A 76 LYS cc_start: 0.9440 (tppt) cc_final: 0.9106 (tppt) REVERT: A 92 ASP cc_start: 0.8753 (p0) cc_final: 0.8493 (p0) REVERT: B 86 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8825 (tp-100) REVERT: B 105 ASP cc_start: 0.9242 (m-30) cc_final: 0.9016 (m-30) REVERT: B 106 GLU cc_start: 0.9322 (tp30) cc_final: 0.8960 (tp30) REVERT: B 124 ASP cc_start: 0.8873 (t0) cc_final: 0.8550 (t0) REVERT: B 131 ASP cc_start: 0.9271 (t0) cc_final: 0.8823 (t0) REVERT: C 13 GLU cc_start: 0.8899 (tp30) cc_final: 0.7820 (tp30) REVERT: C 17 ASN cc_start: 0.9396 (m-40) cc_final: 0.8329 (m-40) REVERT: C 19 PHE cc_start: 0.8787 (m-80) cc_final: 0.8508 (m-80) REVERT: C 30 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: C 38 MET cc_start: 0.9093 (tmm) cc_final: 0.8695 (tmm) REVERT: C 39 CYS cc_start: 0.9282 (p) cc_final: 0.8828 (p) REVERT: C 60 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8628 (mt-10) REVERT: C 83 GLU cc_start: 0.7907 (mp0) cc_final: 0.7566 (mp0) REVERT: C 86 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8313 (tp40) REVERT: C 90 VAL cc_start: 0.9200 (t) cc_final: 0.8923 (p) REVERT: C 102 ASP cc_start: 0.9054 (m-30) cc_final: 0.8773 (m-30) REVERT: C 105 ASP cc_start: 0.9416 (m-30) cc_final: 0.9120 (m-30) REVERT: C 116 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8205 (mmm160) REVERT: C 124 ASP cc_start: 0.7833 (t0) cc_final: 0.7597 (t0) REVERT: D 21 ASP cc_start: 0.7628 (p0) cc_final: 0.7316 (p0) REVERT: D 34 GLU cc_start: 0.8939 (tt0) cc_final: 0.8658 (tt0) REVERT: D 44 ARG cc_start: 0.8796 (ptm160) cc_final: 0.8298 (ptm160) REVERT: D 54 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9168 (pp) REVERT: D 60 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8881 (mm-30) REVERT: D 69 LYS cc_start: 0.9671 (OUTLIER) cc_final: 0.9420 (ttpp) REVERT: D 70 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8584 (tp30) REVERT: D 92 ASP cc_start: 0.9034 (p0) cc_final: 0.8707 (p0) REVERT: D 106 GLU cc_start: 0.8967 (tp30) cc_final: 0.8438 (tp30) REVERT: D 112 LYS cc_start: 0.9449 (mtmm) cc_final: 0.8962 (mtmm) REVERT: D 116 ARG cc_start: 0.8660 (tpp80) cc_final: 0.8250 (tpp80) REVERT: D 132 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7404 (t0) REVERT: E 17 ASN cc_start: 0.9486 (m-40) cc_final: 0.9207 (m110) REVERT: E 83 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8404 (tm-30) REVERT: E 92 ASP cc_start: 0.7725 (p0) cc_final: 0.7137 (p0) REVERT: E 105 ASP cc_start: 0.9234 (m-30) cc_final: 0.8985 (m-30) REVERT: E 124 ASP cc_start: 0.9004 (t70) cc_final: 0.8513 (t0) REVERT: F 13 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8882 (pt0) REVERT: F 34 GLU cc_start: 0.9294 (tt0) cc_final: 0.8958 (tt0) REVERT: F 38 MET cc_start: 0.9138 (tmm) cc_final: 0.8814 (tmm) REVERT: F 46 GLN cc_start: 0.8393 (mt0) cc_final: 0.7772 (pt0) REVERT: F 70 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8552 (mt-10) REVERT: F 86 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8522 (tp40) REVERT: F 110 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8491 (mm-30) REVERT: G 34 GLU cc_start: 0.8822 (tt0) cc_final: 0.8213 (tt0) REVERT: G 70 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8375 (tp30) REVERT: G 86 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8663 (mm-40) REVERT: G 92 ASP cc_start: 0.8920 (p0) cc_final: 0.8555 (p0) REVERT: H 21 ASP cc_start: 0.7580 (p0) cc_final: 0.7209 (p0) REVERT: H 44 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8603 (ttt180) REVERT: H 59 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9191 (pt) REVERT: H 105 ASP cc_start: 0.9199 (m-30) cc_final: 0.8908 (m-30) REVERT: H 116 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8545 (tpp80) REVERT: I 13 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8889 (mt-10) REVERT: I 17 ASN cc_start: 0.9622 (m-40) cc_final: 0.9359 (m-40) REVERT: I 21 ASP cc_start: 0.8240 (p0) cc_final: 0.7823 (p0) REVERT: I 35 PHE cc_start: 0.9638 (t80) cc_final: 0.9001 (t80) REVERT: I 38 MET cc_start: 0.9217 (tmm) cc_final: 0.8927 (tmm) REVERT: I 39 CYS cc_start: 0.9358 (p) cc_final: 0.8717 (p) REVERT: I 60 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8836 (mt-10) REVERT: I 90 VAL cc_start: 0.9142 (t) cc_final: 0.8844 (t) REVERT: I 91 GLU cc_start: 0.8714 (pp20) cc_final: 0.8137 (pp20) REVERT: I 116 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8419 (mmp80) REVERT: J 13 GLU cc_start: 0.8752 (tp30) cc_final: 0.8112 (tp30) REVERT: J 17 ASN cc_start: 0.8656 (m110) cc_final: 0.7643 (m110) REVERT: J 21 ASP cc_start: 0.8583 (p0) cc_final: 0.8073 (p0) REVERT: J 27 GLU cc_start: 0.7275 (mp0) cc_final: 0.6970 (mp0) REVERT: J 60 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8706 (mt-10) REVERT: J 70 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8261 (mm-30) REVERT: J 74 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9212 (mt) REVERT: J 79 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8801 (mtmm) REVERT: J 92 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8607 (p0) REVERT: J 93 ILE cc_start: 0.9143 (mp) cc_final: 0.8828 (mt) REVERT: J 110 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8773 (mm-30) REVERT: J 116 ARG cc_start: 0.9075 (tpp80) cc_final: 0.8823 (tpp80) REVERT: K 69 LYS cc_start: 0.9760 (tttp) cc_final: 0.9437 (ttmm) REVERT: K 86 GLN cc_start: 0.9142 (tp40) cc_final: 0.8713 (tp-100) REVERT: K 105 ASP cc_start: 0.9281 (m-30) cc_final: 0.9012 (m-30) REVERT: L 38 MET cc_start: 0.9211 (tmm) cc_final: 0.9002 (tmm) REVERT: L 39 CYS cc_start: 0.9238 (p) cc_final: 0.8851 (p) REVERT: L 76 LYS cc_start: 0.9393 (mmmm) cc_final: 0.9077 (mmmm) REVERT: L 83 GLU cc_start: 0.8253 (mp0) cc_final: 0.7971 (mp0) REVERT: L 86 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8903 (tp40) REVERT: L 110 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8829 (tp30) REVERT: L 124 ASP cc_start: 0.8722 (t0) cc_final: 0.8013 (t0) REVERT: M 17 ASN cc_start: 0.9536 (m-40) cc_final: 0.9285 (m-40) REVERT: M 34 GLU cc_start: 0.8858 (tt0) cc_final: 0.8583 (tt0) REVERT: M 70 GLU cc_start: 0.9056 (tp30) cc_final: 0.7997 (tp30) REVERT: M 73 ARG cc_start: 0.9375 (tmm-80) cc_final: 0.9172 (tmm-80) REVERT: M 75 ASP cc_start: 0.8989 (p0) cc_final: 0.8483 (p0) REVERT: M 83 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7589 (pp20) REVERT: M 106 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8654 (mt-10) REVERT: M 112 LYS cc_start: 0.9568 (ttmm) cc_final: 0.9066 (mttp) REVERT: M 116 ARG cc_start: 0.8846 (tpp80) cc_final: 0.8499 (tpp80) REVERT: M 131 ASP cc_start: 0.9005 (t0) cc_final: 0.8654 (t0) REVERT: M 132 ASP cc_start: 0.8798 (m-30) cc_final: 0.8202 (m-30) REVERT: N 89 LYS cc_start: 0.8641 (ptmm) cc_final: 0.7923 (ptmm) REVERT: N 90 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (m) REVERT: N 92 ASP cc_start: 0.7711 (p0) cc_final: 0.7069 (p0) REVERT: N 105 ASP cc_start: 0.9204 (m-30) cc_final: 0.8912 (m-30) REVERT: O 13 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8952 (mt-10) REVERT: O 21 ASP cc_start: 0.7525 (p0) cc_final: 0.7173 (p0) REVERT: O 38 MET cc_start: 0.8923 (tmm) cc_final: 0.8581 (tmm) REVERT: O 39 CYS cc_start: 0.9166 (p) cc_final: 0.8710 (p) REVERT: O 86 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8637 (tp40) REVERT: O 92 ASP cc_start: 0.7149 (t70) cc_final: 0.6639 (t0) REVERT: O 94 THR cc_start: 0.9275 (m) cc_final: 0.8939 (p) REVERT: O 97 MET cc_start: 0.9128 (mmm) cc_final: 0.8830 (mmm) REVERT: O 99 TYR cc_start: 0.8391 (t80) cc_final: 0.8175 (t80) REVERT: O 102 ASP cc_start: 0.9059 (m-30) cc_final: 0.8819 (m-30) REVERT: a 62 ASP cc_start: 0.7947 (t0) cc_final: 0.7630 (t0) REVERT: a 108 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9020 (mm) REVERT: a 112 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8782 (mm-30) REVERT: a 113 ASP cc_start: 0.9169 (t70) cc_final: 0.8785 (t0) REVERT: a 117 ASP cc_start: 0.9451 (m-30) cc_final: 0.9171 (m-30) REVERT: b 1 MET cc_start: 0.8578 (tpt) cc_final: 0.8267 (tpt) REVERT: b 18 ASN cc_start: 0.9358 (t0) cc_final: 0.9020 (t0) REVERT: b 55 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8705 (t) REVERT: b 91 VAL cc_start: 0.9624 (t) cc_final: 0.9378 (p) REVERT: c 3 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8111 (ttp80) REVERT: c 103 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8783 (mm-30) REVERT: d 1 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8415 (tpp) REVERT: d 14 GLN cc_start: 0.9017 (mp10) cc_final: 0.8742 (mp10) REVERT: d 17 ILE cc_start: 0.9359 (pt) cc_final: 0.9157 (mm) REVERT: d 29 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8443 (p) REVERT: d 50 GLU cc_start: 0.7504 (tp30) cc_final: 0.7196 (tp30) REVERT: e 5 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8257 (mtmm) REVERT: e 14 GLN cc_start: 0.8942 (mp10) cc_final: 0.8481 (mm-40) REVERT: e 30 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.6946 (p90) REVERT: f 3 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8124 (ttp-110) REVERT: f 50 GLU cc_start: 0.7894 (tp30) cc_final: 0.7566 (tp30) REVERT: f 86 ASP cc_start: 0.8464 (p0) cc_final: 0.8216 (p0) REVERT: f 113 ASP cc_start: 0.9157 (m-30) cc_final: 0.8628 (p0) REVERT: g 14 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8765 (mm-40) REVERT: g 68 LEU cc_start: 0.9644 (tt) cc_final: 0.9403 (tt) REVERT: h 1 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.5563 (tmm) REVERT: h 50 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7785 (mm-30) REVERT: h 74 LYS cc_start: 0.9417 (mmtp) cc_final: 0.9144 (mmmm) REVERT: i 3 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7664 (ttp-110) REVERT: i 73 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8491 (t0) REVERT: j 48 ASN cc_start: 0.8975 (t0) cc_final: 0.8295 (t0) REVERT: j 50 GLU cc_start: 0.8211 (pm20) cc_final: 0.7767 (pm20) REVERT: l 14 GLN cc_start: 0.9305 (mp10) cc_final: 0.9104 (mm110) REVERT: l 27 ASN cc_start: 0.8830 (m-40) cc_final: 0.8548 (m-40) REVERT: l 123 GLN cc_start: 0.8229 (mp10) cc_final: 0.7741 (tp40) REVERT: m 12 ASP cc_start: 0.7716 (p0) cc_final: 0.6901 (p0) REVERT: m 14 GLN cc_start: 0.9023 (pm20) cc_final: 0.8683 (pm20) REVERT: m 29 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7790 (p) REVERT: m 48 ASN cc_start: 0.9087 (t0) cc_final: 0.8665 (t0) REVERT: n 73 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8064 (p0) REVERT: n 107 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7997 (m) REVERT: n 111 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9204 (pp) REVERT: o 1 MET cc_start: 0.8031 (ttp) cc_final: 0.7464 (tmm) REVERT: o 14 GLN cc_start: 0.9462 (mp10) cc_final: 0.9236 (mp10) REVERT: o 50 GLU cc_start: 0.7808 (tp30) cc_final: 0.7518 (tp30) REVERT: o 54 ASN cc_start: 0.7932 (p0) cc_final: 0.7704 (p0) REVERT: o 65 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.5669 (t80) REVERT: o 77 SER cc_start: 0.9435 (p) cc_final: 0.8906 (p) REVERT: o 79 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (p) REVERT: o 93 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8423 (tmt-80) REVERT: o 103 GLU cc_start: 0.7904 (tp30) cc_final: 0.7499 (tm-30) outliers start: 224 outliers final: 159 residues processed: 1240 average time/residue: 0.2180 time to fit residues: 422.3794 Evaluate side-chains 1221 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1037 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 78 ASN Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 3 ARG Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 70 THR Chi-restraints excluded: chain d residue 90 SER Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 16 TRP Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain i residue 73 ASN Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 162 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 357 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 GLN I 78 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 18 ASN g 48 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 42 HIS ** j 73 ASN ** 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 = 0.3396 r_free = 0.3396 target = 0.067748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054062 restraints weight = 148601.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.055655 restraints weight = 90770.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056777 restraints weight = 63862.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.057566 restraints weight = 49197.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058081 restraints weight = 40529.091| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 31470 Z= 0.155 Angle : 0.843 12.864 42780 Z= 0.434 Chirality : 0.048 0.293 4995 Planarity : 0.005 0.066 5565 Dihedral : 7.041 59.952 4218 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 5.45 % Allowed : 27.66 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 3795 helix: 0.40 (0.13), residues: 1612 sheet: -0.29 (0.20), residues: 613 loop : -2.17 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 136 TYR 0.042 0.002 TYR h 114 PHE 0.026 0.002 PHE A 49 TRP 0.008 0.001 TRP d 16 HIS 0.007 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00345 (31470) covalent geometry : angle 0.84346 (42780) hydrogen bonds : bond 0.03931 ( 1420) hydrogen bonds : angle 5.11361 ( 4086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 1166 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8878 (tp30) cc_final: 0.8411 (tp30) REVERT: A 25 THR cc_start: 0.8602 (p) cc_final: 0.8104 (t) REVERT: A 35 PHE cc_start: 0.9653 (t80) cc_final: 0.9451 (t80) REVERT: A 38 MET cc_start: 0.9257 (tmm) cc_final: 0.8624 (tmm) REVERT: A 39 CYS cc_start: 0.9215 (p) cc_final: 0.8948 (p) REVERT: A 53 LEU cc_start: 0.9318 (mm) cc_final: 0.8971 (mt) REVERT: A 76 LYS cc_start: 0.9410 (tppt) cc_final: 0.9043 (tppt) REVERT: A 112 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9080 (mtmm) REVERT: A 124 ASP cc_start: 0.9220 (t0) cc_final: 0.8873 (t0) REVERT: A 132 ASP cc_start: 0.8555 (m-30) cc_final: 0.7908 (t70) REVERT: B 51 ASN cc_start: 0.9483 (m110) cc_final: 0.9197 (p0) REVERT: B 86 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8685 (tp-100) REVERT: B 106 GLU cc_start: 0.9326 (tp30) cc_final: 0.8794 (tp30) REVERT: B 116 ARG cc_start: 0.9172 (tpp80) cc_final: 0.8756 (tpp80) REVERT: B 124 ASP cc_start: 0.8844 (t0) cc_final: 0.8394 (t0) REVERT: B 131 ASP cc_start: 0.9282 (t0) cc_final: 0.8880 (t0) REVERT: C 13 GLU cc_start: 0.8888 (tp30) cc_final: 0.7794 (tp30) REVERT: C 17 ASN cc_start: 0.9450 (m-40) cc_final: 0.8432 (m-40) REVERT: C 19 PHE cc_start: 0.8782 (m-80) cc_final: 0.8555 (m-80) REVERT: C 30 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: C 38 MET cc_start: 0.9064 (tmm) cc_final: 0.8711 (tmm) REVERT: C 60 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 86 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: C 90 VAL cc_start: 0.9020 (t) cc_final: 0.8767 (p) REVERT: C 102 ASP cc_start: 0.9014 (m-30) cc_final: 0.8726 (m-30) REVERT: C 105 ASP cc_start: 0.9425 (m-30) cc_final: 0.9070 (m-30) REVERT: C 116 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8154 (mmm160) REVERT: C 124 ASP cc_start: 0.7808 (t0) cc_final: 0.7566 (t0) REVERT: C 136 ARG cc_start: 0.8853 (tmt170) cc_final: 0.8418 (tmt170) REVERT: D 21 ASP cc_start: 0.7692 (p0) cc_final: 0.7289 (p0) REVERT: D 34 GLU cc_start: 0.8934 (tt0) cc_final: 0.8653 (tt0) REVERT: D 38 MET cc_start: 0.9312 (tpp) cc_final: 0.9085 (tpp) REVERT: D 44 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8390 (ptm160) REVERT: D 60 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8914 (mm-30) REVERT: D 69 LYS cc_start: 0.9658 (OUTLIER) cc_final: 0.9406 (ttpp) REVERT: D 70 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8637 (tp30) REVERT: D 92 ASP cc_start: 0.9034 (p0) cc_final: 0.8704 (p0) REVERT: D 106 GLU cc_start: 0.8884 (tp30) cc_final: 0.8416 (tp30) REVERT: D 116 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8241 (tpp80) REVERT: D 132 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7255 (t0) REVERT: E 17 ASN cc_start: 0.9498 (m-40) cc_final: 0.9165 (m110) REVERT: E 44 ARG cc_start: 0.8386 (tpt170) cc_final: 0.8109 (tpp80) REVERT: E 92 ASP cc_start: 0.7684 (p0) cc_final: 0.7111 (p0) REVERT: E 105 ASP cc_start: 0.9224 (m-30) cc_final: 0.8951 (m-30) REVERT: F 34 GLU cc_start: 0.9304 (tt0) cc_final: 0.9025 (tt0) REVERT: F 38 MET cc_start: 0.9130 (tmm) cc_final: 0.8795 (tmm) REVERT: F 70 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8525 (mt-10) REVERT: F 86 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8477 (tp40) REVERT: F 110 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8509 (mm-30) REVERT: G 21 ASP cc_start: 0.8480 (p0) cc_final: 0.8021 (p0) REVERT: G 34 GLU cc_start: 0.8837 (tt0) cc_final: 0.8226 (tt0) REVERT: G 70 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8247 (tp30) REVERT: G 92 ASP cc_start: 0.8927 (p0) cc_final: 0.8560 (p0) REVERT: H 21 ASP cc_start: 0.7818 (p0) cc_final: 0.7465 (p0) REVERT: H 44 ARG cc_start: 0.9014 (ptm-80) cc_final: 0.8563 (ttt90) REVERT: H 59 ILE cc_start: 0.9657 (OUTLIER) cc_final: 0.9138 (pt) REVERT: H 102 ASP cc_start: 0.9229 (p0) cc_final: 0.8984 (p0) REVERT: H 105 ASP cc_start: 0.9155 (m-30) cc_final: 0.8866 (m-30) REVERT: I 13 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8820 (mt-10) REVERT: I 17 ASN cc_start: 0.9609 (m-40) cc_final: 0.9390 (m-40) REVERT: I 21 ASP cc_start: 0.8107 (p0) cc_final: 0.7542 (p0) REVERT: I 35 PHE cc_start: 0.9598 (t80) cc_final: 0.8942 (t80) REVERT: I 38 MET cc_start: 0.9213 (tmm) cc_final: 0.8924 (tmm) REVERT: I 39 CYS cc_start: 0.9362 (p) cc_final: 0.8680 (p) REVERT: I 60 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8842 (mt-10) REVERT: I 90 VAL cc_start: 0.9144 (t) cc_final: 0.8774 (t) REVERT: I 91 GLU cc_start: 0.8637 (pp20) cc_final: 0.8065 (pp20) REVERT: I 95 MET cc_start: 0.8900 (mmm) cc_final: 0.8609 (mmm) REVERT: I 99 TYR cc_start: 0.8279 (t80) cc_final: 0.8038 (t80) REVERT: I 116 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8411 (mmp80) REVERT: J 21 ASP cc_start: 0.8595 (p0) cc_final: 0.8108 (p0) REVERT: J 27 GLU cc_start: 0.7260 (mp0) cc_final: 0.6967 (mp0) REVERT: J 60 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8751 (mt-10) REVERT: J 70 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8237 (mm-30) REVERT: J 74 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9210 (mt) REVERT: J 75 ASP cc_start: 0.9173 (t70) cc_final: 0.8849 (t70) REVERT: J 83 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7800 (pp20) REVERT: J 92 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8591 (p0) REVERT: J 116 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8785 (tpp80) REVERT: K 44 ARG cc_start: 0.8800 (tpp80) cc_final: 0.8533 (tpp80) REVERT: K 69 LYS cc_start: 0.9760 (tttp) cc_final: 0.9339 (ttmm) REVERT: K 86 GLN cc_start: 0.9091 (tp40) cc_final: 0.8668 (tp-100) REVERT: K 89 LYS cc_start: 0.9305 (ptmm) cc_final: 0.9101 (ptmm) REVERT: K 92 ASP cc_start: 0.8102 (p0) cc_final: 0.7582 (p0) REVERT: K 105 ASP cc_start: 0.9304 (m-30) cc_final: 0.9024 (m-30) REVERT: L 38 MET cc_start: 0.9246 (tmm) cc_final: 0.9031 (tmm) REVERT: L 39 CYS cc_start: 0.9244 (p) cc_final: 0.8862 (p) REVERT: L 70 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8622 (mt-10) REVERT: L 76 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9074 (mmmm) REVERT: L 83 GLU cc_start: 0.8127 (mp0) cc_final: 0.7876 (mp0) REVERT: L 86 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8937 (tp40) REVERT: L 110 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8746 (tp30) REVERT: M 17 ASN cc_start: 0.9534 (m-40) cc_final: 0.9275 (m110) REVERT: M 34 GLU cc_start: 0.8863 (tt0) cc_final: 0.8599 (tt0) REVERT: M 35 PHE cc_start: 0.9498 (t80) cc_final: 0.9163 (t80) REVERT: M 70 GLU cc_start: 0.9014 (tp30) cc_final: 0.8108 (tp30) REVERT: M 73 ARG cc_start: 0.9347 (tmm-80) cc_final: 0.9052 (tmm-80) REVERT: M 75 ASP cc_start: 0.8837 (p0) cc_final: 0.8623 (p0) REVERT: M 83 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7562 (pp20) REVERT: M 102 ASP cc_start: 0.9209 (m-30) cc_final: 0.8956 (p0) REVERT: M 106 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8586 (mp0) REVERT: M 112 LYS cc_start: 0.9560 (ttmm) cc_final: 0.9053 (mttp) REVERT: M 127 TYR cc_start: 0.8939 (m-80) cc_final: 0.8608 (m-80) REVERT: M 131 ASP cc_start: 0.8994 (t0) cc_final: 0.8666 (t0) REVERT: M 132 ASP cc_start: 0.8722 (m-30) cc_final: 0.8081 (m-30) REVERT: N 28 LEU cc_start: 0.9511 (mm) cc_final: 0.9268 (mm) REVERT: N 39 CYS cc_start: 0.9608 (m) cc_final: 0.9164 (m) REVERT: N 79 LYS cc_start: 0.8848 (mptt) cc_final: 0.8647 (mttp) REVERT: N 89 LYS cc_start: 0.8687 (ptmm) cc_final: 0.7897 (ptmm) REVERT: N 90 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8293 (m) REVERT: N 92 ASP cc_start: 0.7728 (p0) cc_final: 0.7091 (p0) REVERT: N 99 TYR cc_start: 0.8877 (t80) cc_final: 0.8584 (t80) REVERT: N 105 ASP cc_start: 0.9221 (m-30) cc_final: 0.8960 (m-30) REVERT: O 13 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8957 (mt-10) REVERT: O 21 ASP cc_start: 0.7454 (p0) cc_final: 0.7102 (p0) REVERT: O 35 PHE cc_start: 0.9585 (t80) cc_final: 0.8982 (t80) REVERT: O 38 MET cc_start: 0.8822 (tmm) cc_final: 0.8473 (tmm) REVERT: O 39 CYS cc_start: 0.9164 (p) cc_final: 0.8717 (p) REVERT: O 86 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8679 (tp40) REVERT: O 94 THR cc_start: 0.9286 (m) cc_final: 0.9004 (p) REVERT: O 97 MET cc_start: 0.9100 (mmm) cc_final: 0.8771 (mmm) REVERT: O 102 ASP cc_start: 0.8980 (m-30) cc_final: 0.8730 (m-30) REVERT: a 14 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8814 (mm-40) REVERT: a 62 ASP cc_start: 0.7870 (t0) cc_final: 0.7556 (t0) REVERT: a 108 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9181 (mm) REVERT: a 112 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9042 (mm-30) REVERT: a 113 ASP cc_start: 0.9150 (t70) cc_final: 0.8814 (t0) REVERT: a 117 ASP cc_start: 0.9430 (m-30) cc_final: 0.9164 (m-30) REVERT: b 1 MET cc_start: 0.8559 (tpt) cc_final: 0.8253 (tpt) REVERT: b 55 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8704 (t) REVERT: b 91 VAL cc_start: 0.9615 (t) cc_final: 0.9376 (p) REVERT: c 3 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.6819 (ttp80) REVERT: c 103 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8439 (mm-30) REVERT: d 1 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: d 14 GLN cc_start: 0.9005 (mp10) cc_final: 0.8728 (mp10) REVERT: d 17 ILE cc_start: 0.9407 (pt) cc_final: 0.9183 (mm) REVERT: d 29 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8412 (p) REVERT: d 50 GLU cc_start: 0.7468 (tp30) cc_final: 0.7258 (tp30) REVERT: e 5 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8265 (mtmm) REVERT: e 14 GLN cc_start: 0.9028 (mp10) cc_final: 0.8529 (mm-40) REVERT: e 30 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.6839 (p90) REVERT: f 3 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8155 (ttp-110) REVERT: f 50 GLU cc_start: 0.7869 (tp30) cc_final: 0.7509 (tp30) REVERT: f 82 ASP cc_start: 0.8391 (t0) cc_final: 0.8136 (m-30) REVERT: f 86 ASP cc_start: 0.8459 (p0) cc_final: 0.8228 (p0) REVERT: g 14 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8608 (mm-40) REVERT: g 29 THR cc_start: 0.8160 (m) cc_final: 0.7907 (p) REVERT: g 68 LEU cc_start: 0.9628 (tt) cc_final: 0.9360 (tt) REVERT: h 1 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6408 (tmm) REVERT: h 74 LYS cc_start: 0.9419 (mmtp) cc_final: 0.9140 (mmmm) REVERT: i 3 ARG cc_start: 0.8385 (mtp-110) cc_final: 0.7840 (ttp-110) REVERT: i 73 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8520 (t0) REVERT: i 114 TYR cc_start: 0.8899 (t80) cc_final: 0.8507 (t80) REVERT: j 14 GLN cc_start: 0.8886 (mp10) cc_final: 0.8555 (mp10) REVERT: j 18 ASN cc_start: 0.8926 (p0) cc_final: 0.8682 (p0) REVERT: j 44 LYS cc_start: 0.9514 (mmmm) cc_final: 0.9054 (tppt) REVERT: j 47 GLN cc_start: 0.9439 (pp30) cc_final: 0.9186 (pp30) REVERT: j 48 ASN cc_start: 0.8732 (t0) cc_final: 0.8193 (t0) REVERT: j 50 GLU cc_start: 0.8288 (pm20) cc_final: 0.7790 (pm20) REVERT: l 14 GLN cc_start: 0.9286 (mp10) cc_final: 0.9056 (mm110) REVERT: l 27 ASN cc_start: 0.8824 (m-40) cc_final: 0.8528 (m-40) REVERT: l 123 GLN cc_start: 0.8166 (mp10) cc_final: 0.7759 (tp40) REVERT: m 12 ASP cc_start: 0.7703 (p0) cc_final: 0.6975 (p0) REVERT: m 14 GLN cc_start: 0.9029 (pm20) cc_final: 0.8265 (pm20) REVERT: m 29 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7622 (p) REVERT: m 48 ASN cc_start: 0.9112 (t0) cc_final: 0.8648 (t0) REVERT: m 117 ASP cc_start: 0.8071 (p0) cc_final: 0.7830 (p0) REVERT: n 111 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9191 (pp) REVERT: o 1 MET cc_start: 0.8069 (ttp) cc_final: 0.7837 (tmm) REVERT: o 14 GLN cc_start: 0.9459 (mp10) cc_final: 0.9182 (mp10) REVERT: o 54 ASN cc_start: 0.7953 (p0) cc_final: 0.7677 (p0) REVERT: o 65 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.5516 (t80) REVERT: o 77 SER cc_start: 0.9399 (p) cc_final: 0.8844 (p) REVERT: o 79 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8214 (p) REVERT: o 103 GLU cc_start: 0.7912 (tp30) cc_final: 0.7615 (tm-30) outliers start: 192 outliers final: 135 residues processed: 1272 average time/residue: 0.2184 time to fit residues: 433.5109 Evaluate side-chains 1242 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1087 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain I residue 78 ASN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 48 ASN Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 73 ASN Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 47 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 86 ASP Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 21 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 253 optimal weight: 0.0970 chunk 106 optimal weight: 0.9990 chunk 340 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN E 18 GLN F 46 GLN ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 48 ASN i 58 ASN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 HIS n 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052505 restraints weight = 152120.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054076 restraints weight = 93251.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055169 restraints weight = 66058.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055930 restraints weight = 51307.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056484 restraints weight = 42605.711| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31470 Z= 0.184 Angle : 0.877 15.171 42780 Z= 0.452 Chirality : 0.048 0.305 4995 Planarity : 0.005 0.067 5565 Dihedral : 7.010 59.748 4215 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.62 % Favored : 91.28 % Rotamer: Outliers : 5.39 % Allowed : 28.85 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.13), residues: 3795 helix: 0.27 (0.12), residues: 1617 sheet: -0.22 (0.20), residues: 604 loop : -2.17 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 3 TYR 0.046 0.002 TYR h 114 PHE 0.026 0.002 PHE H 49 TRP 0.011 0.001 TRP o 16 HIS 0.008 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00415 (31470) covalent geometry : angle 0.87670 (42780) hydrogen bonds : bond 0.04132 ( 1420) hydrogen bonds : angle 5.19725 ( 4086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1128 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8878 (tp30) cc_final: 0.8401 (tp30) REVERT: A 38 MET cc_start: 0.9278 (tmm) cc_final: 0.8680 (tmm) REVERT: A 53 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8933 (mt) REVERT: A 76 LYS cc_start: 0.9418 (tppt) cc_final: 0.9058 (tppt) REVERT: A 92 ASP cc_start: 0.8716 (p0) cc_final: 0.8270 (p0) REVERT: A 112 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9084 (mtmm) REVERT: A 124 ASP cc_start: 0.9229 (t0) cc_final: 0.8844 (t0) REVERT: A 132 ASP cc_start: 0.8589 (m-30) cc_final: 0.7939 (t70) REVERT: B 51 ASN cc_start: 0.9477 (m110) cc_final: 0.9211 (p0) REVERT: B 86 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8697 (tp-100) REVERT: B 106 GLU cc_start: 0.9360 (tp30) cc_final: 0.8814 (tp30) REVERT: B 116 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8722 (tpp80) REVERT: B 124 ASP cc_start: 0.8907 (t0) cc_final: 0.8429 (t0) REVERT: B 131 ASP cc_start: 0.9302 (t0) cc_final: 0.8866 (t0) REVERT: C 13 GLU cc_start: 0.8953 (tp30) cc_final: 0.7851 (tp30) REVERT: C 17 ASN cc_start: 0.9470 (m-40) cc_final: 0.8525 (m-40) REVERT: C 19 PHE cc_start: 0.8817 (m-80) cc_final: 0.8587 (m-80) REVERT: C 38 MET cc_start: 0.9079 (tmm) cc_final: 0.8679 (tmm) REVERT: C 39 CYS cc_start: 0.9282 (p) cc_final: 0.8751 (p) REVERT: C 60 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8663 (mt-10) REVERT: C 69 LYS cc_start: 0.9386 (tppp) cc_final: 0.9134 (ttmm) REVERT: C 86 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8067 (tp40) REVERT: C 90 VAL cc_start: 0.9018 (t) cc_final: 0.8738 (p) REVERT: C 92 ASP cc_start: 0.8238 (p0) cc_final: 0.8016 (p0) REVERT: C 102 ASP cc_start: 0.9061 (m-30) cc_final: 0.8725 (m-30) REVERT: C 105 ASP cc_start: 0.9433 (m-30) cc_final: 0.9060 (m-30) REVERT: C 108 VAL cc_start: 0.9578 (p) cc_final: 0.9183 (m) REVERT: C 112 LYS cc_start: 0.9627 (mttp) cc_final: 0.9234 (mtmm) REVERT: C 116 ARG cc_start: 0.8559 (mmm160) cc_final: 0.8165 (mmm160) REVERT: D 21 ASP cc_start: 0.7698 (p0) cc_final: 0.7324 (p0) REVERT: D 34 GLU cc_start: 0.8946 (tt0) cc_final: 0.8661 (tt0) REVERT: D 44 ARG cc_start: 0.8859 (ptm160) cc_final: 0.8354 (ptm160) REVERT: D 60 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8937 (mm-30) REVERT: D 69 LYS cc_start: 0.9651 (OUTLIER) cc_final: 0.9395 (ttpp) REVERT: D 70 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8522 (tp30) REVERT: D 92 ASP cc_start: 0.8995 (p0) cc_final: 0.8621 (p0) REVERT: D 106 GLU cc_start: 0.9007 (tp30) cc_final: 0.8582 (tp30) REVERT: D 116 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8270 (tpp80) REVERT: D 132 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7341 (t0) REVERT: E 17 ASN cc_start: 0.9492 (m-40) cc_final: 0.9192 (m110) REVERT: E 44 ARG cc_start: 0.8404 (tpt170) cc_final: 0.8103 (tpp80) REVERT: E 92 ASP cc_start: 0.7706 (p0) cc_final: 0.7144 (p0) REVERT: E 105 ASP cc_start: 0.9225 (m-30) cc_final: 0.8954 (m-30) REVERT: E 124 ASP cc_start: 0.9265 (t0) cc_final: 0.8753 (t0) REVERT: F 38 MET cc_start: 0.9124 (tmm) cc_final: 0.8745 (tmm) REVERT: F 70 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8536 (mt-10) REVERT: F 86 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8543 (tp40) REVERT: F 110 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8516 (mm-30) REVERT: F 116 ARG cc_start: 0.8469 (mmp80) cc_final: 0.8239 (mmp80) REVERT: F 124 ASP cc_start: 0.8316 (t70) cc_final: 0.7971 (t70) REVERT: G 21 ASP cc_start: 0.8480 (p0) cc_final: 0.8074 (p0) REVERT: G 34 GLU cc_start: 0.8855 (tt0) cc_final: 0.8345 (tt0) REVERT: G 60 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8889 (mt-10) REVERT: G 70 GLU cc_start: 0.8778 (mm-30) cc_final: 0.7973 (tp30) REVERT: G 86 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8871 (mm-40) REVERT: G 92 ASP cc_start: 0.8872 (p0) cc_final: 0.8494 (p0) REVERT: G 116 ARG cc_start: 0.8807 (tpp80) cc_final: 0.8577 (tpp80) REVERT: H 21 ASP cc_start: 0.7794 (p0) cc_final: 0.7442 (p0) REVERT: H 44 ARG cc_start: 0.9081 (ptm-80) cc_final: 0.8631 (ttt90) REVERT: H 59 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9229 (pt) REVERT: H 89 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8518 (mmmm) REVERT: H 92 ASP cc_start: 0.8301 (p0) cc_final: 0.7557 (p0) REVERT: H 102 ASP cc_start: 0.9205 (p0) cc_final: 0.8937 (p0) REVERT: H 105 ASP cc_start: 0.9112 (m-30) cc_final: 0.8814 (m-30) REVERT: H 116 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8496 (tpp80) REVERT: I 13 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8772 (mt-10) REVERT: I 17 ASN cc_start: 0.9617 (m-40) cc_final: 0.9354 (m-40) REVERT: I 21 ASP cc_start: 0.8125 (p0) cc_final: 0.7594 (p0) REVERT: I 35 PHE cc_start: 0.9602 (t80) cc_final: 0.8915 (t80) REVERT: I 38 MET cc_start: 0.9217 (tmm) cc_final: 0.8885 (tmm) REVERT: I 39 CYS cc_start: 0.9369 (p) cc_final: 0.8674 (p) REVERT: I 60 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8798 (mt-10) REVERT: I 76 LYS cc_start: 0.9469 (mmmm) cc_final: 0.9225 (mmmm) REVERT: I 90 VAL cc_start: 0.9140 (t) cc_final: 0.8707 (t) REVERT: I 91 GLU cc_start: 0.8697 (pp20) cc_final: 0.8121 (pp20) REVERT: I 95 MET cc_start: 0.8833 (mmm) cc_final: 0.8593 (mmm) REVERT: I 99 TYR cc_start: 0.8499 (t80) cc_final: 0.8200 (t80) REVERT: I 116 ARG cc_start: 0.8675 (mmm160) cc_final: 0.8378 (mmp80) REVERT: J 21 ASP cc_start: 0.8583 (p0) cc_final: 0.8052 (p0) REVERT: J 27 GLU cc_start: 0.7312 (mp0) cc_final: 0.7010 (mp0) REVERT: J 29 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8313 (tm-30) REVERT: J 30 GLU cc_start: 0.8893 (pm20) cc_final: 0.8556 (pm20) REVERT: J 60 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8774 (mt-10) REVERT: J 83 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7787 (pp20) REVERT: J 92 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8569 (p0) REVERT: J 116 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8745 (tpp80) REVERT: K 44 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8617 (tpp80) REVERT: K 69 LYS cc_start: 0.9766 (tttp) cc_final: 0.9360 (ttmm) REVERT: K 86 GLN cc_start: 0.9105 (tp40) cc_final: 0.8710 (tp-100) REVERT: K 105 ASP cc_start: 0.9294 (m-30) cc_final: 0.9007 (m-30) REVERT: K 116 ARG cc_start: 0.9228 (mmp80) cc_final: 0.8730 (tpp80) REVERT: L 38 MET cc_start: 0.9226 (tmm) cc_final: 0.9008 (tmm) REVERT: L 39 CYS cc_start: 0.9271 (p) cc_final: 0.8861 (p) REVERT: L 70 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8680 (mt-10) REVERT: L 75 ASP cc_start: 0.9136 (t0) cc_final: 0.8574 (t0) REVERT: L 76 LYS cc_start: 0.9426 (mmmm) cc_final: 0.9197 (mmtt) REVERT: L 83 GLU cc_start: 0.8180 (mp0) cc_final: 0.7689 (mp0) REVERT: L 86 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8957 (tp40) REVERT: L 110 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8810 (tp30) REVERT: M 17 ASN cc_start: 0.9561 (m-40) cc_final: 0.9303 (m110) REVERT: M 34 GLU cc_start: 0.8894 (tt0) cc_final: 0.8633 (tt0) REVERT: M 49 PHE cc_start: 0.9421 (t80) cc_final: 0.9164 (t80) REVERT: M 70 GLU cc_start: 0.8948 (tp30) cc_final: 0.8137 (tp30) REVERT: M 73 ARG cc_start: 0.9355 (tmm-80) cc_final: 0.8357 (ttp80) REVERT: M 75 ASP cc_start: 0.8820 (p0) cc_final: 0.8358 (p0) REVERT: M 83 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7520 (pp20) REVERT: M 106 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8655 (mt-10) REVERT: M 112 LYS cc_start: 0.9585 (ttmm) cc_final: 0.9080 (mttp) REVERT: M 116 ARG cc_start: 0.8737 (tpp80) cc_final: 0.8531 (tpp80) REVERT: M 127 TYR cc_start: 0.9001 (m-80) cc_final: 0.8656 (m-80) REVERT: M 131 ASP cc_start: 0.9015 (t0) cc_final: 0.8683 (t0) REVERT: M 132 ASP cc_start: 0.8769 (m-30) cc_final: 0.8196 (m-30) REVERT: N 39 CYS cc_start: 0.9605 (m) cc_final: 0.9153 (m) REVERT: N 92 ASP cc_start: 0.7616 (p0) cc_final: 0.7107 (p0) REVERT: N 99 TYR cc_start: 0.8792 (t80) cc_final: 0.8479 (t80) REVERT: N 105 ASP cc_start: 0.9222 (m-30) cc_final: 0.8927 (m-30) REVERT: O 21 ASP cc_start: 0.7508 (p0) cc_final: 0.7161 (p0) REVERT: O 34 GLU cc_start: 0.9337 (tt0) cc_final: 0.9000 (tt0) REVERT: O 35 PHE cc_start: 0.9611 (t80) cc_final: 0.8969 (t80) REVERT: O 38 MET cc_start: 0.8843 (tmm) cc_final: 0.8487 (tmm) REVERT: O 39 CYS cc_start: 0.9118 (p) cc_final: 0.8678 (p) REVERT: O 86 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8705 (tp40) REVERT: O 94 THR cc_start: 0.9279 (m) cc_final: 0.9061 (p) REVERT: O 97 MET cc_start: 0.9107 (mmm) cc_final: 0.8813 (mmm) REVERT: O 102 ASP cc_start: 0.8954 (m-30) cc_final: 0.8726 (m-30) REVERT: a 62 ASP cc_start: 0.8012 (t0) cc_final: 0.7697 (t0) REVERT: a 75 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7874 (mmmt) REVERT: a 108 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9211 (mm) REVERT: a 112 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9059 (mm-30) REVERT: a 113 ASP cc_start: 0.9167 (t70) cc_final: 0.8831 (t0) REVERT: a 117 ASP cc_start: 0.9440 (m-30) cc_final: 0.9183 (m-30) REVERT: b 1 MET cc_start: 0.8652 (tpt) cc_final: 0.8330 (tpt) REVERT: b 55 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8736 (t) REVERT: b 91 VAL cc_start: 0.9629 (t) cc_final: 0.9390 (p) REVERT: c 3 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8094 (ttp80) REVERT: c 5 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8015 (pttm) REVERT: c 50 GLU cc_start: 0.7946 (tp30) cc_final: 0.7404 (tp30) REVERT: c 103 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8329 (mm-30) REVERT: c 109 ASN cc_start: 0.9123 (m-40) cc_final: 0.8827 (m110) REVERT: d 1 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8527 (tpp) REVERT: d 14 GLN cc_start: 0.9040 (mp10) cc_final: 0.8786 (mp10) REVERT: d 17 ILE cc_start: 0.9405 (pt) cc_final: 0.9186 (mm) REVERT: d 29 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8482 (p) REVERT: e 14 GLN cc_start: 0.9034 (mp10) cc_final: 0.8528 (mm-40) REVERT: e 30 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.6741 (p90) REVERT: e 77 SER cc_start: 0.9259 (m) cc_final: 0.8694 (t) REVERT: f 3 ARG cc_start: 0.8646 (mtp-110) cc_final: 0.8159 (ttp-110) REVERT: f 50 GLU cc_start: 0.7957 (tp30) cc_final: 0.7632 (tp30) REVERT: f 82 ASP cc_start: 0.8453 (t0) cc_final: 0.8196 (m-30) REVERT: f 86 ASP cc_start: 0.8517 (p0) cc_final: 0.8272 (p0) REVERT: g 14 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8729 (mm-40) REVERT: g 50 GLU cc_start: 0.8547 (pm20) cc_final: 0.8089 (pm20) REVERT: g 68 LEU cc_start: 0.9641 (tt) cc_final: 0.9386 (tt) REVERT: h 1 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6285 (tmm) REVERT: h 3 ARG cc_start: 0.8608 (mtp180) cc_final: 0.8329 (ttp-110) REVERT: h 74 LYS cc_start: 0.9448 (mmtp) cc_final: 0.9181 (mmmm) REVERT: i 3 ARG cc_start: 0.8338 (mtp-110) cc_final: 0.7734 (ttp-110) REVERT: i 73 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8507 (t0) REVERT: i 114 TYR cc_start: 0.8951 (t80) cc_final: 0.8588 (t80) REVERT: j 14 GLN cc_start: 0.8882 (mp10) cc_final: 0.8501 (mp10) REVERT: j 18 ASN cc_start: 0.9034 (p0) cc_final: 0.8813 (p0) REVERT: j 44 LYS cc_start: 0.9537 (mmmm) cc_final: 0.9005 (tppt) REVERT: j 47 GLN cc_start: 0.9453 (pp30) cc_final: 0.9147 (pp30) REVERT: j 48 ASN cc_start: 0.8770 (t0) cc_final: 0.8277 (t0) REVERT: j 50 GLU cc_start: 0.8151 (pm20) cc_final: 0.7630 (pm20) REVERT: l 14 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9092 (mm110) REVERT: l 27 ASN cc_start: 0.8857 (m-40) cc_final: 0.8624 (m-40) REVERT: l 123 GLN cc_start: 0.8166 (mp10) cc_final: 0.7863 (tp40) REVERT: m 12 ASP cc_start: 0.7698 (p0) cc_final: 0.7005 (p0) REVERT: m 13 ASP cc_start: 0.7952 (m-30) cc_final: 0.7741 (m-30) REVERT: m 14 GLN cc_start: 0.8953 (pm20) cc_final: 0.8145 (pm20) REVERT: m 29 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7779 (p) REVERT: m 48 ASN cc_start: 0.9164 (t0) cc_final: 0.8697 (t0) REVERT: m 117 ASP cc_start: 0.8135 (p0) cc_final: 0.7871 (p0) REVERT: n 107 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7920 (m) REVERT: n 111 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9172 (pp) REVERT: o 14 GLN cc_start: 0.9465 (mp10) cc_final: 0.9205 (mp10) REVERT: o 54 ASN cc_start: 0.7990 (p0) cc_final: 0.7695 (p0) REVERT: o 65 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.5605 (t80) REVERT: o 77 SER cc_start: 0.9425 (p) cc_final: 0.8896 (p) REVERT: o 93 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8396 (tmt-80) REVERT: o 103 GLU cc_start: 0.7939 (tp30) cc_final: 0.7674 (tm-30) outliers start: 190 outliers final: 139 residues processed: 1233 average time/residue: 0.2179 time to fit residues: 419.8208 Evaluate side-chains 1220 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1060 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 113 ASP Chi-restraints excluded: chain c residue 3 ARG Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 106 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 94 GLU Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 73 ASN Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 114 TYR Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 14 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 86 ASP Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 111 LEU Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 320 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 chunk 156 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 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 = 0.3374 r_free = 0.3374 target = 0.066776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.052646 restraints weight = 152900.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054204 restraints weight = 93746.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055292 restraints weight = 66611.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056057 restraints weight = 51888.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.056603 restraints weight = 43278.695| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 31470 Z= 0.181 Angle : 0.902 16.869 42780 Z= 0.466 Chirality : 0.049 0.395 4995 Planarity : 0.005 0.068 5565 Dihedral : 7.053 59.800 4213 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 4.74 % Allowed : 29.84 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 3795 helix: 0.21 (0.12), residues: 1617 sheet: -0.22 (0.20), residues: 605 loop : -2.18 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 3 TYR 0.047 0.002 TYR h 114 PHE 0.025 0.002 PHE H 49 TRP 0.010 0.001 TRP a 16 HIS 0.007 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00411 (31470) covalent geometry : angle 0.90202 (42780) hydrogen bonds : bond 0.04130 ( 1420) hydrogen bonds : angle 5.23269 ( 4086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7590 Ramachandran restraints generated. 3795 Oldfield, 0 Emsley, 3795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1124 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 13 GLU cc_start: 0.8868 (tp30) cc_final: 0.8411 (tp30) REVERT: A 38 MET cc_start: 0.9266 (tmm) cc_final: 0.8686 (tmm) REVERT: A 46 GLN cc_start: 0.8787 (pt0) cc_final: 0.8520 (pt0) REVERT: A 53 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8930 (mt) REVERT: A 76 LYS cc_start: 0.9423 (tppt) cc_final: 0.9008 (tppt) REVERT: A 92 ASP cc_start: 0.8828 (p0) cc_final: 0.8468 (p0) REVERT: A 124 ASP cc_start: 0.9207 (t0) cc_final: 0.9003 (t0) REVERT: A 132 ASP cc_start: 0.8618 (m-30) cc_final: 0.7965 (t70) REVERT: B 51 ASN cc_start: 0.9489 (m110) cc_final: 0.9252 (p0) REVERT: B 86 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8764 (tp-100) REVERT: B 89 LYS cc_start: 0.8981 (tppt) cc_final: 0.8627 (mmmt) REVERT: B 95 MET cc_start: 0.8641 (mmm) cc_final: 0.8399 (mmm) REVERT: B 124 ASP cc_start: 0.8910 (t0) cc_final: 0.8524 (t0) REVERT: B 131 ASP cc_start: 0.9296 (t0) cc_final: 0.8872 (t0) REVERT: C 13 GLU cc_start: 0.8953 (tp30) cc_final: 0.7832 (tp30) REVERT: C 17 ASN cc_start: 0.9473 (m-40) cc_final: 0.8500 (m-40) REVERT: C 19 PHE cc_start: 0.8779 (m-80) cc_final: 0.8573 (m-80) REVERT: C 38 MET cc_start: 0.9059 (tmm) cc_final: 0.8691 (tmm) REVERT: C 60 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8664 (mt-10) REVERT: C 83 GLU cc_start: 0.7851 (mp0) cc_final: 0.7507 (mp0) REVERT: C 86 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8071 (tp40) REVERT: C 90 VAL cc_start: 0.8979 (t) cc_final: 0.8721 (p) REVERT: C 102 ASP cc_start: 0.9017 (m-30) cc_final: 0.8679 (m-30) REVERT: C 105 ASP cc_start: 0.9427 (m-30) cc_final: 0.9059 (m-30) REVERT: C 108 VAL cc_start: 0.9589 (p) cc_final: 0.9159 (m) REVERT: C 109 THR cc_start: 0.9481 (p) cc_final: 0.9244 (p) REVERT: C 112 LYS cc_start: 0.9602 (mttp) cc_final: 0.9188 (mtmm) REVERT: C 116 ARG cc_start: 0.8552 (mmm160) cc_final: 0.8176 (mmm160) REVERT: C 128 VAL cc_start: 0.8928 (p) cc_final: 0.8440 (m) REVERT: D 21 ASP cc_start: 0.7691 (p0) cc_final: 0.7203 (p0) REVERT: D 44 ARG cc_start: 0.8926 (ptm160) cc_final: 0.8430 (ptm160) REVERT: D 60 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8938 (mm-30) REVERT: D 69 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9374 (ttpp) REVERT: D 74 LEU cc_start: 0.9802 (OUTLIER) cc_final: 0.9482 (mt) REVERT: D 92 ASP cc_start: 0.9021 (p0) cc_final: 0.8708 (p0) REVERT: D 106 GLU cc_start: 0.9024 (tp30) cc_final: 0.8580 (tp30) REVERT: D 132 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7253 (t0) REVERT: E 17 ASN cc_start: 0.9480 (m-40) cc_final: 0.9261 (m-40) REVERT: E 44 ARG cc_start: 0.8409 (tpt170) cc_final: 0.8104 (tpp80) REVERT: E 92 ASP cc_start: 0.7767 (p0) cc_final: 0.7168 (t70) REVERT: E 124 ASP cc_start: 0.9246 (t0) cc_final: 0.8748 (t0) REVERT: F 38 MET cc_start: 0.9125 (tmm) cc_final: 0.8763 (tmm) REVERT: F 70 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8514 (mt-10) REVERT: F 86 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8524 (tp40) REVERT: F 110 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8554 (mm-30) REVERT: F 116 ARG cc_start: 0.8476 (mmp80) cc_final: 0.8247 (mmp80) REVERT: F 124 ASP cc_start: 0.8338 (t70) cc_final: 0.8008 (t70) REVERT: G 21 ASP cc_start: 0.8529 (p0) cc_final: 0.8039 (p0) REVERT: G 34 GLU cc_start: 0.8866 (tt0) cc_final: 0.8363 (tt0) REVERT: G 60 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8868 (mt-10) REVERT: G 70 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8137 (tp30) REVERT: G 92 ASP cc_start: 0.8852 (p0) cc_final: 0.8449 (p0) REVERT: G 116 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8601 (tpp80) REVERT: H 21 ASP cc_start: 0.7910 (p0) cc_final: 0.7534 (p0) REVERT: H 44 ARG cc_start: 0.9112 (ptm-80) cc_final: 0.8601 (ttt90) REVERT: H 59 ILE cc_start: 0.9634 (OUTLIER) cc_final: 0.9189 (pt) REVERT: H 89 LYS cc_start: 0.8904 (mmmm) cc_final: 0.8639 (mmmm) REVERT: H 92 ASP cc_start: 0.8250 (p0) cc_final: 0.7428 (p0) REVERT: H 102 ASP cc_start: 0.9187 (p0) cc_final: 0.8896 (p0) REVERT: H 105 ASP cc_start: 0.9098 (m-30) cc_final: 0.8814 (m-30) REVERT: I 21 ASP cc_start: 0.8112 (p0) cc_final: 0.7511 (p0) REVERT: I 35 PHE cc_start: 0.9597 (t80) cc_final: 0.9119 (t80) REVERT: I 38 MET cc_start: 0.9217 (tmm) cc_final: 0.8968 (tmm) REVERT: I 39 CYS cc_start: 0.9337 (p) cc_final: 0.8746 (p) REVERT: I 90 VAL cc_start: 0.9097 (t) cc_final: 0.8736 (p) REVERT: I 91 GLU cc_start: 0.8531 (pp20) cc_final: 0.8115 (pp20) REVERT: I 95 MET cc_start: 0.8848 (mmm) cc_final: 0.8633 (mmm) REVERT: I 99 TYR cc_start: 0.8622 (t80) cc_final: 0.8303 (t80) REVERT: J 21 ASP cc_start: 0.8538 (p0) cc_final: 0.7961 (p0) REVERT: J 27 GLU cc_start: 0.7292 (mp0) cc_final: 0.6963 (mp0) REVERT: J 30 GLU cc_start: 0.8826 (pm20) cc_final: 0.8550 (pm20) REVERT: J 34 GLU cc_start: 0.9024 (tt0) cc_final: 0.8508 (tt0) REVERT: J 60 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8784 (mt-10) REVERT: J 69 LYS cc_start: 0.9613 (OUTLIER) cc_final: 0.9400 (ttpp) REVERT: J 70 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8361 (tp30) REVERT: J 83 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7722 (pp20) REVERT: J 92 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8474 (p0) REVERT: K 44 ARG cc_start: 0.8837 (tpp80) cc_final: 0.8604 (tpp80) REVERT: K 86 GLN cc_start: 0.9063 (tp40) cc_final: 0.8672 (tp-100) REVERT: K 102 ASP cc_start: 0.9225 (p0) cc_final: 0.8900 (p0) REVERT: K 105 ASP cc_start: 0.9275 (m-30) cc_final: 0.8892 (m-30) REVERT: K 116 ARG cc_start: 0.9221 (mmp80) cc_final: 0.8717 (tpp80) REVERT: L 38 MET cc_start: 0.9239 (tmm) cc_final: 0.9018 (tmm) REVERT: L 39 CYS cc_start: 0.9281 (p) cc_final: 0.8858 (p) REVERT: L 75 ASP cc_start: 0.9072 (t0) cc_final: 0.8470 (t0) REVERT: L 76 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9209 (mmtt) REVERT: L 83 GLU cc_start: 0.8165 (mp0) cc_final: 0.7727 (mp0) REVERT: L 86 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8930 (tp40) REVERT: L 110 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8797 (tp30) REVERT: M 17 ASN cc_start: 0.9564 (m-40) cc_final: 0.9301 (m110) REVERT: M 34 GLU cc_start: 0.8905 (tt0) cc_final: 0.8634 (tt0) REVERT: M 70 GLU cc_start: 0.8937 (tp30) cc_final: 0.8139 (tp30) REVERT: M 73 ARG cc_start: 0.9342 (tmm-80) cc_final: 0.8359 (ttp80) REVERT: M 83 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7428 (pp20) REVERT: M 106 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8645 (mt-10) REVERT: M 112 LYS cc_start: 0.9588 (ttmm) cc_final: 0.9084 (mttp) REVERT: M 131 ASP cc_start: 0.9073 (t0) cc_final: 0.8740 (t0) REVERT: M 132 ASP cc_start: 0.8759 (m-30) cc_final: 0.8186 (m-30) REVERT: N 39 CYS cc_start: 0.9626 (m) cc_final: 0.9169 (m) REVERT: N 44 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8207 (tpp80) REVERT: N 89 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8596 (ptmm) REVERT: N 92 ASP cc_start: 0.7614 (p0) cc_final: 0.6970 (p0) REVERT: N 105 ASP cc_start: 0.9217 (m-30) cc_final: 0.8922 (m-30) REVERT: O 21 ASP cc_start: 0.7473 (p0) cc_final: 0.7132 (p0) REVERT: O 35 PHE cc_start: 0.9604 (t80) cc_final: 0.8860 (t80) REVERT: O 38 MET cc_start: 0.8856 (tmm) cc_final: 0.8503 (tmm) REVERT: O 39 CYS cc_start: 0.9153 (p) cc_final: 0.8675 (p) REVERT: O 86 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8597 (tp40) REVERT: O 90 VAL cc_start: 0.8966 (t) cc_final: 0.8547 (t) REVERT: O 97 MET cc_start: 0.9104 (mmm) cc_final: 0.8796 (mmm) REVERT: O 102 ASP cc_start: 0.8935 (m-30) cc_final: 0.8701 (m-30) REVERT: a 1 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8701 (tmm) REVERT: a 62 ASP cc_start: 0.8072 (t0) cc_final: 0.7744 (t0) REVERT: a 108 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9206 (mm) REVERT: a 112 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9108 (mm-30) REVERT: a 113 ASP cc_start: 0.9175 (t70) cc_final: 0.8858 (t0) REVERT: a 117 ASP cc_start: 0.9459 (m-30) cc_final: 0.9203 (m-30) REVERT: b 1 MET cc_start: 0.8685 (tpt) cc_final: 0.8318 (tpt) REVERT: b 55 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8766 (t) REVERT: b 91 VAL cc_start: 0.9632 (t) cc_final: 0.9401 (p) REVERT: c 3 ARG cc_start: 0.8488 (ttp-110) cc_final: 0.8014 (ttp80) REVERT: c 5 LYS cc_start: 0.8782 (mtmm) cc_final: 0.7781 (pttm) REVERT: c 46 ASP cc_start: 0.7809 (p0) cc_final: 0.7562 (p0) REVERT: c 50 GLU cc_start: 0.7980 (tp30) cc_final: 0.7497 (tp30) REVERT: c 103 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8325 (mm-30) REVERT: c 109 ASN cc_start: 0.9067 (m-40) cc_final: 0.8639 (m110) REVERT: d 14 GLN cc_start: 0.9020 (mp10) cc_final: 0.8679 (mp10) REVERT: d 17 ILE cc_start: 0.9427 (pt) cc_final: 0.9208 (mm) REVERT: d 29 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8538 (p) REVERT: d 50 GLU cc_start: 0.7369 (tp30) cc_final: 0.7072 (tp30) REVERT: e 14 GLN cc_start: 0.9054 (mp10) cc_final: 0.8550 (mm-40) REVERT: e 30 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.6701 (p90) REVERT: e 77 SER cc_start: 0.9249 (m) cc_final: 0.8664 (t) REVERT: f 3 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8199 (ttp-110) REVERT: f 82 ASP cc_start: 0.8483 (t0) cc_final: 0.8226 (m-30) REVERT: g 14 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8699 (mm-40) REVERT: g 68 LEU cc_start: 0.9652 (tt) cc_final: 0.9390 (tt) REVERT: h 1 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6233 (tmm) REVERT: h 3 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8303 (ttp-110) REVERT: h 74 LYS cc_start: 0.9459 (mmtp) cc_final: 0.9208 (mmmm) REVERT: i 5 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8684 (mmmt) REVERT: i 73 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8500 (t0) REVERT: i 74 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7875 (tptp) REVERT: i 114 TYR cc_start: 0.8986 (t80) cc_final: 0.8643 (t80) REVERT: j 14 GLN cc_start: 0.8951 (mp10) cc_final: 0.8567 (mp10) REVERT: j 44 LYS cc_start: 0.9567 (mmmm) cc_final: 0.8946 (tppt) REVERT: j 47 GLN cc_start: 0.9443 (pp30) cc_final: 0.9162 (pp30) REVERT: j 48 ASN cc_start: 0.8898 (t0) cc_final: 0.8452 (t0) REVERT: j 50 GLU cc_start: 0.8135 (pm20) cc_final: 0.7618 (pm20) REVERT: j 112 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8793 (tm-30) REVERT: l 14 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9031 (mm110) REVERT: l 27 ASN cc_start: 0.8817 (m-40) cc_final: 0.8529 (m-40) REVERT: l 123 GLN cc_start: 0.8213 (mp10) cc_final: 0.7973 (tp40) REVERT: m 12 ASP cc_start: 0.7776 (p0) cc_final: 0.7146 (p0) REVERT: m 13 ASP cc_start: 0.7798 (m-30) cc_final: 0.7588 (m-30) REVERT: m 14 GLN cc_start: 0.8952 (pm20) cc_final: 0.8172 (pm20) REVERT: m 29 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7873 (p) REVERT: m 48 ASN cc_start: 0.9195 (t0) cc_final: 0.8705 (t0) REVERT: m 117 ASP cc_start: 0.8256 (p0) cc_final: 0.7981 (p0) REVERT: n 111 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9233 (pp) REVERT: o 14 GLN cc_start: 0.9444 (mp10) cc_final: 0.9184 (mp10) REVERT: o 54 ASN cc_start: 0.8036 (p0) cc_final: 0.7555 (p0) REVERT: o 65 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5790 (t80) REVERT: o 77 SER cc_start: 0.9377 (p) cc_final: 0.8926 (p) REVERT: o 82 ASP cc_start: 0.8322 (m-30) cc_final: 0.7097 (p0) REVERT: o 103 GLU cc_start: 0.8023 (tp30) cc_final: 0.7750 (tm-30) outliers start: 167 outliers final: 131 residues processed: 1214 average time/residue: 0.2182 time to fit residues: 414.0311 Evaluate side-chains 1237 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1086 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 46 GLN Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 ILE Chi-restraints excluded: chain c residue 106 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU Chi-restraints excluded: chain g residue 86 ASP Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 65 TYR Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 73 ASN Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 114 TYR Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 87 ILE Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain l residue 14 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 86 ASP Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 36 TYR Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 84 THR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 250 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 356 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 chunk 64 optimal weight: 30.0000 chunk 211 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 GLN ** N 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 109 ASN ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 ASN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.067584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054148 restraints weight = 148684.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055788 restraints weight = 89287.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.056935 restraints weight = 61824.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.057728 restraints weight = 46966.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058297 restraints weight = 38376.377| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31470 Z= 0.169 Angle : 0.918 14.047 42780 Z= 0.473 Chirality : 0.050 0.372 4995 Planarity : 0.005 0.069 5565 Dihedral : 6.961 59.422 4210 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.48 % Favored : 91.41 % Rotamer: Outliers : 4.51 % Allowed : 30.70 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.13), residues: 3795 helix: 0.21 (0.12), residues: 1617 sheet: -0.05 (0.21), residues: 603 loop : -2.17 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 136 TYR 0.047 0.002 TYR h 114 PHE 0.024 0.002 PHE H 49 TRP 0.009 0.001 TRP a 16 HIS 0.007 0.001 HIS b 42 Details of bonding type rmsd covalent geometry : bond 0.00380 (31470) covalent geometry : angle 0.91807 (42780) hydrogen bonds : bond 0.04158 ( 1420) hydrogen bonds : angle 5.21391 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8244.62 seconds wall clock time: 143 minutes 4.65 seconds (8584.65 seconds total)