Starting phenix.real_space_refine on Thu Jun 26 15:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8keg_37155/06_2025/8keg_37155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8keg_37155/06_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_37155/06_2025/8keg_37155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8keg_37155/06_2025/8keg_37155.map" model { file = "/net/cci-nas-00/data/ceres_data/8keg_37155/06_2025/8keg_37155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8keg_37155/06_2025/8keg_37155_neut.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.26, per 1000 atoms: 0.62 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: 9.14 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 3.53 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: 9.61 Time building geometry restraints manager: 10.56 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: 0.01 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: 2.220 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: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.210 Set scattering table: 0.320 Process input model: 68.680 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.230 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.310 ------------------------------------------------------------------------------- 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 : 21.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP o 16 HIS 0.006 0.001 HIS o 10 PHE 0.009 0.001 PHE I 42 TYR 0.012 0.001 TYR n 104 ARG 0.004 0.001 ARG M 65 Details of bonding type rmsd hydrogen bonds : bond 0.13310 ( 1420) hydrogen bonds : angle 6.33352 ( 4086) covalent geometry : bond 0.00316 (31470) covalent geometry : angle 0.88681 (42780) *********************** 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 : 4.013 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: 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: 0.8671 (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: 0.6913 (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: 0.7793 (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: 0.8974 (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: 0.8010 (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: 0.8491 (tmm) REVERT: I 39 CYS cc_start: 0.9169 (p) cc_final: 0.8561 (p) REVERT: I 83 GLU cc_start: 0.7512 (mp0) cc_final: 0.7309 (mp0) REVERT: I 86 GLN cc_start: 0.8710 (tp40) cc_final: 0.8480 (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: 0.8865 (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: 0.7658 (t) REVERT: J 60 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8363 (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: 0.9063 (ptmm) REVERT: J 80 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7752 (mt-10) REVERT: J 83 GLU cc_start: 0.7839 (pp20) cc_final: 0.7634 (tm-30) REVERT: J 92 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8371 (p0) REVERT: K 15 TYR cc_start: 0.9002 (t80) cc_final: 0.8701 (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: 0.8050 (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: 0.9335 (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: 0.8761 (mt-10) REVERT: L 83 GLU cc_start: 0.8212 (mp0) cc_final: 0.7989 (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: 0.8670 (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: 0.8870 (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: 0.8962 (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: 0.7601 (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: 0.8659 (t0) REVERT: d 48 ASN cc_start: 0.9041 (t0) cc_final: 0.8742 (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: 0.5572 (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: 0.8486 (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: 0.8309 (t0) REVERT: m 50 GLU cc_start: 0.7848 (pm20) cc_final: 0.7270 (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: 0.8453 (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: 0.4557 time to fit residues: 988.7755 Evaluate side-chains 1137 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1025 time to evaluate : 3.828 ------------------------------------------------------------------------------- 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 316 optimal weight: 8.9990 chunk 284 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 293 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 340 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 98 ASN C 86 GLN F 51 ASN F 86 GLN G 47 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 HIS N 17 ASN N 140 ASN O 17 ASN O 78 ASN a 10 HIS a 18 ASN a 58 ASN ** 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 f 73 ASN g 121 ASN h 31 ASN 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 j 73 ASN k 18 ASN m 18 ASN m 76 HIS 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 = 0.3536 r_free = 0.3536 target = 0.073586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059393 restraints weight = 147154.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.061020 restraints weight = 92719.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.062167 restraints weight = 66215.906| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31470 Z= 0.175 Angle : 0.777 10.106 42780 Z= 0.406 Chirality : 0.048 0.256 4995 Planarity : 0.005 0.067 5565 Dihedral : 8.806 98.803 4390 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.41 % Favored : 91.46 % Rotamer: Outliers : 5.30 % Allowed : 17.76 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3795 helix: 0.86 (0.13), residues: 1596 sheet: -0.80 (0.20), residues: 603 loop : -2.19 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP o 16 HIS 0.017 0.002 HIS b 42 PHE 0.026 0.002 PHE I 19 TYR 0.029 0.002 TYR f 36 ARG 0.015 0.001 ARG l 9 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 1420) hydrogen bonds : angle 5.48344 ( 4086) covalent geometry : bond 0.00389 (31470) covalent geometry : angle 0.77678 (42780) *********************** 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 1404 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 1217 time to evaluate : 3.929 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: 0.8946 (tp30) cc_final: 0.8491 (tp30) REVERT: A 17 ASN cc_start: 0.8904 (m110) cc_final: 0.8189 (m110) REVERT: A 35 PHE cc_start: 0.9665 (t80) cc_final: 0.9066 (t80) REVERT: A 38 MET cc_start: 0.9237 (tmm) cc_final: 0.8608 (tmm) REVERT: A 39 CYS cc_start: 0.8951 (p) cc_final: 0.8658 (p) REVERT: A 92 ASP cc_start: 0.8316 (p0) cc_final: 0.7934 (p0) REVERT: A 109 THR cc_start: 0.9648 (p) cc_final: 0.9281 (p) REVERT: A 112 LYS cc_start: 0.9406 (mttm) cc_final: 0.9170 (mmtm) REVERT: A 116 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7975 (tpp80) REVERT: A 122 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8583 (m) REVERT: B 42 PHE cc_start: 0.9432 (m-80) cc_final: 0.9099 (m-80) REVERT: B 49 PHE cc_start: 0.9766 (t80) cc_final: 0.9454 (t80) REVERT: B 86 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8898 (tp-100) REVERT: B 89 LYS cc_start: 0.8702 (tppt) cc_final: 0.8498 (tppt) REVERT: B 131 ASP cc_start: 0.9226 (t0) cc_final: 0.8780 (t0) REVERT: C 13 GLU cc_start: 0.8879 (tp30) cc_final: 0.7787 (tp30) REVERT: C 17 ASN cc_start: 0.9351 (m-40) cc_final: 0.7957 (m-40) REVERT: C 19 PHE cc_start: 0.8750 (m-80) cc_final: 0.8479 (m-80) REVERT: C 30 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: C 38 MET cc_start: 0.8991 (tmm) cc_final: 0.8705 (tmm) REVERT: C 39 CYS cc_start: 0.9320 (p) cc_final: 0.8984 (p) REVERT: C 60 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8658 (mt-10) REVERT: C 92 ASP cc_start: 0.7869 (p0) cc_final: 0.7004 (p0) REVERT: C 105 ASP cc_start: 0.9428 (m-30) cc_final: 0.9141 (m-30) REVERT: D 44 ARG cc_start: 0.8850 (ptm160) cc_final: 0.8373 (ptm160) REVERT: D 60 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8985 (mm-30) REVERT: D 70 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8521 (tp30) REVERT: D 76 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8675 (mppt) REVERT: D 79 LYS cc_start: 0.9373 (mppt) cc_final: 0.9158 (mmtm) REVERT: D 106 GLU cc_start: 0.8917 (tp30) cc_final: 0.8690 (tp30) REVERT: D 116 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8381 (tpp80) REVERT: D 132 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7610 (t0) REVERT: E 46 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8485 (tm-30) REVERT: E 49 PHE cc_start: 0.9674 (t80) cc_final: 0.9171 (t80) REVERT: E 75 ASP cc_start: 0.8817 (t0) cc_final: 0.8579 (t0) REVERT: E 92 ASP cc_start: 0.8013 (p0) cc_final: 0.7726 (p0) REVERT: E 105 ASP cc_start: 0.9302 (m-30) cc_final: 0.9063 (m-30) REVERT: F 38 MET cc_start: 0.9069 (tmm) cc_final: 0.8813 (tmm) REVERT: F 39 CYS cc_start: 0.9352 (p) cc_final: 0.8968 (p) REVERT: F 60 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8771 (mt-10) REVERT: F 92 ASP cc_start: 0.7595 (t70) cc_final: 0.7386 (t0) REVERT: F 106 GLU cc_start: 0.9425 (tp30) cc_final: 0.9129 (mm-30) REVERT: F 110 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8225 (mm-30) REVERT: F 127 TYR cc_start: 0.8876 (m-80) cc_final: 0.8675 (m-80) REVERT: G 70 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8042 (tp30) REVERT: G 92 ASP cc_start: 0.8688 (p0) cc_final: 0.8449 (p0) REVERT: G 110 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9072 (mm-30) REVERT: G 132 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: H 17 ASN cc_start: 0.8905 (m110) cc_final: 0.8440 (m110) REVERT: H 21 ASP cc_start: 0.7520 (p0) cc_final: 0.7126 (p0) REVERT: H 42 PHE cc_start: 0.9391 (m-80) cc_final: 0.9171 (m-80) REVERT: H 44 ARG cc_start: 0.8763 (ptm-80) cc_final: 0.7925 (ttt180) REVERT: H 46 GLN cc_start: 0.7654 (mt0) cc_final: 0.7218 (mt0) REVERT: H 89 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8280 (ttmm) REVERT: H 92 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7427 (p0) REVERT: H 104 LYS cc_start: 0.9386 (mttm) cc_final: 0.9149 (mmtt) REVERT: H 105 ASP cc_start: 0.9138 (m-30) cc_final: 0.8906 (m-30) REVERT: H 124 ASP cc_start: 0.8985 (t0) cc_final: 0.8665 (t0) REVERT: I 17 ASN cc_start: 0.9660 (m-40) cc_final: 0.9405 (m-40) REVERT: I 21 ASP cc_start: 0.8277 (p0) cc_final: 0.7930 (p0) REVERT: I 38 MET cc_start: 0.9191 (tmm) cc_final: 0.8909 (tmm) REVERT: I 39 CYS cc_start: 0.9306 (p) cc_final: 0.8691 (p) REVERT: I 83 GLU cc_start: 0.7621 (mp0) cc_final: 0.7394 (mp0) REVERT: I 86 GLN cc_start: 0.8778 (tp40) cc_final: 0.8572 (tp40) REVERT: I 89 LYS cc_start: 0.9542 (ttpp) cc_final: 0.9224 (ttpp) REVERT: I 91 GLU cc_start: 0.8488 (pp20) cc_final: 0.8228 (pp20) REVERT: I 95 MET cc_start: 0.8883 (mmm) cc_final: 0.8615 (mmm) REVERT: I 102 ASP cc_start: 0.8947 (m-30) cc_final: 0.8732 (m-30) REVERT: I 106 GLU cc_start: 0.9343 (tp30) cc_final: 0.9057 (mm-30) REVERT: I 116 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8076 (mmm160) REVERT: J 13 GLU cc_start: 0.8765 (tp30) cc_final: 0.8199 (tp30) REVERT: J 17 ASN cc_start: 0.8773 (m110) cc_final: 0.7973 (m110) REVERT: J 21 ASP cc_start: 0.8646 (p0) cc_final: 0.8336 (p0) REVERT: J 27 GLU cc_start: 0.7139 (mp0) cc_final: 0.6910 (mp0) REVERT: J 60 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8595 (mt-10) REVERT: J 76 LYS cc_start: 0.9395 (tttt) cc_final: 0.8969 (ptmm) REVERT: J 80 GLU cc_start: 0.8868 (mt-10) cc_final: 0.7974 (mt-10) REVERT: J 92 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8544 (p0) REVERT: K 69 LYS cc_start: 0.9756 (tttp) cc_final: 0.9480 (ttmm) REVERT: K 79 LYS cc_start: 0.9041 (mppt) cc_final: 0.8660 (mmtm) REVERT: K 86 GLN cc_start: 0.9091 (tp40) cc_final: 0.8812 (tp-100) REVERT: K 89 LYS cc_start: 0.9139 (ptmm) cc_final: 0.8823 (ptmm) REVERT: K 116 ARG cc_start: 0.9252 (mmt-90) cc_final: 0.8840 (tpp80) REVERT: L 17 ASN cc_start: 0.9418 (m110) cc_final: 0.9076 (m-40) REVERT: L 21 ASP cc_start: 0.7495 (p0) cc_final: 0.7009 (p0) REVERT: L 38 MET cc_start: 0.9063 (tmm) cc_final: 0.8755 (tmm) REVERT: L 39 CYS cc_start: 0.9256 (p) cc_final: 0.8701 (p) REVERT: L 75 ASP cc_start: 0.8927 (t0) cc_final: 0.8217 (t0) REVERT: L 76 LYS cc_start: 0.9365 (mmmm) cc_final: 0.9123 (mmtt) REVERT: L 83 GLU cc_start: 0.8384 (mp0) cc_final: 0.8006 (mp0) REVERT: L 86 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8860 (tp40) REVERT: L 89 LYS cc_start: 0.8475 (ptmm) cc_final: 0.7969 (ptmm) REVERT: L 102 ASP cc_start: 0.9152 (m-30) cc_final: 0.8873 (m-30) REVERT: L 124 ASP cc_start: 0.8556 (t0) cc_final: 0.8198 (t0) REVERT: M 34 GLU cc_start: 0.9067 (tt0) cc_final: 0.8784 (tt0) REVERT: M 46 GLN cc_start: 0.6794 (tm-30) cc_final: 0.6069 (tm-30) REVERT: M 51 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.9037 (p0) REVERT: M 83 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7570 (pp20) REVERT: M 102 ASP cc_start: 0.9320 (m-30) cc_final: 0.8891 (m-30) REVERT: M 106 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8622 (mp0) REVERT: M 116 ARG cc_start: 0.8849 (tpp80) cc_final: 0.8534 (tpp80) REVERT: M 131 ASP cc_start: 0.8805 (t0) cc_final: 0.8496 (t0) REVERT: N 15 TYR cc_start: 0.9109 (t80) cc_final: 0.8852 (t80) REVERT: N 89 LYS cc_start: 0.8172 (ptmm) cc_final: 0.7642 (ptmm) REVERT: N 90 VAL cc_start: 0.9027 (m) cc_final: 0.8657 (p) REVERT: N 105 ASP cc_start: 0.9232 (m-30) cc_final: 0.8947 (m-30) REVERT: O 21 ASP cc_start: 0.7547 (p0) cc_final: 0.7229 (p0) REVERT: O 35 PHE cc_start: 0.9506 (t80) cc_final: 0.8975 (t80) REVERT: O 38 MET cc_start: 0.8850 (tmm) cc_final: 0.8588 (tmm) REVERT: O 39 CYS cc_start: 0.9202 (p) cc_final: 0.8860 (p) REVERT: O 70 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8386 (mm-30) REVERT: O 91 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: O 92 ASP cc_start: 0.6728 (t70) cc_final: 0.6390 (t0) REVERT: O 94 THR cc_start: 0.9142 (m) cc_final: 0.8705 (p) REVERT: O 102 ASP cc_start: 0.9054 (m-30) cc_final: 0.8734 (m-30) REVERT: O 105 ASP cc_start: 0.9311 (m-30) cc_final: 0.9108 (m-30) REVERT: O 131 ASP cc_start: 0.9355 (p0) cc_final: 0.8948 (m-30) REVERT: a 62 ASP cc_start: 0.7766 (t0) cc_final: 0.7564 (t0) REVERT: a 68 LEU cc_start: 0.9650 (tt) cc_final: 0.9283 (tt) REVERT: a 113 ASP cc_start: 0.9100 (t70) cc_final: 0.8805 (t0) REVERT: a 117 ASP cc_start: 0.9393 (m-30) cc_final: 0.9145 (m-30) REVERT: b 1 MET cc_start: 0.7653 (tpt) cc_final: 0.6552 (tpt) REVERT: c 5 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7050 (mtmm) REVERT: d 17 ILE cc_start: 0.8946 (pt) cc_final: 0.8662 (mm) REVERT: d 50 GLU cc_start: 0.7166 (tp30) cc_final: 0.6769 (tp30) REVERT: e 5 LYS cc_start: 0.8610 (mtmm) cc_final: 0.7910 (mtmm) REVERT: e 16 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.4935 (m100) REVERT: e 30 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7272 (p90) REVERT: f 5 LYS cc_start: 0.8088 (mtmm) cc_final: 0.7631 (mtmm) REVERT: f 17 ILE cc_start: 0.7968 (mp) cc_final: 0.7504 (mm) REVERT: f 27 ASN cc_start: 0.8286 (m-40) cc_final: 0.7792 (m-40) REVERT: f 54 ASN cc_start: 0.7344 (p0) cc_final: 0.7043 (t0) REVERT: f 59 VAL cc_start: 0.7276 (p) cc_final: 0.6734 (p) REVERT: f 82 ASP cc_start: 0.8144 (t0) cc_final: 0.7693 (m-30) REVERT: f 91 VAL cc_start: 0.9533 (t) cc_final: 0.9243 (m) REVERT: f 109 ASN cc_start: 0.8939 (m-40) cc_final: 0.8424 (m110) REVERT: f 110 TYR cc_start: 0.9360 (t80) cc_final: 0.9077 (t80) REVERT: g 14 GLN cc_start: 0.9133 (mp10) cc_final: 0.8841 (mm-40) REVERT: g 48 ASN cc_start: 0.9333 (t0) cc_final: 0.8820 (t0) REVERT: g 50 GLU cc_start: 0.8507 (mp0) cc_final: 0.7889 (mp0) REVERT: g 68 LEU cc_start: 0.9502 (tt) cc_final: 0.9274 (tt) REVERT: h 1 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.5607 (tmm) REVERT: h 36 TYR cc_start: 0.8736 (m-80) cc_final: 0.8189 (m-10) REVERT: i 69 THR cc_start: 0.8492 (p) cc_final: 0.8287 (t) REVERT: j 13 ASP cc_start: 0.7216 (m-30) cc_final: 0.7004 (m-30) REVERT: j 48 ASN cc_start: 0.9139 (t0) cc_final: 0.8848 (t0) REVERT: j 50 GLU cc_start: 0.8403 (pm20) cc_final: 0.7595 (pm20) REVERT: k 58 ASN cc_start: 0.6847 (OUTLIER) cc_final: 0.6356 (m-40) REVERT: l 14 GLN cc_start: 0.9145 (mp10) cc_final: 0.8795 (mp10) REVERT: l 110 TYR cc_start: 0.9152 (t80) cc_final: 0.8907 (t80) REVERT: m 48 ASN cc_start: 0.8855 (t0) cc_final: 0.8474 (t0) REVERT: m 50 GLU cc_start: 0.8175 (pm20) cc_final: 0.7494 (mp0) REVERT: n 42 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8097 (t70) REVERT: n 62 ASP cc_start: 0.9160 (t70) cc_final: 0.8803 (t0) REVERT: n 94 GLU cc_start: 0.8029 (pm20) cc_final: 0.7799 (pm20) REVERT: n 111 LEU cc_start: 0.9484 (mm) cc_final: 0.9076 (pp) outliers start: 187 outliers final: 99 residues processed: 1314 average time/residue: 0.4476 time to fit residues: 915.8175 Evaluate side-chains 1164 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1052 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 59 ILE Chi-restraints excluded: chain B residue 81 SER 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 122 VAL Chi-restraints excluded: chain I residue 129 SER 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 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 133 VAL Chi-restraints excluded: chain L residue 134 GLU 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 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 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 72 ASP Chi-restraints excluded: chain b residue 87 ILE Chi-restraints excluded: chain c residue 56 VAL 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 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 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 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 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 108 LEU Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 107 VAL 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 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 108 optimal weight: 8.9990 chunk 370 optimal weight: 4.9990 chunk 318 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 281 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 354 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 18 GLN A 98 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN F 10 HIS F 51 ASN G 17 ASN ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** K 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** 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** ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 HIS ** i 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 18 ASN j 35 GLN ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 58 ASN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.056850 restraints weight = 148865.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058453 restraints weight = 93740.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059588 restraints weight = 66504.439| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31470 Z= 0.205 Angle : 0.763 13.665 42780 Z= 0.403 Chirality : 0.046 0.190 4995 Planarity : 0.005 0.071 5565 Dihedral : 7.692 83.337 4253 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.06 % Favored : 91.81 % Rotamer: Outliers : 6.10 % Allowed : 20.96 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 3795 helix: 0.60 (0.13), residues: 1609 sheet: -0.85 (0.20), residues: 613 loop : -2.21 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP o 16 HIS 0.017 0.002 HIS b 42 PHE 0.032 0.002 PHE I 19 TYR 0.042 0.002 TYR h 114 ARG 0.008 0.001 ARG l 9 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1420) hydrogen bonds : angle 5.40418 ( 4086) covalent geometry : bond 0.00448 (31470) covalent geometry : angle 0.76286 (42780) *********************** 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 1349 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 1134 time to evaluate : 3.661 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: 0.8973 (tp30) cc_final: 0.8534 (tp30) REVERT: A 29 GLU cc_start: 0.9043 (tp30) cc_final: 0.8739 (tp30) REVERT: A 30 GLU cc_start: 0.8885 (pm20) cc_final: 0.8193 (pm20) REVERT: A 38 MET cc_start: 0.9277 (tmm) cc_final: 0.8631 (tmm) REVERT: A 70 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8638 (tp30) REVERT: A 92 ASP cc_start: 0.8588 (p0) cc_final: 0.8160 (p0) REVERT: A 112 LYS cc_start: 0.9436 (mttm) cc_final: 0.9191 (mmtm) REVERT: B 49 PHE cc_start: 0.9733 (t80) cc_final: 0.9519 (t80) REVERT: B 51 ASN cc_start: 0.9371 (m110) cc_final: 0.9043 (p0) REVERT: B 86 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8823 (tp-100) REVERT: B 105 ASP cc_start: 0.9285 (m-30) cc_final: 0.8991 (m-30) REVERT: B 106 GLU cc_start: 0.9282 (tp30) cc_final: 0.9058 (tp30) REVERT: B 124 ASP cc_start: 0.8703 (t0) cc_final: 0.8187 (t0) REVERT: B 131 ASP cc_start: 0.9298 (t0) cc_final: 0.8873 (t0) REVERT: C 13 GLU cc_start: 0.8868 (tp30) cc_final: 0.7642 (tp30) REVERT: C 17 ASN cc_start: 0.9384 (m-40) cc_final: 0.8012 (m-40) REVERT: C 19 PHE cc_start: 0.8804 (m-80) cc_final: 0.8542 (m-80) REVERT: C 30 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: C 38 MET cc_start: 0.9062 (tmm) cc_final: 0.8704 (tmm) REVERT: C 39 CYS cc_start: 0.9313 (p) cc_final: 0.8894 (p) REVERT: C 60 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8699 (mt-10) REVERT: C 70 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8839 (mm-30) REVERT: C 86 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8650 (tp40) REVERT: C 105 ASP cc_start: 0.9456 (m-30) cc_final: 0.9183 (m-30) REVERT: C 124 ASP cc_start: 0.7859 (t0) cc_final: 0.7549 (t0) REVERT: D 44 ARG cc_start: 0.8832 (ptm160) cc_final: 0.8332 (ptm160) REVERT: D 60 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8982 (mm-30) REVERT: D 90 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8579 (m) REVERT: D 106 GLU cc_start: 0.8985 (tp30) cc_final: 0.8692 (tp30) REVERT: D 113 LYS cc_start: 0.9480 (mtpt) cc_final: 0.9187 (mtmt) REVERT: D 116 ARG cc_start: 0.8670 (tpp80) cc_final: 0.8350 (tpp80) REVERT: E 46 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8568 (tm-30) REVERT: E 49 PHE cc_start: 0.9706 (t80) cc_final: 0.9265 (t80) REVERT: E 75 ASP cc_start: 0.8845 (t0) cc_final: 0.8554 (t0) REVERT: E 105 ASP cc_start: 0.9280 (m-30) cc_final: 0.9040 (m-30) REVERT: F 38 MET cc_start: 0.9230 (tmm) cc_final: 0.8957 (tmm) REVERT: F 39 CYS cc_start: 0.9406 (p) cc_final: 0.8985 (p) REVERT: F 60 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8787 (mt-10) REVERT: F 70 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8613 (mt-10) REVERT: F 86 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8516 (tp40) REVERT: F 102 ASP cc_start: 0.9046 (m-30) cc_final: 0.8839 (m-30) REVERT: F 106 GLU cc_start: 0.9394 (tp30) cc_final: 0.9190 (mm-30) REVERT: F 110 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8323 (mm-30) REVERT: F 119 LYS cc_start: 0.9342 (mmmt) cc_final: 0.9020 (mmmt) REVERT: G 29 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8532 (tm-30) REVERT: G 70 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8154 (tp30) REVERT: G 92 ASP cc_start: 0.8772 (p0) cc_final: 0.8474 (p0) REVERT: G 110 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9084 (mm-30) REVERT: H 21 ASP cc_start: 0.7562 (p0) cc_final: 0.7183 (p0) REVERT: H 31 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9028 (tp) REVERT: H 44 ARG cc_start: 0.8861 (ptm-80) cc_final: 0.8252 (ttt180) REVERT: H 49 PHE cc_start: 0.9712 (t80) cc_final: 0.9499 (t80) REVERT: H 53 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9150 (mm) REVERT: H 75 ASP cc_start: 0.8702 (m-30) cc_final: 0.8496 (m-30) REVERT: H 89 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8394 (ttmm) REVERT: H 105 ASP cc_start: 0.9135 (m-30) cc_final: 0.8897 (m-30) REVERT: H 124 ASP cc_start: 0.8933 (t0) cc_final: 0.8624 (t0) REVERT: I 13 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8886 (mt-10) REVERT: I 17 ASN cc_start: 0.9655 (m-40) cc_final: 0.9360 (m-40) REVERT: I 21 ASP cc_start: 0.8491 (p0) cc_final: 0.8122 (p0) REVERT: I 38 MET cc_start: 0.9249 (tmm) cc_final: 0.8942 (tmm) REVERT: I 39 CYS cc_start: 0.9341 (p) cc_final: 0.8848 (p) REVERT: I 60 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8620 (mt-10) REVERT: I 70 GLU cc_start: 0.8476 (tt0) cc_final: 0.8274 (mt-10) REVERT: I 89 LYS cc_start: 0.9510 (ttpp) cc_final: 0.9229 (ttpp) REVERT: I 102 ASP cc_start: 0.8940 (m-30) cc_final: 0.8706 (m-30) REVERT: I 106 GLU cc_start: 0.9325 (tp30) cc_final: 0.9015 (mm-30) REVERT: I 116 ARG cc_start: 0.8655 (mmm160) cc_final: 0.7936 (mmm160) REVERT: J 13 GLU cc_start: 0.8731 (tp30) cc_final: 0.8164 (tp30) REVERT: J 17 ASN cc_start: 0.8691 (m110) cc_final: 0.7864 (m110) REVERT: J 21 ASP cc_start: 0.8641 (p0) cc_final: 0.8295 (p0) REVERT: J 27 GLU cc_start: 0.7211 (mp0) cc_final: 0.6969 (mp0) REVERT: J 60 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8652 (mt-10) REVERT: J 79 LYS cc_start: 0.9147 (mtmm) cc_final: 0.8835 (mtmm) REVERT: J 83 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7871 (pp20) REVERT: J 92 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8710 (p0) REVERT: J 110 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8564 (mm-30) REVERT: K 42 PHE cc_start: 0.9365 (m-10) cc_final: 0.9002 (m-10) REVERT: K 51 ASN cc_start: 0.9403 (m110) cc_final: 0.9159 (p0) REVERT: K 69 LYS cc_start: 0.9761 (tttp) cc_final: 0.9469 (ttmm) REVERT: K 86 GLN cc_start: 0.9168 (tp40) cc_final: 0.8799 (tp-100) REVERT: K 89 LYS cc_start: 0.9216 (ptmm) cc_final: 0.9000 (ptmm) REVERT: K 98 ASN cc_start: 0.8798 (p0) cc_final: 0.8497 (p0) REVERT: K 105 ASP cc_start: 0.9325 (m-30) cc_final: 0.9018 (m-30) REVERT: K 116 ARG cc_start: 0.9311 (mmt-90) cc_final: 0.8911 (tpp80) REVERT: L 17 ASN cc_start: 0.9522 (m-40) cc_final: 0.9174 (m-40) REVERT: L 21 ASP cc_start: 0.7629 (p0) cc_final: 0.7358 (p0) REVERT: L 26 SER cc_start: 0.7660 (t) cc_final: 0.6939 (p) REVERT: L 38 MET cc_start: 0.9144 (tmm) cc_final: 0.8873 (tmm) REVERT: L 39 CYS cc_start: 0.9226 (p) cc_final: 0.8687 (p) REVERT: L 83 GLU cc_start: 0.8341 (mp0) cc_final: 0.7962 (mp0) REVERT: L 86 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8826 (tp40) REVERT: L 89 LYS cc_start: 0.8488 (ptmm) cc_final: 0.8253 (ptmm) REVERT: L 124 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8379 (t0) REVERT: M 34 GLU cc_start: 0.9113 (tt0) cc_final: 0.8790 (tt0) REVERT: M 70 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8149 (tp30) REVERT: M 83 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7566 (pp20) REVERT: M 102 ASP cc_start: 0.9226 (m-30) cc_final: 0.8989 (m-30) REVERT: M 106 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8619 (mp0) REVERT: M 116 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8540 (tpp80) REVERT: M 131 ASP cc_start: 0.8838 (t0) cc_final: 0.8518 (t0) REVERT: N 44 ARG cc_start: 0.8470 (ttt90) cc_final: 0.8246 (ttt180) REVERT: N 89 LYS cc_start: 0.8398 (ptmm) cc_final: 0.7660 (ptmm) REVERT: N 105 ASP cc_start: 0.9237 (m-30) cc_final: 0.8952 (m-30) REVERT: O 21 ASP cc_start: 0.7588 (p0) cc_final: 0.7287 (p0) REVERT: O 38 MET cc_start: 0.8904 (tmm) cc_final: 0.8644 (tmm) REVERT: O 39 CYS cc_start: 0.9172 (p) cc_final: 0.8866 (p) REVERT: O 91 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: O 92 ASP cc_start: 0.6880 (t70) cc_final: 0.6350 (t0) REVERT: O 94 THR cc_start: 0.9199 (m) cc_final: 0.8819 (p) REVERT: O 95 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8219 (mtm) REVERT: O 102 ASP cc_start: 0.9086 (m-30) cc_final: 0.8722 (m-30) REVERT: O 105 ASP cc_start: 0.9340 (m-30) cc_final: 0.9056 (m-30) REVERT: O 112 LYS cc_start: 0.9558 (ptpp) cc_final: 0.9340 (mttp) REVERT: a 62 ASP cc_start: 0.7774 (t0) cc_final: 0.7382 (t0) REVERT: a 112 GLU cc_start: 0.9291 (OUTLIER) cc_final: 0.8668 (mm-30) REVERT: a 113 ASP cc_start: 0.9074 (t70) cc_final: 0.8743 (t0) REVERT: a 117 ASP cc_start: 0.9412 (m-30) cc_final: 0.9133 (m-30) REVERT: b 1 MET cc_start: 0.7932 (tpt) cc_final: 0.6744 (tpt) REVERT: b 55 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8189 (t) REVERT: b 91 VAL cc_start: 0.9623 (t) cc_final: 0.9402 (p) REVERT: c 5 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7382 (mtmm) REVERT: c 82 ASP cc_start: 0.7791 (t0) cc_final: 0.7516 (m-30) REVERT: c 114 TYR cc_start: 0.9104 (t80) cc_final: 0.8863 (t80) REVERT: d 17 ILE cc_start: 0.9129 (pt) cc_final: 0.8824 (mm) REVERT: d 29 THR cc_start: 0.8776 (m) cc_final: 0.8410 (p) REVERT: d 50 GLU cc_start: 0.7326 (tp30) cc_final: 0.7035 (tp30) REVERT: d 58 ASN cc_start: 0.7080 (t0) cc_final: 0.6845 (t0) REVERT: e 5 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8200 (mtmm) REVERT: e 16 TRP cc_start: 0.7932 (OUTLIER) cc_final: 0.5029 (m100) REVERT: e 30 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7109 (p90) REVERT: f 3 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8123 (ttp-110) REVERT: f 5 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7281 (ptpp) REVERT: f 14 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8866 (pm20) REVERT: f 17 ILE cc_start: 0.8538 (mp) cc_final: 0.8172 (mm) REVERT: f 27 ASN cc_start: 0.8511 (m-40) cc_final: 0.8023 (m-40) REVERT: f 46 ASP cc_start: 0.8360 (p0) cc_final: 0.7957 (p0) REVERT: f 59 VAL cc_start: 0.7556 (p) cc_final: 0.6953 (p) REVERT: f 82 ASP cc_start: 0.8221 (t0) cc_final: 0.7736 (m-30) REVERT: f 86 ASP cc_start: 0.8461 (p0) cc_final: 0.8088 (p0) REVERT: f 109 ASN cc_start: 0.8976 (m-40) cc_final: 0.8656 (m110) REVERT: g 14 GLN cc_start: 0.9190 (mp10) cc_final: 0.8930 (mm-40) REVERT: g 48 ASN cc_start: 0.9386 (t0) cc_final: 0.8843 (t0) REVERT: g 50 GLU cc_start: 0.8436 (mp0) cc_final: 0.7764 (mp0) REVERT: g 58 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6702 (m-40) REVERT: g 68 LEU cc_start: 0.9570 (tt) cc_final: 0.9370 (tt) REVERT: h 1 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.5647 (tmm) REVERT: h 21 LEU cc_start: 0.9556 (mt) cc_final: 0.9321 (mt) REVERT: h 36 TYR cc_start: 0.8790 (m-80) cc_final: 0.8266 (m-10) REVERT: i 1 MET cc_start: 0.7903 (mtp) cc_final: 0.7641 (ttt) REVERT: j 1 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5636 (ttt) REVERT: j 12 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7669 (p0) REVERT: k 25 LEU cc_start: 0.8656 (tp) cc_final: 0.8397 (tp) REVERT: k 58 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6563 (m-40) REVERT: l 14 GLN cc_start: 0.9243 (mp10) cc_final: 0.8860 (mp10) REVERT: l 110 TYR cc_start: 0.9132 (t80) cc_final: 0.8865 (t80) REVERT: m 12 ASP cc_start: 0.7326 (p0) cc_final: 0.6808 (p0) REVERT: m 14 GLN cc_start: 0.8738 (mp10) cc_final: 0.8488 (mp10) REVERT: m 29 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7463 (p) REVERT: m 48 ASN cc_start: 0.9033 (t0) cc_final: 0.8759 (t0) REVERT: m 50 GLU cc_start: 0.8200 (pm20) cc_final: 0.7950 (mp0) REVERT: n 13 ASP cc_start: 0.8492 (t0) cc_final: 0.8181 (t0) REVERT: n 42 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8401 (t70) REVERT: n 111 LEU cc_start: 0.9470 (mm) cc_final: 0.9084 (pp) REVERT: o 14 GLN cc_start: 0.9427 (mp10) cc_final: 0.9157 (mp10) REVERT: o 54 ASN cc_start: 0.7697 (p0) cc_final: 0.7340 (p0) REVERT: o 93 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8302 (tmt-80) outliers start: 215 outliers final: 128 residues processed: 1261 average time/residue: 0.4474 time to fit residues: 884.0590 Evaluate side-chains 1187 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1037 time to evaluate : 3.901 ------------------------------------------------------------------------------- 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 9 THR Chi-restraints excluded: chain B residue 33 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 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 90 VAL 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 122 VAL Chi-restraints excluded: chain G residue 46 GLN Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 53 LEU 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 33 ILE 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 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 124 ASP 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 70 GLU 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 130 TYR Chi-restraints excluded: chain O residue 31 LEU 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 118 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 4 LEU 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 68 LEU 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 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 110 TYR Chi-restraints excluded: chain f residue 14 GLN 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 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 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS 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 58 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 30 PHE Chi-restraints excluded: chain m residue 54 ASN 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 64 SER Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 247 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 359 optimal weight: 0.0970 chunk 151 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 chunk 251 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS E 51 ASN G 98 ASN K 18 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 18 GLN O 78 ASN a 58 ASN a 73 ASN b 42 HIS c 10 HIS ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 HIS i 73 ASN j 14 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN l 58 ASN ** m 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.067891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054074 restraints weight = 150559.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.055629 restraints weight = 93459.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056728 restraints weight = 66177.769| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31470 Z= 0.209 Angle : 0.761 11.997 42780 Z= 0.402 Chirality : 0.046 0.209 4995 Planarity : 0.005 0.055 5565 Dihedral : 7.636 82.751 4247 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.38 % Favored : 91.49 % Rotamer: Outliers : 7.01 % Allowed : 21.84 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3795 helix: 0.52 (0.12), residues: 1615 sheet: -0.79 (0.20), residues: 627 loop : -2.22 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP o 16 HIS 0.013 0.002 HIS b 42 PHE 0.033 0.002 PHE M 49 TYR 0.039 0.002 TYR m 110 ARG 0.012 0.001 ARG g 3 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1420) hydrogen bonds : angle 5.29170 ( 4086) covalent geometry : bond 0.00457 (31470) covalent geometry : angle 0.76075 (42780) *********************** 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 1371 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 1124 time to evaluate : 3.737 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: A 13 GLU cc_start: 0.8852 (tp30) cc_final: 0.8349 (tp30) REVERT: A 17 ASN cc_start: 0.8968 (m110) cc_final: 0.8161 (m110) REVERT: A 29 GLU cc_start: 0.9017 (tp30) cc_final: 0.8690 (tp30) REVERT: A 30 GLU cc_start: 0.8829 (pm20) cc_final: 0.8111 (pm20) REVERT: A 38 MET cc_start: 0.9236 (tmm) cc_final: 0.8579 (tmm) REVERT: A 70 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8719 (tp30) REVERT: A 92 ASP cc_start: 0.8728 (p0) cc_final: 0.8487 (p0) REVERT: A 122 VAL cc_start: 0.9489 (p) cc_final: 0.9098 (p) REVERT: A 132 ASP cc_start: 0.8542 (m-30) cc_final: 0.7844 (t70) REVERT: B 49 PHE cc_start: 0.9736 (t80) cc_final: 0.9507 (t80) REVERT: B 86 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8816 (tp-100) REVERT: B 106 GLU cc_start: 0.9325 (tp30) cc_final: 0.9008 (tp30) REVERT: B 124 ASP cc_start: 0.8809 (t0) cc_final: 0.8165 (t0) REVERT: B 131 ASP cc_start: 0.9253 (t0) cc_final: 0.8832 (t0) REVERT: C 13 GLU cc_start: 0.8901 (tp30) cc_final: 0.7832 (tp30) REVERT: C 17 ASN cc_start: 0.9384 (m-40) cc_final: 0.8372 (m-40) REVERT: C 19 PHE cc_start: 0.8797 (m-80) cc_final: 0.8499 (m-80) REVERT: C 30 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: C 38 MET cc_start: 0.9034 (tmm) cc_final: 0.8697 (tmm) REVERT: C 60 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 70 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8684 (mm-30) REVERT: C 83 GLU cc_start: 0.7882 (mp0) cc_final: 0.7652 (mp0) REVERT: C 86 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8691 (tp40) REVERT: C 102 ASP cc_start: 0.9168 (m-30) cc_final: 0.8669 (m-30) REVERT: C 105 ASP cc_start: 0.9438 (m-30) cc_final: 0.9218 (m-30) REVERT: C 116 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8244 (mmm160) REVERT: D 60 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8951 (mm-30) REVERT: D 112 LYS cc_start: 0.9470 (mtmm) cc_final: 0.9072 (mtmm) REVERT: D 113 LYS cc_start: 0.9468 (mtpt) cc_final: 0.9199 (mtmt) REVERT: D 116 ARG cc_start: 0.8706 (tpp80) cc_final: 0.8500 (tpp80) REVERT: E 46 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8990 (tm-30) REVERT: E 49 PHE cc_start: 0.9742 (t80) cc_final: 0.9435 (t80) REVERT: E 75 ASP cc_start: 0.8832 (t0) cc_final: 0.8588 (t0) REVERT: E 89 LYS cc_start: 0.8986 (ptmm) cc_final: 0.8694 (ptmm) REVERT: E 92 ASP cc_start: 0.7806 (p0) cc_final: 0.7318 (p0) REVERT: E 105 ASP cc_start: 0.9262 (m-30) cc_final: 0.9023 (m-30) REVERT: E 116 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8969 (tpp80) REVERT: E 124 ASP cc_start: 0.8797 (t70) cc_final: 0.8524 (t0) REVERT: E 132 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: F 38 MET cc_start: 0.9256 (tmm) cc_final: 0.8973 (tmm) REVERT: F 39 CYS cc_start: 0.9366 (p) cc_final: 0.9023 (p) REVERT: F 70 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8671 (mt-10) REVERT: F 86 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8582 (tp40) REVERT: F 110 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8337 (mm-30) REVERT: G 29 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8454 (tm-30) REVERT: G 46 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: G 60 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8821 (mt-10) REVERT: G 70 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8186 (tp30) REVERT: G 79 LYS cc_start: 0.9414 (mppt) cc_final: 0.9094 (mtmm) REVERT: G 92 ASP cc_start: 0.8888 (p0) cc_final: 0.8603 (p0) REVERT: G 110 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9089 (mm-30) REVERT: G 132 ASP cc_start: 0.8622 (m-30) cc_final: 0.8345 (t70) REVERT: H 21 ASP cc_start: 0.7624 (p0) cc_final: 0.7245 (p0) REVERT: H 31 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9047 (tp) REVERT: H 44 ARG cc_start: 0.8906 (ptm-80) cc_final: 0.8545 (ttt180) REVERT: H 49 PHE cc_start: 0.9691 (t80) cc_final: 0.9433 (t80) REVERT: H 53 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9099 (mm) REVERT: H 95 MET cc_start: 0.8898 (mmm) cc_final: 0.8683 (mmm) REVERT: H 105 ASP cc_start: 0.9123 (m-30) cc_final: 0.8881 (m-30) REVERT: H 124 ASP cc_start: 0.8927 (t0) cc_final: 0.8726 (t0) REVERT: H 131 ASP cc_start: 0.9140 (p0) cc_final: 0.8818 (p0) REVERT: I 13 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8970 (mt-10) REVERT: I 27 GLU cc_start: 0.7755 (mp0) cc_final: 0.7511 (pm20) REVERT: I 38 MET cc_start: 0.9223 (tmm) cc_final: 0.8896 (tmm) REVERT: I 39 CYS cc_start: 0.9343 (p) cc_final: 0.8842 (p) REVERT: I 60 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8784 (mt-10) REVERT: I 102 ASP cc_start: 0.8959 (m-30) cc_final: 0.8757 (m-30) REVERT: I 116 ARG cc_start: 0.8708 (mmm160) cc_final: 0.7990 (mmm160) REVERT: J 13 GLU cc_start: 0.8745 (tp30) cc_final: 0.8143 (tp30) REVERT: J 17 ASN cc_start: 0.8673 (m110) cc_final: 0.7788 (m110) REVERT: J 21 ASP cc_start: 0.8641 (p0) cc_final: 0.8395 (p0) REVERT: J 27 GLU cc_start: 0.7163 (mp0) cc_final: 0.6942 (mp0) REVERT: J 60 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8653 (mt-10) REVERT: J 70 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8426 (mm-30) REVERT: J 124 ASP cc_start: 0.9048 (t0) cc_final: 0.8666 (t0) REVERT: K 44 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8297 (tpp80) REVERT: K 69 LYS cc_start: 0.9749 (tttp) cc_final: 0.9447 (ttmm) REVERT: K 86 GLN cc_start: 0.9180 (tp40) cc_final: 0.8799 (tp-100) REVERT: K 105 ASP cc_start: 0.9303 (m-30) cc_final: 0.8980 (m-30) REVERT: K 116 ARG cc_start: 0.9266 (mmt-90) cc_final: 0.8895 (tpp80) REVERT: L 13 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8877 (mt-10) REVERT: L 17 ASN cc_start: 0.9592 (m-40) cc_final: 0.9271 (m-40) REVERT: L 18 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8968 (mp10) REVERT: L 38 MET cc_start: 0.9225 (tmm) cc_final: 0.8941 (tmm) REVERT: L 39 CYS cc_start: 0.9213 (p) cc_final: 0.8662 (p) REVERT: L 83 GLU cc_start: 0.8309 (mp0) cc_final: 0.7996 (mp0) REVERT: L 86 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8864 (tp40) REVERT: L 124 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.7986 (t0) REVERT: M 17 ASN cc_start: 0.9502 (m-40) cc_final: 0.9275 (m110) REVERT: M 51 ASN cc_start: 0.9533 (OUTLIER) cc_final: 0.9317 (p0) REVERT: M 70 GLU cc_start: 0.9034 (tp30) cc_final: 0.8266 (tp30) REVERT: M 83 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7574 (pp20) REVERT: M 86 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8528 (mm110) REVERT: M 102 ASP cc_start: 0.9245 (m-30) cc_final: 0.8996 (m-30) REVERT: M 106 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8647 (mp0) REVERT: M 116 ARG cc_start: 0.8869 (tpp80) cc_final: 0.8472 (tpp80) REVERT: N 89 LYS cc_start: 0.8520 (ptmm) cc_final: 0.7663 (ptmm) REVERT: N 90 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8542 (m) REVERT: N 92 ASP cc_start: 0.7728 (p0) cc_final: 0.7319 (p0) REVERT: N 105 ASP cc_start: 0.9215 (m-30) cc_final: 0.8918 (m-30) REVERT: O 21 ASP cc_start: 0.7679 (p0) cc_final: 0.7306 (p0) REVERT: O 38 MET cc_start: 0.8939 (tmm) cc_final: 0.8641 (tmm) REVERT: O 39 CYS cc_start: 0.9177 (p) cc_final: 0.8797 (p) REVERT: O 91 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: O 92 ASP cc_start: 0.6974 (t70) cc_final: 0.6521 (t0) REVERT: O 97 MET cc_start: 0.9072 (mmm) cc_final: 0.8872 (mmm) REVERT: O 102 ASP cc_start: 0.9075 (m-30) cc_final: 0.8735 (m-30) REVERT: O 105 ASP cc_start: 0.9400 (m-30) cc_final: 0.9183 (m-30) REVERT: a 62 ASP cc_start: 0.7909 (t0) cc_final: 0.7585 (t0) REVERT: a 101 ASP cc_start: 0.9090 (p0) cc_final: 0.8865 (p0) REVERT: a 112 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8962 (mm-30) REVERT: a 113 ASP cc_start: 0.9161 (t70) cc_final: 0.8811 (t0) REVERT: a 117 ASP cc_start: 0.9473 (m-30) cc_final: 0.9201 (m-30) REVERT: b 1 MET cc_start: 0.8135 (tpt) cc_final: 0.7274 (tpt) REVERT: b 55 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8443 (t) REVERT: b 91 VAL cc_start: 0.9635 (t) cc_final: 0.9402 (p) REVERT: b 117 ASP cc_start: 0.9030 (m-30) cc_final: 0.8623 (t0) REVERT: c 5 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7788 (mtmm) REVERT: d 17 ILE cc_start: 0.9282 (pt) cc_final: 0.9009 (mm) REVERT: d 29 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8449 (p) REVERT: d 50 GLU cc_start: 0.7583 (tp30) cc_final: 0.7361 (tp30) REVERT: e 1 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7457 (tpp) REVERT: e 5 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8163 (mtmm) REVERT: e 14 GLN cc_start: 0.8819 (mp10) cc_final: 0.8563 (mm-40) REVERT: e 30 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.6879 (p90) REVERT: f 3 ARG cc_start: 0.8665 (mtp-110) cc_final: 0.8269 (ttp-110) REVERT: f 27 ASN cc_start: 0.8735 (m-40) cc_final: 0.8367 (m-40) REVERT: f 109 ASN cc_start: 0.8817 (m-40) cc_final: 0.8482 (m110) REVERT: g 24 THR cc_start: 0.9358 (m) cc_final: 0.9100 (p) REVERT: g 48 ASN cc_start: 0.9407 (t0) cc_final: 0.8823 (t0) REVERT: g 50 GLU cc_start: 0.8368 (mp0) cc_final: 0.7753 (mp0) REVERT: g 68 LEU cc_start: 0.9614 (tt) cc_final: 0.9398 (tt) REVERT: h 1 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.5761 (ttp) REVERT: h 36 TYR cc_start: 0.8777 (m-80) cc_final: 0.8259 (m-10) REVERT: i 1 MET cc_start: 0.8026 (mtp) cc_final: 0.7801 (ttp) REVERT: j 1 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5759 (ttt) REVERT: j 48 ASN cc_start: 0.8805 (t0) cc_final: 0.8383 (t0) REVERT: j 50 GLU cc_start: 0.8179 (pm20) cc_final: 0.7852 (pm20) REVERT: l 14 GLN cc_start: 0.9243 (mp10) cc_final: 0.8911 (mp10) REVERT: m 12 ASP cc_start: 0.7680 (p0) cc_final: 0.7327 (p0) REVERT: m 29 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7529 (p) REVERT: m 48 ASN cc_start: 0.9103 (t0) cc_final: 0.8730 (t0) REVERT: m 50 GLU cc_start: 0.8411 (pm20) cc_final: 0.7852 (pm20) REVERT: n 94 GLU cc_start: 0.8015 (pm20) cc_final: 0.7795 (pm20) REVERT: n 111 LEU cc_start: 0.9487 (mm) cc_final: 0.9151 (pp) REVERT: o 54 ASN cc_start: 0.7790 (p0) cc_final: 0.7260 (p0) outliers start: 247 outliers final: 147 residues processed: 1272 average time/residue: 0.4456 time to fit residues: 881.8167 Evaluate side-chains 1191 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1027 time to evaluate : 3.600 ------------------------------------------------------------------------------- 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 44 ARG 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 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 33 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 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 56 LEU 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 46 GLN Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 98 ASN Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 53 LEU 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 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 90 VAL 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 80 GLU 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 124 ASP 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 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 74 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 58 THR 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 118 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 b residue 17 ILE 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 69 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASN 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 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 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 f residue 110 TYR Chi-restraints excluded: chain g residue 23 LEU 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 59 VAL Chi-restraints excluded: chain h residue 100 THR Chi-restraints excluded: chain h residue 121 ASN Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 44 LYS 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 24 THR 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 107 VAL 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 64 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 103 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 90 optimal weight: 0.0970 chunk 336 optimal weight: 2.9990 chunk 348 optimal weight: 30.0000 chunk 374 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 337 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN H 78 ASN I 78 ASN L 78 ASN N 140 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** 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** l 123 GLN ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.053465 restraints weight = 150606.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055011 restraints weight = 93466.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.056112 restraints weight = 66427.608| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31470 Z= 0.185 Angle : 0.768 14.284 42780 Z= 0.402 Chirality : 0.046 0.193 4995 Planarity : 0.005 0.064 5565 Dihedral : 7.345 65.637 4231 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.48 % Favored : 91.38 % Rotamer: Outliers : 6.98 % Allowed : 23.89 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3795 helix: 0.57 (0.12), residues: 1610 sheet: -0.67 (0.20), residues: 620 loop : -2.23 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP o 16 HIS 0.007 0.001 HIS o 10 PHE 0.020 0.002 PHE m 53 TYR 0.040 0.002 TYR h 114 ARG 0.010 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1420) hydrogen bonds : angle 5.19054 ( 4086) covalent geometry : bond 0.00408 (31470) covalent geometry : angle 0.76792 (42780) *********************** 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 1390 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1144 time to evaluate : 3.591 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: 0.8855 (tp30) cc_final: 0.8318 (tp30) REVERT: A 17 ASN cc_start: 0.9001 (m110) cc_final: 0.8153 (m110) REVERT: A 29 GLU cc_start: 0.9019 (tp30) cc_final: 0.8516 (tp30) REVERT: A 30 GLU cc_start: 0.8917 (pm20) cc_final: 0.8215 (pm20) REVERT: A 38 MET cc_start: 0.9275 (tmm) cc_final: 0.8701 (tmm) REVERT: A 69 LYS cc_start: 0.9654 (tptm) cc_final: 0.9428 (tptm) REVERT: A 70 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8203 (tp30) REVERT: A 73 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8794 (ttp80) REVERT: A 92 ASP cc_start: 0.8799 (p0) cc_final: 0.8502 (p0) REVERT: A 112 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9134 (mmtm) REVERT: A 124 ASP cc_start: 0.9223 (t0) cc_final: 0.8919 (t0) REVERT: B 86 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8869 (tp-100) REVERT: B 105 ASP cc_start: 0.9257 (m-30) cc_final: 0.9048 (m-30) REVERT: B 106 GLU cc_start: 0.9348 (tp30) cc_final: 0.8997 (tp30) REVERT: B 116 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8781 (tpp80) REVERT: B 124 ASP cc_start: 0.8669 (t0) cc_final: 0.7945 (t0) REVERT: B 131 ASP cc_start: 0.9315 (t0) cc_final: 0.8856 (t0) REVERT: C 13 GLU cc_start: 0.8943 (tp30) cc_final: 0.7853 (tp30) REVERT: C 17 ASN cc_start: 0.9415 (m-40) cc_final: 0.8386 (m-40) REVERT: C 19 PHE cc_start: 0.8821 (m-80) cc_final: 0.8466 (m-80) REVERT: C 30 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: C 38 MET cc_start: 0.9073 (tmm) cc_final: 0.8704 (tmm) REVERT: C 60 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8707 (mt-10) REVERT: C 70 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8615 (mm-30) REVERT: C 83 GLU cc_start: 0.7912 (mp0) cc_final: 0.7594 (mp0) REVERT: C 86 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8613 (tp40) REVERT: C 102 ASP cc_start: 0.9161 (m-30) cc_final: 0.8888 (m-30) REVERT: C 105 ASP cc_start: 0.9443 (m-30) cc_final: 0.9216 (m-30) REVERT: C 113 LYS cc_start: 0.9635 (mtpt) cc_final: 0.9284 (ttmm) REVERT: C 116 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8161 (mmm160) REVERT: D 60 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8926 (mm-30) REVERT: D 69 LYS cc_start: 0.9664 (ttmm) cc_final: 0.9373 (ttpp) REVERT: D 113 LYS cc_start: 0.9470 (mtpt) cc_final: 0.9206 (mtmt) REVERT: D 116 ARG cc_start: 0.8774 (tpp80) cc_final: 0.8547 (tpp80) REVERT: E 17 ASN cc_start: 0.9468 (m-40) cc_final: 0.9071 (m110) REVERT: E 79 LYS cc_start: 0.9062 (mppt) cc_final: 0.8808 (mmtp) REVERT: E 89 LYS cc_start: 0.9015 (ptmm) cc_final: 0.8710 (ptmm) REVERT: E 92 ASP cc_start: 0.7737 (p0) cc_final: 0.7130 (p0) REVERT: E 105 ASP cc_start: 0.9286 (m-30) cc_final: 0.9034 (m-30) REVERT: E 116 ARG cc_start: 0.9239 (tpp80) cc_final: 0.9028 (tpp80) REVERT: E 132 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: F 34 GLU cc_start: 0.9281 (tt0) cc_final: 0.8909 (tt0) REVERT: F 38 MET cc_start: 0.9323 (tmm) cc_final: 0.8992 (tmm) REVERT: F 39 CYS cc_start: 0.9382 (p) cc_final: 0.9023 (p) REVERT: F 60 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8958 (mt-10) REVERT: F 86 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8547 (tp40) REVERT: F 110 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8350 (mm-30) REVERT: F 116 ARG cc_start: 0.8520 (mmm160) cc_final: 0.7916 (mmp80) REVERT: G 29 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8616 (tm-30) REVERT: G 34 GLU cc_start: 0.8860 (tt0) cc_final: 0.8291 (tt0) REVERT: G 60 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8909 (mt-10) REVERT: G 70 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8084 (tp30) REVERT: G 79 LYS cc_start: 0.9496 (mppt) cc_final: 0.9111 (mtmm) REVERT: G 86 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8594 (mm-40) REVERT: G 92 ASP cc_start: 0.8925 (p0) cc_final: 0.8582 (p0) REVERT: H 21 ASP cc_start: 0.7645 (p0) cc_final: 0.7266 (p0) REVERT: H 31 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9037 (tp) REVERT: H 44 ARG cc_start: 0.9057 (ptm-80) cc_final: 0.8405 (ttt180) REVERT: H 95 MET cc_start: 0.8924 (mmm) cc_final: 0.8685 (mmm) REVERT: H 105 ASP cc_start: 0.9173 (m-30) cc_final: 0.8923 (m-30) REVERT: I 13 GLU cc_start: 0.9226 (mt-10) cc_final: 0.9009 (mt-10) REVERT: I 27 GLU cc_start: 0.7914 (mp0) cc_final: 0.7707 (pm20) REVERT: I 35 PHE cc_start: 0.9619 (t80) cc_final: 0.9003 (t80) REVERT: I 38 MET cc_start: 0.9252 (tmm) cc_final: 0.8928 (tmm) REVERT: I 39 CYS cc_start: 0.9360 (p) cc_final: 0.8728 (p) REVERT: I 60 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8905 (mt-10) REVERT: I 90 VAL cc_start: 0.9013 (t) cc_final: 0.8546 (t) REVERT: I 92 ASP cc_start: 0.8395 (t0) cc_final: 0.8187 (t0) REVERT: I 116 ARG cc_start: 0.8701 (mmm160) cc_final: 0.7907 (mmm160) REVERT: J 13 GLU cc_start: 0.8753 (tp30) cc_final: 0.8370 (tp30) REVERT: J 21 ASP cc_start: 0.8664 (p0) cc_final: 0.8255 (p0) REVERT: J 27 GLU cc_start: 0.7273 (mp0) cc_final: 0.7008 (mp0) REVERT: J 60 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8734 (mt-10) REVERT: J 70 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8302 (tp30) REVERT: J 79 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8856 (mtmm) REVERT: J 83 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7959 (pp20) REVERT: J 92 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8504 (p0) REVERT: K 44 ARG cc_start: 0.8667 (tpp80) cc_final: 0.8364 (tpp80) REVERT: K 69 LYS cc_start: 0.9754 (tttp) cc_final: 0.9440 (ttmm) REVERT: K 86 GLN cc_start: 0.9146 (tp40) cc_final: 0.8742 (tp-100) REVERT: K 105 ASP cc_start: 0.9318 (m-30) cc_final: 0.9116 (m-30) REVERT: L 13 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8908 (mt-10) REVERT: L 17 ASN cc_start: 0.9618 (m-40) cc_final: 0.9280 (m-40) REVERT: L 38 MET cc_start: 0.9232 (tmm) cc_final: 0.8932 (tmm) REVERT: L 39 CYS cc_start: 0.9238 (p) cc_final: 0.8658 (p) REVERT: L 76 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9044 (mmmm) REVERT: L 83 GLU cc_start: 0.8284 (mp0) cc_final: 0.7937 (mp0) REVERT: L 86 GLN cc_start: 0.9333 (mm-40) cc_final: 0.8829 (tp40) REVERT: L 124 ASP cc_start: 0.8774 (t70) cc_final: 0.8132 (t0) REVERT: M 17 ASN cc_start: 0.9530 (m-40) cc_final: 0.9283 (m110) REVERT: M 46 GLN cc_start: 0.6433 (tm-30) cc_final: 0.6210 (tm-30) REVERT: M 69 LYS cc_start: 0.9679 (OUTLIER) cc_final: 0.9465 (ttpp) REVERT: M 70 GLU cc_start: 0.8996 (tp30) cc_final: 0.8499 (tp30) REVERT: M 75 ASP cc_start: 0.8946 (p0) cc_final: 0.8734 (p0) REVERT: M 83 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7554 (pp20) REVERT: M 86 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8519 (mm110) REVERT: M 102 ASP cc_start: 0.9228 (m-30) cc_final: 0.9002 (m-30) REVERT: M 106 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8623 (mp0) REVERT: M 116 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8504 (tpp80) REVERT: M 131 ASP cc_start: 0.8970 (t0) cc_final: 0.8647 (t0) REVERT: N 86 GLN cc_start: 0.8504 (mp10) cc_final: 0.8209 (mp10) REVERT: N 89 LYS cc_start: 0.8581 (ptmm) cc_final: 0.7773 (ptmm) REVERT: N 90 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8534 (m) REVERT: N 92 ASP cc_start: 0.7656 (p0) cc_final: 0.7142 (p0) REVERT: N 105 ASP cc_start: 0.9241 (m-30) cc_final: 0.8943 (m-30) REVERT: O 21 ASP cc_start: 0.7619 (p0) cc_final: 0.7266 (p0) REVERT: O 38 MET cc_start: 0.8947 (tmm) cc_final: 0.8609 (tmm) REVERT: O 39 CYS cc_start: 0.9162 (p) cc_final: 0.8777 (p) REVERT: O 91 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: O 92 ASP cc_start: 0.7066 (t70) cc_final: 0.6627 (t0) REVERT: O 102 ASP cc_start: 0.9104 (m-30) cc_final: 0.8735 (m-30) REVERT: O 105 ASP cc_start: 0.9411 (m-30) cc_final: 0.9187 (m-30) REVERT: O 112 LYS cc_start: 0.9520 (ptpp) cc_final: 0.9309 (mttp) REVERT: O 116 ARG cc_start: 0.8435 (mmp80) cc_final: 0.8234 (mmp80) REVERT: a 62 ASP cc_start: 0.7964 (t0) cc_final: 0.7677 (t0) REVERT: a 108 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9057 (mm) REVERT: a 112 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8867 (mm-30) REVERT: a 113 ASP cc_start: 0.9175 (t70) cc_final: 0.8839 (t0) REVERT: a 117 ASP cc_start: 0.9466 (m-30) cc_final: 0.9213 (m-30) REVERT: b 1 MET cc_start: 0.8318 (tpt) cc_final: 0.7578 (tpt) REVERT: b 55 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8468 (t) REVERT: b 91 VAL cc_start: 0.9629 (t) cc_final: 0.9394 (p) REVERT: b 117 ASP cc_start: 0.9047 (m-30) cc_final: 0.8678 (t0) REVERT: c 5 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7877 (mtmm) REVERT: d 1 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8514 (tpp) REVERT: d 14 GLN cc_start: 0.9026 (mp10) cc_final: 0.8735 (mp10) REVERT: d 17 ILE cc_start: 0.9361 (pt) cc_final: 0.9076 (mm) REVERT: d 29 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8517 (p) REVERT: d 50 GLU cc_start: 0.7518 (tp30) cc_final: 0.7258 (tp30) REVERT: e 5 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8354 (mtmm) REVERT: e 14 GLN cc_start: 0.8875 (mp10) cc_final: 0.8554 (mp10) REVERT: e 30 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.6809 (p90) REVERT: f 5 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7782 (mtmm) REVERT: f 27 ASN cc_start: 0.8657 (m-40) cc_final: 0.8358 (m-40) REVERT: f 59 VAL cc_start: 0.7969 (p) cc_final: 0.7508 (m) REVERT: f 86 ASP cc_start: 0.8580 (p0) cc_final: 0.8353 (p0) REVERT: f 109 ASN cc_start: 0.8893 (m-40) cc_final: 0.8563 (m110) REVERT: f 113 ASP cc_start: 0.9137 (m-30) cc_final: 0.8619 (p0) REVERT: g 50 GLU cc_start: 0.8327 (mp0) cc_final: 0.8080 (pm20) REVERT: g 68 LEU cc_start: 0.9640 (tt) cc_final: 0.9424 (tt) REVERT: h 1 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.5758 (tmm) REVERT: h 36 TYR cc_start: 0.8801 (m-80) cc_final: 0.8510 (m-10) REVERT: i 112 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8921 (mm-30) REVERT: j 1 MET cc_start: 0.6654 (OUTLIER) cc_final: 0.6249 (ttt) REVERT: j 12 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8230 (p0) REVERT: j 48 ASN cc_start: 0.8943 (t0) cc_final: 0.8415 (t0) REVERT: j 50 GLU cc_start: 0.8300 (pm20) cc_final: 0.7766 (pm20) REVERT: k 17 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9379 (mm) REVERT: l 14 GLN cc_start: 0.9304 (mp10) cc_final: 0.8934 (mp10) REVERT: m 12 ASP cc_start: 0.7776 (p0) cc_final: 0.7045 (p0) REVERT: m 13 ASP cc_start: 0.8281 (m-30) cc_final: 0.7827 (m-30) REVERT: m 14 GLN cc_start: 0.8944 (mp10) cc_final: 0.8507 (mp10) REVERT: m 29 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7596 (p) REVERT: m 48 ASN cc_start: 0.9209 (t0) cc_final: 0.8828 (t0) REVERT: m 50 GLU cc_start: 0.8502 (pm20) cc_final: 0.7839 (pm20) REVERT: n 14 GLN cc_start: 0.9296 (mm-40) cc_final: 0.8780 (mm110) REVERT: n 111 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9170 (pp) REVERT: o 1 MET cc_start: 0.8005 (ttp) cc_final: 0.7343 (tmm) REVERT: o 54 ASN cc_start: 0.7992 (p0) cc_final: 0.7543 (p0) REVERT: o 65 TYR cc_start: 0.5969 (OUTLIER) cc_final: 0.4613 (t80) outliers start: 246 outliers final: 163 residues processed: 1287 average time/residue: 0.4543 time to fit residues: 906.0195 Evaluate side-chains 1246 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1061 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG 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 110 GLU Chi-restraints excluded: chain B residue 33 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 47 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER 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 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 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 80 GLU 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 118 LEU Chi-restraints excluded: chain F residue 122 VAL 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 G residue 98 ASN Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 53 LEU 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 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 79 LYS Chi-restraints excluded: chain J residue 90 VAL 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 56 LEU Chi-restraints excluded: chain K residue 80 GLU 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 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 132 ASP Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 69 LYS 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 74 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 44 ARG 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 91 GLU 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 10 HIS 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 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 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASN 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 70 THR 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 97 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 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain f residue 110 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 h residue 106 ASN 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 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 12 ASP 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 67 ILE 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 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 64 SER Chi-restraints excluded: chain n residue 91 VAL 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 65 TYR Chi-restraints excluded: chain o residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 368 optimal weight: 0.0060 chunk 271 optimal weight: 0.0770 chunk 262 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 370 optimal weight: 0.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN G 98 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN O 18 GLN O 78 ASN d 48 ASN ** e 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** 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** l 123 GLN ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055558 restraints weight = 147300.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.057169 restraints weight = 91966.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.058296 restraints weight = 64905.628| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31470 Z= 0.149 Angle : 0.793 13.100 42780 Z= 0.409 Chirality : 0.047 0.268 4995 Planarity : 0.005 0.065 5565 Dihedral : 7.157 66.082 4226 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.12 % Favored : 91.75 % Rotamer: Outliers : 5.87 % Allowed : 26.07 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3795 helix: 0.54 (0.13), residues: 1609 sheet: -0.51 (0.20), residues: 613 loop : -2.20 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP o 16 HIS 0.006 0.001 HIS o 10 PHE 0.018 0.002 PHE B 42 TYR 0.039 0.002 TYR h 114 ARG 0.008 0.001 ARG f 93 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 1420) hydrogen bonds : angle 5.09129 ( 4086) covalent geometry : bond 0.00326 (31470) covalent geometry : angle 0.79349 (42780) *********************** 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 1377 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1170 time to evaluate : 3.581 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: A 13 GLU cc_start: 0.8884 (tp30) cc_final: 0.8441 (tp30) REVERT: A 29 GLU cc_start: 0.9033 (tp30) cc_final: 0.8393 (tp30) REVERT: A 30 GLU cc_start: 0.8934 (pm20) cc_final: 0.8298 (pm20) REVERT: A 35 PHE cc_start: 0.9669 (t80) cc_final: 0.9255 (t80) REVERT: A 38 MET cc_start: 0.9254 (tmm) cc_final: 0.8610 (tmm) REVERT: A 70 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8415 (tp30) REVERT: A 79 LYS cc_start: 0.9473 (mtmm) cc_final: 0.9217 (mppt) REVERT: A 92 ASP cc_start: 0.8787 (p0) cc_final: 0.8475 (p0) REVERT: A 112 LYS cc_start: 0.9358 (mtmm) cc_final: 0.9058 (mtmm) REVERT: B 76 LYS cc_start: 0.9429 (tppt) cc_final: 0.9096 (mmmm) REVERT: B 86 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8744 (tp-100) REVERT: B 105 ASP cc_start: 0.9256 (m-30) cc_final: 0.9029 (m-30) REVERT: B 106 GLU cc_start: 0.9324 (tp30) cc_final: 0.8964 (tp30) REVERT: B 116 ARG cc_start: 0.9136 (tpp80) cc_final: 0.8924 (tpp80) REVERT: B 124 ASP cc_start: 0.8668 (t0) cc_final: 0.8025 (t0) REVERT: B 131 ASP cc_start: 0.9304 (t0) cc_final: 0.8866 (t0) REVERT: C 13 GLU cc_start: 0.8895 (tp30) cc_final: 0.7807 (tp30) REVERT: C 17 ASN cc_start: 0.9459 (m-40) cc_final: 0.8468 (m-40) REVERT: C 19 PHE cc_start: 0.8769 (m-80) cc_final: 0.8478 (m-80) REVERT: C 30 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: C 38 MET cc_start: 0.9089 (tmm) cc_final: 0.8712 (tmm) REVERT: C 60 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8649 (mt-10) REVERT: C 70 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8642 (mm-30) REVERT: C 86 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8392 (tp40) REVERT: C 102 ASP cc_start: 0.9159 (m-30) cc_final: 0.8866 (m-30) REVERT: C 105 ASP cc_start: 0.9438 (m-30) cc_final: 0.9204 (m-30) REVERT: C 116 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8230 (mmm160) REVERT: D 15 TYR cc_start: 0.9044 (t80) cc_final: 0.8761 (t80) REVERT: D 21 ASP cc_start: 0.7652 (p0) cc_final: 0.7425 (p0) REVERT: D 44 ARG cc_start: 0.8729 (ptm160) cc_final: 0.8219 (ptm160) REVERT: D 54 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9169 (pp) REVERT: D 60 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8928 (mm-30) REVERT: D 69 LYS cc_start: 0.9658 (OUTLIER) cc_final: 0.9373 (ttpp) REVERT: D 73 ARG cc_start: 0.9255 (ttp80) cc_final: 0.9024 (ttp80) REVERT: D 106 GLU cc_start: 0.8996 (tp30) cc_final: 0.8654 (tp30) REVERT: D 116 ARG cc_start: 0.8664 (tpp80) cc_final: 0.8451 (tpp80) REVERT: D 132 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7309 (t0) REVERT: E 17 ASN cc_start: 0.9479 (m-40) cc_final: 0.9149 (m110) REVERT: E 46 GLN cc_start: 0.9334 (tp-100) cc_final: 0.8842 (tp-100) REVERT: E 83 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8383 (tm-30) REVERT: E 92 ASP cc_start: 0.7795 (p0) cc_final: 0.7264 (p0) REVERT: E 105 ASP cc_start: 0.9260 (m-30) cc_final: 0.8989 (m-30) REVERT: E 116 ARG cc_start: 0.9239 (tpp80) cc_final: 0.8969 (tpp80) REVERT: E 132 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: F 13 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8903 (pt0) REVERT: F 34 GLU cc_start: 0.9307 (tt0) cc_final: 0.8929 (tt0) REVERT: F 38 MET cc_start: 0.9313 (tmm) cc_final: 0.8968 (tmm) REVERT: F 39 CYS cc_start: 0.9335 (p) cc_final: 0.9025 (p) REVERT: F 86 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8475 (tp40) REVERT: F 110 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8334 (mm-30) REVERT: G 29 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8657 (tm-30) REVERT: G 34 GLU cc_start: 0.8846 (tt0) cc_final: 0.8241 (tt0) REVERT: G 60 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8897 (mt-10) REVERT: G 70 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8338 (mm-30) REVERT: G 86 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8575 (mm-40) REVERT: G 92 ASP cc_start: 0.8931 (p0) cc_final: 0.8577 (p0) REVERT: G 124 ASP cc_start: 0.8693 (t0) cc_final: 0.8431 (t0) REVERT: H 21 ASP cc_start: 0.7734 (p0) cc_final: 0.7348 (p0) REVERT: H 31 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8992 (tp) REVERT: H 44 ARG cc_start: 0.9068 (ptm-80) cc_final: 0.8490 (ttt90) REVERT: H 82 ILE cc_start: 0.9316 (tp) cc_final: 0.9045 (mt) REVERT: H 105 ASP cc_start: 0.9161 (m-30) cc_final: 0.8909 (m-30) REVERT: H 116 ARG cc_start: 0.8972 (tpp80) cc_final: 0.8600 (tpp80) REVERT: I 21 ASP cc_start: 0.8376 (p0) cc_final: 0.8107 (p0) REVERT: I 35 PHE cc_start: 0.9603 (t80) cc_final: 0.8974 (t80) REVERT: I 38 MET cc_start: 0.9253 (tmm) cc_final: 0.8957 (tmm) REVERT: I 39 CYS cc_start: 0.9346 (p) cc_final: 0.8697 (p) REVERT: I 60 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8921 (mt-10) REVERT: I 90 VAL cc_start: 0.9031 (t) cc_final: 0.8731 (p) REVERT: I 99 TYR cc_start: 0.8441 (t80) cc_final: 0.8082 (t80) REVERT: I 104 LYS cc_start: 0.9505 (mmtt) cc_final: 0.9293 (mmtt) REVERT: I 116 ARG cc_start: 0.8588 (mmm160) cc_final: 0.8121 (mmm160) REVERT: J 13 GLU cc_start: 0.8772 (tp30) cc_final: 0.8419 (tp30) REVERT: J 21 ASP cc_start: 0.8678 (p0) cc_final: 0.8290 (p0) REVERT: J 27 GLU cc_start: 0.7098 (mp0) cc_final: 0.6792 (mp0) REVERT: J 34 GLU cc_start: 0.9066 (tt0) cc_final: 0.8528 (tt0) REVERT: J 60 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8688 (mt-10) REVERT: J 69 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9393 (ttpp) REVERT: J 70 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8362 (tp30) REVERT: J 79 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8849 (mtmm) REVERT: J 83 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7927 (tm-30) REVERT: J 92 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8645 (p0) REVERT: J 110 GLU cc_start: 0.8982 (tt0) cc_final: 0.8605 (tt0) REVERT: K 46 GLN cc_start: 0.9172 (mp10) cc_final: 0.8881 (mp10) REVERT: K 69 LYS cc_start: 0.9737 (tttp) cc_final: 0.9412 (ttmm) REVERT: K 75 ASP cc_start: 0.9094 (t0) cc_final: 0.8862 (t0) REVERT: K 86 GLN cc_start: 0.9077 (tp40) cc_final: 0.8671 (tp-100) REVERT: K 105 ASP cc_start: 0.9326 (m-30) cc_final: 0.9050 (m-30) REVERT: K 116 ARG cc_start: 0.9112 (mmt-90) cc_final: 0.8729 (tpp80) REVERT: L 13 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8827 (mt-10) REVERT: L 17 ASN cc_start: 0.9623 (m-40) cc_final: 0.9293 (m-40) REVERT: L 21 ASP cc_start: 0.7774 (p0) cc_final: 0.7395 (p0) REVERT: L 38 MET cc_start: 0.9253 (tmm) cc_final: 0.8933 (tmm) REVERT: L 39 CYS cc_start: 0.9256 (p) cc_final: 0.8670 (p) REVERT: L 76 LYS cc_start: 0.9351 (mmmm) cc_final: 0.9026 (mmmm) REVERT: L 79 LYS cc_start: 0.9404 (mmmm) cc_final: 0.8882 (mmmm) REVERT: L 83 GLU cc_start: 0.8246 (mp0) cc_final: 0.7602 (mp0) REVERT: L 86 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8814 (tp40) REVERT: L 124 ASP cc_start: 0.8805 (t70) cc_final: 0.8352 (t0) REVERT: M 17 ASN cc_start: 0.9514 (m-40) cc_final: 0.9277 (m110) REVERT: M 49 PHE cc_start: 0.9212 (t80) cc_final: 0.8998 (t80) REVERT: M 69 LYS cc_start: 0.9671 (OUTLIER) cc_final: 0.9386 (ttpp) REVERT: M 70 GLU cc_start: 0.9000 (tp30) cc_final: 0.8661 (tp30) REVERT: M 73 ARG cc_start: 0.9338 (tmm-80) cc_final: 0.8590 (ttp80) REVERT: M 83 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7439 (pp20) REVERT: M 106 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8669 (mp0) REVERT: M 116 ARG cc_start: 0.8848 (tpp80) cc_final: 0.8539 (tpp80) REVERT: M 131 ASP cc_start: 0.8990 (t0) cc_final: 0.8582 (t0) REVERT: M 132 ASP cc_start: 0.8769 (m-30) cc_final: 0.8123 (m-30) REVERT: N 35 PHE cc_start: 0.9489 (t80) cc_final: 0.9244 (t80) REVERT: N 44 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7831 (tpt170) REVERT: N 89 LYS cc_start: 0.8644 (ptmm) cc_final: 0.7841 (ptmm) REVERT: N 92 ASP cc_start: 0.7818 (p0) cc_final: 0.7203 (p0) REVERT: N 105 ASP cc_start: 0.9234 (m-30) cc_final: 0.8925 (m-30) REVERT: O 13 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8977 (mt-10) REVERT: O 21 ASP cc_start: 0.7583 (p0) cc_final: 0.7232 (p0) REVERT: O 38 MET cc_start: 0.8908 (tmm) cc_final: 0.8555 (tmm) REVERT: O 39 CYS cc_start: 0.9168 (p) cc_final: 0.8802 (p) REVERT: O 92 ASP cc_start: 0.7089 (t70) cc_final: 0.6582 (t0) REVERT: O 94 THR cc_start: 0.9243 (m) cc_final: 0.8946 (p) REVERT: O 102 ASP cc_start: 0.9054 (m-30) cc_final: 0.8661 (m-30) REVERT: O 105 ASP cc_start: 0.9379 (m-30) cc_final: 0.9090 (m-30) REVERT: O 112 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9238 (mttp) REVERT: O 116 ARG cc_start: 0.8411 (mmp80) cc_final: 0.8143 (mmp80) REVERT: a 62 ASP cc_start: 0.7980 (t0) cc_final: 0.7710 (t0) REVERT: a 75 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8051 (mmmt) REVERT: a 108 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9009 (mm) REVERT: a 112 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8722 (mm-30) REVERT: a 113 ASP cc_start: 0.9151 (t70) cc_final: 0.8772 (t0) REVERT: a 117 ASP cc_start: 0.9444 (m-30) cc_final: 0.9166 (m-30) REVERT: b 1 MET cc_start: 0.8170 (tpt) cc_final: 0.7434 (tpt) REVERT: b 18 ASN cc_start: 0.9328 (t0) cc_final: 0.9126 (t0) REVERT: b 55 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8472 (t) REVERT: b 91 VAL cc_start: 0.9623 (t) cc_final: 0.9382 (p) REVERT: b 117 ASP cc_start: 0.9003 (m-30) cc_final: 0.8658 (t0) REVERT: c 5 LYS cc_start: 0.8455 (mtmm) cc_final: 0.7808 (mtmm) REVERT: c 50 GLU cc_start: 0.7939 (tp30) cc_final: 0.7251 (tp30) REVERT: c 82 ASP cc_start: 0.8371 (t0) cc_final: 0.8120 (m-30) REVERT: c 103 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8607 (mm-30) REVERT: c 114 TYR cc_start: 0.9139 (t80) cc_final: 0.8894 (t80) REVERT: d 1 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8491 (tpp) REVERT: d 14 GLN cc_start: 0.8902 (mp10) cc_final: 0.8622 (mp10) REVERT: d 29 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8427 (p) REVERT: d 50 GLU cc_start: 0.7453 (tp30) cc_final: 0.7103 (tp30) REVERT: e 14 GLN cc_start: 0.8949 (mp10) cc_final: 0.8632 (mm-40) REVERT: e 30 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.6543 (p90) REVERT: f 5 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7731 (mtmm) REVERT: f 27 ASN cc_start: 0.8716 (m-40) cc_final: 0.8405 (m-40) REVERT: f 82 ASP cc_start: 0.8409 (t0) cc_final: 0.8106 (m-30) REVERT: f 86 ASP cc_start: 0.8548 (p0) cc_final: 0.8320 (p0) REVERT: f 109 ASN cc_start: 0.8885 (m-40) cc_final: 0.8578 (m110) REVERT: g 1 MET cc_start: 0.8574 (tpp) cc_final: 0.8350 (tpp) REVERT: g 68 LEU cc_start: 0.9621 (tt) cc_final: 0.9382 (tt) REVERT: g 86 ASP cc_start: 0.8827 (m-30) cc_final: 0.8554 (t0) REVERT: h 1 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6072 (tmm) REVERT: h 11 LEU cc_start: 0.9223 (tt) cc_final: 0.9008 (tt) REVERT: h 36 TYR cc_start: 0.8714 (m-80) cc_final: 0.8489 (m-10) REVERT: h 74 LYS cc_start: 0.9380 (mmtp) cc_final: 0.9110 (mmmm) REVERT: i 114 TYR cc_start: 0.8933 (t80) cc_final: 0.8535 (t80) REVERT: j 1 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6045 (ttt) REVERT: j 12 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8252 (p0) REVERT: j 48 ASN cc_start: 0.9014 (t0) cc_final: 0.8489 (t0) REVERT: j 50 GLU cc_start: 0.8359 (pm20) cc_final: 0.7737 (pm20) REVERT: k 17 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9378 (mm) REVERT: l 14 GLN cc_start: 0.9272 (mp10) cc_final: 0.8913 (mp10) REVERT: l 27 ASN cc_start: 0.8624 (m-40) cc_final: 0.8378 (m-40) REVERT: m 12 ASP cc_start: 0.7756 (p0) cc_final: 0.7252 (p0) REVERT: m 13 ASP cc_start: 0.8151 (m-30) cc_final: 0.7865 (m-30) REVERT: m 29 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7498 (p) REVERT: m 48 ASN cc_start: 0.9251 (t0) cc_final: 0.8745 (t0) REVERT: m 50 GLU cc_start: 0.8495 (pm20) cc_final: 0.7768 (pm20) REVERT: n 111 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9184 (pp) REVERT: o 54 ASN cc_start: 0.8034 (p0) cc_final: 0.7590 (p0) REVERT: o 65 TYR cc_start: 0.5966 (OUTLIER) cc_final: 0.4740 (t80) outliers start: 207 outliers final: 126 residues processed: 1284 average time/residue: 0.5002 time to fit residues: 1007.0241 Evaluate side-chains 1218 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1067 time to evaluate : 3.606 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 94 THR 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 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 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 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 133 VAL 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 31 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain I residue 47 ASN 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 79 LYS Chi-restraints excluded: chain J residue 90 VAL 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 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 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 53 LEU Chi-restraints excluded: chain M residue 69 LYS 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 18 GLN Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 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 10 HIS 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 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS 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 90 SER 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 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 106 ASN Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain i residue 52 VAL 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 1 MET Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 42 HIS 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 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 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 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 81 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 373 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 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 51 ASN E 18 GLN E 51 ASN F 46 GLN ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 ASN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN a 48 ASN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** 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** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 109 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053389 restraints weight = 149477.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054923 restraints weight = 92802.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056021 restraints weight = 65459.889| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 31470 Z= 0.196 Angle : 0.809 15.808 42780 Z= 0.423 Chirality : 0.047 0.214 4995 Planarity : 0.005 0.064 5565 Dihedral : 7.010 63.340 4211 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.38 % Rotamer: Outliers : 6.21 % Allowed : 26.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3795 helix: 0.39 (0.12), residues: 1611 sheet: -0.39 (0.21), residues: 600 loop : -2.19 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 16 HIS 0.008 0.001 HIS j 10 PHE 0.038 0.002 PHE A 49 TYR 0.042 0.002 TYR h 114 ARG 0.009 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1420) hydrogen bonds : angle 5.18537 ( 4086) covalent geometry : bond 0.00439 (31470) covalent geometry : angle 0.80890 (42780) *********************** 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 1317 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1098 time to evaluate : 3.816 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: A 13 GLU cc_start: 0.8904 (tp30) cc_final: 0.8460 (tp30) REVERT: A 29 GLU cc_start: 0.9039 (tp30) cc_final: 0.8304 (tp30) REVERT: A 30 GLU cc_start: 0.8870 (pm20) cc_final: 0.8190 (pm20) REVERT: A 35 PHE cc_start: 0.9629 (t80) cc_final: 0.9213 (t80) REVERT: A 38 MET cc_start: 0.9273 (tmm) cc_final: 0.8676 (tmm) REVERT: A 70 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8226 (tp30) REVERT: A 73 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8605 (ttp80) REVERT: A 76 LYS cc_start: 0.9411 (tppt) cc_final: 0.9163 (tppt) REVERT: A 79 LYS cc_start: 0.9524 (mtmm) cc_final: 0.9313 (mtmm) REVERT: A 92 ASP cc_start: 0.8864 (p0) cc_final: 0.8583 (p0) REVERT: A 124 ASP cc_start: 0.9237 (t0) cc_final: 0.8875 (t0) REVERT: A 132 ASP cc_start: 0.8680 (m-30) cc_final: 0.8054 (t70) REVERT: B 76 LYS cc_start: 0.9425 (tppt) cc_final: 0.9097 (mmmm) REVERT: B 86 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8745 (tp-100) REVERT: B 105 ASP cc_start: 0.9272 (m-30) cc_final: 0.9062 (m-30) REVERT: B 106 GLU cc_start: 0.9378 (tp30) cc_final: 0.8839 (tp30) REVERT: B 116 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8768 (tpp80) REVERT: B 124 ASP cc_start: 0.8822 (t0) cc_final: 0.8261 (t0) REVERT: B 131 ASP cc_start: 0.9297 (t0) cc_final: 0.8890 (t0) REVERT: C 13 GLU cc_start: 0.8935 (tp30) cc_final: 0.7850 (tp30) REVERT: C 17 ASN cc_start: 0.9459 (m-40) cc_final: 0.8576 (m-40) REVERT: C 19 PHE cc_start: 0.8813 (m-80) cc_final: 0.8499 (m-80) REVERT: C 30 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: C 38 MET cc_start: 0.9147 (tmm) cc_final: 0.8771 (tmm) REVERT: C 60 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8873 (mt-10) REVERT: C 70 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8592 (mm-30) REVERT: C 83 GLU cc_start: 0.7953 (mp0) cc_final: 0.7482 (mp0) REVERT: C 86 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8504 (tp40) REVERT: C 92 ASP cc_start: 0.8213 (p0) cc_final: 0.7618 (p0) REVERT: C 102 ASP cc_start: 0.9169 (m-30) cc_final: 0.8859 (m-30) REVERT: C 105 ASP cc_start: 0.9446 (m-30) cc_final: 0.9214 (m-30) REVERT: C 116 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8287 (mmm160) REVERT: D 21 ASP cc_start: 0.7717 (p0) cc_final: 0.7435 (p0) REVERT: D 29 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8620 (tm-30) REVERT: D 44 ARG cc_start: 0.8730 (ptm160) cc_final: 0.8195 (ptm160) REVERT: D 54 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9126 (pp) REVERT: D 60 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8939 (mm-30) REVERT: D 69 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9379 (ttpp) REVERT: D 73 ARG cc_start: 0.9267 (ttp80) cc_final: 0.8907 (ttp80) REVERT: D 76 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8754 (mmtm) REVERT: D 79 LYS cc_start: 0.9387 (mppt) cc_final: 0.9126 (mmtm) REVERT: D 106 GLU cc_start: 0.8961 (tp30) cc_final: 0.8672 (tp30) REVERT: D 112 LYS cc_start: 0.9432 (mtmm) cc_final: 0.8948 (mtmm) REVERT: D 132 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7406 (t0) REVERT: E 17 ASN cc_start: 0.9502 (m-40) cc_final: 0.9198 (m110) REVERT: E 46 GLN cc_start: 0.9378 (tp-100) cc_final: 0.8834 (tp-100) REVERT: E 92 ASP cc_start: 0.7757 (p0) cc_final: 0.7175 (p0) REVERT: E 116 ARG cc_start: 0.9216 (tpp80) cc_final: 0.8920 (tpp80) REVERT: E 132 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: E 136 ARG cc_start: 0.8519 (ttt180) cc_final: 0.8248 (tmm160) REVERT: F 13 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8921 (pt0) REVERT: F 38 MET cc_start: 0.9342 (tmm) cc_final: 0.9047 (tmm) REVERT: F 39 CYS cc_start: 0.9361 (p) cc_final: 0.9078 (p) REVERT: F 86 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8555 (tp40) REVERT: F 110 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8376 (mm-30) REVERT: F 116 ARG cc_start: 0.8506 (mmp80) cc_final: 0.8271 (mmp80) REVERT: G 21 ASP cc_start: 0.8442 (p0) cc_final: 0.8026 (p0) REVERT: G 34 GLU cc_start: 0.8837 (tt0) cc_final: 0.8220 (tt0) REVERT: G 70 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8148 (tp30) REVERT: G 79 LYS cc_start: 0.9495 (mppt) cc_final: 0.9097 (mtmm) REVERT: G 92 ASP cc_start: 0.8908 (p0) cc_final: 0.8552 (p0) REVERT: G 127 TYR cc_start: 0.8600 (m-80) cc_final: 0.8269 (m-80) REVERT: H 21 ASP cc_start: 0.7698 (p0) cc_final: 0.7311 (p0) REVERT: H 44 ARG cc_start: 0.9057 (ptm-80) cc_final: 0.8517 (ttt180) REVERT: H 82 ILE cc_start: 0.9343 (tp) cc_final: 0.9071 (mt) REVERT: H 92 ASP cc_start: 0.8331 (p0) cc_final: 0.7515 (p0) REVERT: H 105 ASP cc_start: 0.9223 (m-30) cc_final: 0.8937 (m-30) REVERT: I 21 ASP cc_start: 0.8389 (p0) cc_final: 0.8100 (p0) REVERT: I 35 PHE cc_start: 0.9621 (t80) cc_final: 0.8992 (t80) REVERT: I 38 MET cc_start: 0.9256 (tmm) cc_final: 0.8949 (tmm) REVERT: I 39 CYS cc_start: 0.9388 (p) cc_final: 0.8755 (p) REVERT: I 60 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8732 (mt-10) REVERT: I 90 VAL cc_start: 0.9121 (t) cc_final: 0.8803 (p) REVERT: I 95 MET cc_start: 0.8913 (mmm) cc_final: 0.8702 (mmm) REVERT: I 116 ARG cc_start: 0.8662 (mmm160) cc_final: 0.8416 (mmp80) REVERT: J 13 GLU cc_start: 0.8786 (tp30) cc_final: 0.8167 (tp30) REVERT: J 17 ASN cc_start: 0.8688 (m110) cc_final: 0.7666 (m110) REVERT: J 21 ASP cc_start: 0.8676 (p0) cc_final: 0.8319 (p0) REVERT: J 27 GLU cc_start: 0.7348 (mp0) cc_final: 0.7027 (mp0) REVERT: J 34 GLU cc_start: 0.9041 (tt0) cc_final: 0.8523 (tt0) REVERT: J 60 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8767 (mt-10) REVERT: J 69 LYS cc_start: 0.9618 (OUTLIER) cc_final: 0.9393 (ttpp) REVERT: J 70 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8458 (tp30) REVERT: J 92 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8458 (p0) REVERT: J 110 GLU cc_start: 0.9051 (tt0) cc_final: 0.8595 (tt0) REVERT: J 112 LYS cc_start: 0.9423 (mtmm) cc_final: 0.9191 (mttm) REVERT: K 44 ARG cc_start: 0.8648 (tpp80) cc_final: 0.8310 (tpp80) REVERT: K 69 LYS cc_start: 0.9756 (tttp) cc_final: 0.9419 (ttmm) REVERT: K 79 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8446 (mttp) REVERT: K 86 GLN cc_start: 0.9124 (tp40) cc_final: 0.8715 (tp-100) REVERT: K 92 ASP cc_start: 0.8096 (p0) cc_final: 0.7709 (p0) REVERT: L 13 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8911 (mt-10) REVERT: L 17 ASN cc_start: 0.9632 (m-40) cc_final: 0.9298 (m-40) REVERT: L 38 MET cc_start: 0.9268 (tmm) cc_final: 0.9060 (tmm) REVERT: L 39 CYS cc_start: 0.9224 (p) cc_final: 0.8816 (p) REVERT: L 76 LYS cc_start: 0.9400 (mmmm) cc_final: 0.9061 (mmmm) REVERT: L 83 GLU cc_start: 0.8318 (mp0) cc_final: 0.7981 (mp0) REVERT: L 86 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8867 (tp40) REVERT: L 110 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8987 (tp30) REVERT: M 17 ASN cc_start: 0.9545 (m-40) cc_final: 0.9299 (m-40) REVERT: M 69 LYS cc_start: 0.9679 (OUTLIER) cc_final: 0.9472 (ttpp) REVERT: M 70 GLU cc_start: 0.9014 (tp30) cc_final: 0.8190 (tp30) REVERT: M 83 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7527 (pp20) REVERT: M 106 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8665 (mp0) REVERT: M 131 ASP cc_start: 0.9022 (t0) cc_final: 0.8641 (t0) REVERT: M 132 ASP cc_start: 0.8770 (m-30) cc_final: 0.8164 (m-30) REVERT: N 35 PHE cc_start: 0.9533 (t80) cc_final: 0.9304 (t80) REVERT: N 86 GLN cc_start: 0.8652 (mp10) cc_final: 0.8232 (mp10) REVERT: N 89 LYS cc_start: 0.8722 (ptmm) cc_final: 0.7921 (ptmm) REVERT: N 92 ASP cc_start: 0.7636 (p0) cc_final: 0.6881 (p0) REVERT: N 105 ASP cc_start: 0.9242 (m-30) cc_final: 0.8949 (m-30) REVERT: O 21 ASP cc_start: 0.7662 (p0) cc_final: 0.7272 (p0) REVERT: O 38 MET cc_start: 0.8906 (tmm) cc_final: 0.8549 (tmm) REVERT: O 39 CYS cc_start: 0.9200 (p) cc_final: 0.8791 (p) REVERT: O 92 ASP cc_start: 0.7283 (t70) cc_final: 0.6785 (t0) REVERT: O 99 TYR cc_start: 0.8344 (t80) cc_final: 0.8111 (t80) REVERT: O 102 ASP cc_start: 0.9055 (m-30) cc_final: 0.8682 (m-30) REVERT: O 105 ASP cc_start: 0.9415 (m-30) cc_final: 0.9176 (m-30) REVERT: a 62 ASP cc_start: 0.8083 (t0) cc_final: 0.7773 (t0) REVERT: a 75 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7817 (mmmt) REVERT: a 108 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8942 (mm) REVERT: a 112 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: a 113 ASP cc_start: 0.9174 (t70) cc_final: 0.8793 (t0) REVERT: a 117 ASP cc_start: 0.9451 (m-30) cc_final: 0.9185 (m-30) REVERT: b 1 MET cc_start: 0.8504 (tpt) cc_final: 0.8062 (tpt) REVERT: b 18 ASN cc_start: 0.9380 (t0) cc_final: 0.9174 (t0) REVERT: b 55 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8666 (t) REVERT: b 91 VAL cc_start: 0.9646 (t) cc_final: 0.9409 (p) REVERT: b 117 ASP cc_start: 0.9011 (m-30) cc_final: 0.8585 (t0) REVERT: c 5 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8220 (mtmm) REVERT: c 50 GLU cc_start: 0.7962 (tp30) cc_final: 0.7391 (tp30) REVERT: d 14 GLN cc_start: 0.8972 (mp10) cc_final: 0.8677 (mp10) REVERT: d 17 ILE cc_start: 0.9451 (pt) cc_final: 0.9159 (mm) REVERT: d 29 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8540 (p) REVERT: d 50 GLU cc_start: 0.7697 (tp30) cc_final: 0.7405 (tp30) REVERT: e 14 GLN cc_start: 0.8909 (mp10) cc_final: 0.8523 (mm-40) REVERT: e 30 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.6797 (p90) REVERT: f 27 ASN cc_start: 0.8729 (m-40) cc_final: 0.8375 (m-40) REVERT: g 48 ASN cc_start: 0.9342 (t0) cc_final: 0.9068 (t0) REVERT: g 68 LEU cc_start: 0.9649 (tt) cc_final: 0.9425 (tt) REVERT: g 86 ASP cc_start: 0.8885 (m-30) cc_final: 0.8542 (t0) REVERT: h 1 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6193 (tmm) REVERT: h 74 LYS cc_start: 0.9415 (mmtp) cc_final: 0.9130 (mmmm) REVERT: i 114 TYR cc_start: 0.8952 (t80) cc_final: 0.8573 (t80) REVERT: j 12 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8258 (p0) REVERT: j 48 ASN cc_start: 0.9000 (t0) cc_final: 0.8514 (t0) REVERT: j 50 GLU cc_start: 0.8196 (pm20) cc_final: 0.7585 (pm20) REVERT: j 101 ASP cc_start: 0.8331 (p0) cc_final: 0.8023 (p0) REVERT: j 112 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8784 (tm-30) REVERT: l 14 GLN cc_start: 0.9285 (mp10) cc_final: 0.8952 (mm-40) REVERT: l 27 ASN cc_start: 0.8684 (m-40) cc_final: 0.8415 (m-40) REVERT: l 123 GLN cc_start: 0.8092 (mp10) cc_final: 0.7514 (tp40) REVERT: m 12 ASP cc_start: 0.7786 (p0) cc_final: 0.7264 (p0) REVERT: m 13 ASP cc_start: 0.8129 (m-30) cc_final: 0.7762 (m-30) REVERT: m 29 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7749 (p) REVERT: m 48 ASN cc_start: 0.9337 (t0) cc_final: 0.8770 (t0) REVERT: m 50 GLU cc_start: 0.8484 (pm20) cc_final: 0.7756 (pm20) REVERT: n 107 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8060 (m) REVERT: n 111 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9177 (pp) REVERT: o 50 GLU cc_start: 0.7824 (tp30) cc_final: 0.6970 (tp30) REVERT: o 54 ASN cc_start: 0.8254 (p0) cc_final: 0.7731 (p0) REVERT: o 65 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.4687 (t80) REVERT: o 93 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8427 (tmt-80) outliers start: 219 outliers final: 159 residues processed: 1230 average time/residue: 0.4648 time to fit residues: 889.4507 Evaluate side-chains 1227 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1045 time to evaluate : 4.887 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 86 GLN 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 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 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 E residue 132 ASP Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 46 GLN 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 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 94 THR Chi-restraints excluded: chain H residue 118 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 94 THR Chi-restraints excluded: chain I residue 107 LEU 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 90 VAL 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 28 LEU Chi-restraints excluded: chain K residue 46 GLN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 GLU 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 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 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 69 LYS 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 18 GLN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain N residue 140 ASN Chi-restraints excluded: chain O residue 17 ASN Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 LEU 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 10 HIS 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 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 87 ILE Chi-restraints excluded: chain b residue 97 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASN 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 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 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 106 ASN 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 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 12 ASP Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 67 ILE 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 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 91 VAL 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 n residue 115 ILE Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 69 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 63 optimal weight: 0.0670 chunk 306 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 272 optimal weight: 30.0000 overall best weight: 5.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 ASN O 18 GLN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 GLN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** k 27 ASN ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 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 = 0.3310 r_free = 0.3310 target = 0.063667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050474 restraints weight = 151745.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.051990 restraints weight = 92074.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053047 restraints weight = 64564.252| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 31470 Z= 0.236 Angle : 0.851 13.681 42780 Z= 0.446 Chirality : 0.047 0.248 4995 Planarity : 0.005 0.063 5565 Dihedral : 7.078 58.690 4209 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.80 % Favored : 91.09 % Rotamer: Outliers : 6.24 % Allowed : 27.66 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 3795 helix: 0.29 (0.12), residues: 1612 sheet: -0.52 (0.21), residues: 609 loop : -2.20 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP o 16 HIS 0.012 0.001 HIS e 76 PHE 0.039 0.002 PHE A 49 TYR 0.041 0.002 TYR h 114 ARG 0.009 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 1420) hydrogen bonds : angle 5.27347 ( 4086) covalent geometry : bond 0.00524 (31470) covalent geometry : angle 0.85058 (42780) *********************** 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 1312 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1092 time to evaluate : 4.094 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: A 13 GLU cc_start: 0.8935 (tp30) cc_final: 0.8506 (tp30) REVERT: A 29 GLU cc_start: 0.9034 (tp30) cc_final: 0.8237 (tp30) REVERT: A 30 GLU cc_start: 0.8771 (pm20) cc_final: 0.7947 (pm20) REVERT: A 38 MET cc_start: 0.9306 (tmm) cc_final: 0.8757 (tmm) REVERT: A 70 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8530 (tp30) REVERT: A 73 ARG cc_start: 0.8924 (ttp80) cc_final: 0.8697 (ttp80) REVERT: A 76 LYS cc_start: 0.9406 (tppt) cc_final: 0.9152 (tppt) REVERT: A 79 LYS cc_start: 0.9539 (mtmm) cc_final: 0.9308 (mtmm) REVERT: A 92 ASP cc_start: 0.8855 (p0) cc_final: 0.8607 (p0) REVERT: A 124 ASP cc_start: 0.9249 (t0) cc_final: 0.8725 (t0) REVERT: A 132 ASP cc_start: 0.8794 (m-30) cc_final: 0.7785 (t70) REVERT: B 86 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8860 (tp-100) REVERT: B 91 GLU cc_start: 0.8251 (pp20) cc_final: 0.7573 (pp20) REVERT: B 105 ASP cc_start: 0.9329 (m-30) cc_final: 0.9121 (m-30) REVERT: B 116 ARG cc_start: 0.9172 (tpp80) cc_final: 0.8690 (tpp80) REVERT: B 124 ASP cc_start: 0.8900 (t0) cc_final: 0.8315 (t0) REVERT: B 131 ASP cc_start: 0.9281 (t0) cc_final: 0.9039 (t0) REVERT: C 13 GLU cc_start: 0.8934 (tp30) cc_final: 0.7894 (tp30) REVERT: C 17 ASN cc_start: 0.9410 (m-40) cc_final: 0.8438 (m-40) REVERT: C 19 PHE cc_start: 0.8791 (m-80) cc_final: 0.8508 (m-80) REVERT: C 30 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: C 38 MET cc_start: 0.9190 (tmm) cc_final: 0.8715 (tmm) REVERT: C 39 CYS cc_start: 0.9227 (p) cc_final: 0.8834 (p) REVERT: C 70 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8623 (mm-30) REVERT: C 79 LYS cc_start: 0.9345 (mmmm) cc_final: 0.9138 (mmmm) REVERT: C 83 GLU cc_start: 0.8047 (mp0) cc_final: 0.7736 (mp0) REVERT: C 86 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8690 (tp40) REVERT: C 102 ASP cc_start: 0.9160 (m-30) cc_final: 0.8852 (m-30) REVERT: C 105 ASP cc_start: 0.9455 (m-30) cc_final: 0.9209 (m-30) REVERT: C 116 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8316 (mmm160) REVERT: D 21 ASP cc_start: 0.7737 (p0) cc_final: 0.7375 (p0) REVERT: D 44 ARG cc_start: 0.8772 (ptm160) cc_final: 0.8205 (ptm160) REVERT: D 60 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8926 (mm-30) REVERT: D 69 LYS cc_start: 0.9680 (OUTLIER) cc_final: 0.9430 (ttpp) REVERT: D 75 ASP cc_start: 0.8616 (p0) cc_final: 0.8348 (p0) REVERT: D 106 GLU cc_start: 0.8998 (tp30) cc_final: 0.8589 (tp30) REVERT: E 17 ASN cc_start: 0.9505 (m-40) cc_final: 0.9216 (m110) REVERT: E 46 GLN cc_start: 0.9385 (tp-100) cc_final: 0.8825 (tp-100) REVERT: E 92 ASP cc_start: 0.7770 (p0) cc_final: 0.7165 (p0) REVERT: E 116 ARG cc_start: 0.9275 (tpp80) cc_final: 0.8964 (tpp80) REVERT: E 132 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7215 (m-30) REVERT: F 38 MET cc_start: 0.9357 (tmm) cc_final: 0.9045 (tmm) REVERT: F 86 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8579 (tp40) REVERT: F 110 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8469 (mm-30) REVERT: F 116 ARG cc_start: 0.8469 (mmp80) cc_final: 0.8255 (mmp80) REVERT: G 21 ASP cc_start: 0.8457 (p0) cc_final: 0.8060 (p0) REVERT: G 34 GLU cc_start: 0.8867 (tt0) cc_final: 0.8177 (tt0) REVERT: G 60 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8839 (mt-10) REVERT: G 70 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8179 (tp30) REVERT: G 79 LYS cc_start: 0.9512 (mppt) cc_final: 0.9158 (mtmm) REVERT: G 92 ASP cc_start: 0.8890 (p0) cc_final: 0.8506 (p0) REVERT: H 44 ARG cc_start: 0.9041 (ptm-80) cc_final: 0.8584 (ttt90) REVERT: H 102 ASP cc_start: 0.9285 (p0) cc_final: 0.9079 (p0) REVERT: H 105 ASP cc_start: 0.9184 (m-30) cc_final: 0.8892 (m-30) REVERT: H 116 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8690 (tpp80) REVERT: I 35 PHE cc_start: 0.9617 (t80) cc_final: 0.9180 (t80) REVERT: I 38 MET cc_start: 0.9278 (tmm) cc_final: 0.9062 (tmm) REVERT: I 39 CYS cc_start: 0.9360 (p) cc_final: 0.8917 (p) REVERT: I 60 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8844 (mt-10) REVERT: I 89 LYS cc_start: 0.9495 (ttpp) cc_final: 0.9188 (tttp) REVERT: I 90 VAL cc_start: 0.9166 (t) cc_final: 0.8821 (t) REVERT: I 116 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8191 (mmm160) REVERT: J 13 GLU cc_start: 0.8852 (tp30) cc_final: 0.8209 (tp30) REVERT: J 17 ASN cc_start: 0.8718 (m110) cc_final: 0.7728 (m110) REVERT: J 21 ASP cc_start: 0.8612 (p0) cc_final: 0.8204 (p0) REVERT: J 34 GLU cc_start: 0.9077 (tt0) cc_final: 0.8535 (tt0) REVERT: J 60 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8761 (mt-10) REVERT: J 69 LYS cc_start: 0.9627 (OUTLIER) cc_final: 0.9407 (ttpp) REVERT: J 70 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8433 (tp30) REVERT: J 92 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8628 (p0) REVERT: J 110 GLU cc_start: 0.9101 (tt0) cc_final: 0.8648 (tt0) REVERT: K 44 ARG cc_start: 0.8700 (tpp80) cc_final: 0.8459 (tpp80) REVERT: K 69 LYS cc_start: 0.9757 (tttp) cc_final: 0.9435 (ttmm) REVERT: K 86 GLN cc_start: 0.9078 (tp40) cc_final: 0.8624 (tp-100) REVERT: K 92 ASP cc_start: 0.7953 (p0) cc_final: 0.7563 (p0) REVERT: K 105 ASP cc_start: 0.9334 (m-30) cc_final: 0.9097 (m-30) REVERT: L 13 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8933 (mt-10) REVERT: L 17 ASN cc_start: 0.9653 (m-40) cc_final: 0.9329 (m-40) REVERT: L 38 MET cc_start: 0.9283 (tmm) cc_final: 0.9073 (tmm) REVERT: L 39 CYS cc_start: 0.9218 (p) cc_final: 0.8795 (p) REVERT: L 46 GLN cc_start: 0.9047 (mt0) cc_final: 0.8691 (mt0) REVERT: L 76 LYS cc_start: 0.9446 (mmmm) cc_final: 0.9056 (mmmm) REVERT: L 83 GLU cc_start: 0.8295 (mp0) cc_final: 0.7894 (mp0) REVERT: L 86 GLN cc_start: 0.9349 (mm-40) cc_final: 0.8901 (tp40) REVERT: L 124 ASP cc_start: 0.8803 (t0) cc_final: 0.8223 (t0) REVERT: M 17 ASN cc_start: 0.9566 (m-40) cc_final: 0.9310 (m110) REVERT: M 35 PHE cc_start: 0.9542 (t80) cc_final: 0.9268 (t80) REVERT: M 70 GLU cc_start: 0.9078 (tp30) cc_final: 0.8431 (tp30) REVERT: M 73 ARG cc_start: 0.9351 (tmm-80) cc_final: 0.8704 (ttp80) REVERT: M 83 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7632 (pp20) REVERT: M 106 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8667 (mp0) REVERT: M 112 LYS cc_start: 0.9578 (ttmm) cc_final: 0.9079 (mttp) REVERT: M 116 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8537 (tpp80) REVERT: M 131 ASP cc_start: 0.9026 (t0) cc_final: 0.8684 (t0) REVERT: M 132 ASP cc_start: 0.8741 (m-30) cc_final: 0.8119 (m-30) REVERT: N 35 PHE cc_start: 0.9542 (t80) cc_final: 0.9313 (t80) REVERT: N 86 GLN cc_start: 0.8680 (mp10) cc_final: 0.8091 (mp10) REVERT: N 89 LYS cc_start: 0.8761 (ptmm) cc_final: 0.7992 (ptmm) REVERT: N 92 ASP cc_start: 0.7738 (p0) cc_final: 0.7003 (p0) REVERT: N 97 MET cc_start: 0.9188 (mmm) cc_final: 0.8696 (mmm) REVERT: N 98 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8694 (p0) REVERT: N 105 ASP cc_start: 0.9259 (m-30) cc_final: 0.8960 (m-30) REVERT: O 13 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8982 (mt-10) REVERT: O 21 ASP cc_start: 0.7667 (p0) cc_final: 0.7304 (p0) REVERT: O 38 MET cc_start: 0.8952 (tmm) cc_final: 0.8605 (tmm) REVERT: O 39 CYS cc_start: 0.9209 (p) cc_final: 0.8754 (p) REVERT: O 75 ASP cc_start: 0.8894 (t0) cc_final: 0.8518 (t0) REVERT: O 76 LYS cc_start: 0.9406 (mmmm) cc_final: 0.9094 (mmtm) REVERT: O 92 ASP cc_start: 0.7252 (t70) cc_final: 0.6778 (t0) REVERT: O 99 TYR cc_start: 0.8482 (t80) cc_final: 0.8251 (t80) REVERT: O 102 ASP cc_start: 0.9067 (m-30) cc_final: 0.8736 (m-30) REVERT: O 105 ASP cc_start: 0.9434 (m-30) cc_final: 0.9195 (m-30) REVERT: O 116 ARG cc_start: 0.8415 (mmp80) cc_final: 0.7965 (mmp80) REVERT: a 62 ASP cc_start: 0.8052 (t0) cc_final: 0.7777 (t0) REVERT: a 108 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9243 (mm) REVERT: a 112 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9072 (mm-30) REVERT: a 113 ASP cc_start: 0.9150 (t70) cc_final: 0.8835 (t0) REVERT: a 117 ASP cc_start: 0.9433 (m-30) cc_final: 0.9188 (m-30) REVERT: b 1 MET cc_start: 0.8699 (tpt) cc_final: 0.8182 (tpt) REVERT: b 23 LEU cc_start: 0.9210 (tp) cc_final: 0.8985 (tp) REVERT: b 55 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8673 (t) REVERT: b 117 ASP cc_start: 0.9029 (m-30) cc_final: 0.8632 (t0) REVERT: c 3 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.7947 (ttp80) REVERT: c 50 GLU cc_start: 0.8046 (tp30) cc_final: 0.7637 (tp30) REVERT: d 14 GLN cc_start: 0.9056 (mp10) cc_final: 0.8716 (mp10) REVERT: d 17 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9166 (mm) REVERT: d 29 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8652 (p) REVERT: d 50 GLU cc_start: 0.7914 (tp30) cc_final: 0.7668 (tp30) REVERT: e 5 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8128 (mtmm) REVERT: e 14 GLN cc_start: 0.8860 (mp10) cc_final: 0.8438 (mm-40) REVERT: e 30 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7107 (p90) REVERT: g 50 GLU cc_start: 0.8274 (pm20) cc_final: 0.7921 (pm20) REVERT: g 68 LEU cc_start: 0.9651 (tt) cc_final: 0.9426 (tt) REVERT: g 86 ASP cc_start: 0.8974 (m-30) cc_final: 0.8639 (t0) REVERT: h 1 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6100 (tmm) REVERT: j 12 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8328 (p0) REVERT: j 13 ASP cc_start: 0.7589 (m-30) cc_final: 0.7300 (m-30) REVERT: j 44 LYS cc_start: 0.9609 (mmmm) cc_final: 0.9136 (tppt) REVERT: j 47 GLN cc_start: 0.9487 (pp30) cc_final: 0.9179 (pp30) REVERT: j 48 ASN cc_start: 0.8976 (t0) cc_final: 0.8495 (t0) REVERT: j 50 GLU cc_start: 0.8105 (pm20) cc_final: 0.7533 (pm20) REVERT: j 101 ASP cc_start: 0.8473 (p0) cc_final: 0.8199 (p0) REVERT: j 112 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8816 (tm-30) REVERT: l 14 GLN cc_start: 0.9276 (mp10) cc_final: 0.8953 (mm-40) REVERT: l 123 GLN cc_start: 0.8128 (mp10) cc_final: 0.7784 (tp40) REVERT: m 12 ASP cc_start: 0.7962 (p0) cc_final: 0.7445 (p0) REVERT: m 13 ASP cc_start: 0.8162 (m-30) cc_final: 0.7844 (m-30) REVERT: m 29 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8033 (p) REVERT: m 48 ASN cc_start: 0.9401 (t0) cc_final: 0.8780 (t0) REVERT: m 50 GLU cc_start: 0.8616 (pm20) cc_final: 0.7898 (pm20) REVERT: n 107 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8005 (m) REVERT: n 111 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9191 (pp) REVERT: o 50 GLU cc_start: 0.7992 (tp30) cc_final: 0.7431 (tp30) REVERT: o 54 ASN cc_start: 0.8286 (p0) cc_final: 0.7802 (p0) REVERT: o 65 TYR cc_start: 0.5993 (OUTLIER) cc_final: 0.4805 (t80) outliers start: 220 outliers final: 162 residues processed: 1219 average time/residue: 0.4533 time to fit residues: 854.1322 Evaluate side-chains 1207 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1026 time to evaluate : 3.437 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 94 THR 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 40 ILE Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER 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 E residue 9 THR Chi-restraints excluded: chain E residue 28 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 122 VAL Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain F residue 46 GLN 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 56 LEU Chi-restraints excluded: chain G residue 83 GLU 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 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 107 LEU 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 90 VAL Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 46 GLN 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 129 SER Chi-restraints excluded: chain K residue 130 TYR 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 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 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 18 GLN Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 47 ASN Chi-restraints excluded: chain O residue 58 THR 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 21 LEU 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 106 ASN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 17 ILE Chi-restraints excluded: chain d residue 18 ASN 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 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 31 ASN 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 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 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 106 ASN 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 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 12 ASP 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 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 91 VAL 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 Chi-restraints excluded: chain o residue 109 ASN Chi-restraints excluded: chain o residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 30 optimal weight: 0.0670 chunk 108 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** 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 18 GLN O 18 GLN O 51 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 109 ASN g 48 ASN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 10 HIS n 34 ASN ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052208 restraints weight = 149327.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053751 restraints weight = 90567.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054849 restraints weight = 63499.526| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 31470 Z= 0.168 Angle : 0.861 14.337 42780 Z= 0.446 Chirality : 0.048 0.240 4995 Planarity : 0.005 0.063 5565 Dihedral : 7.043 61.056 4207 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.46 % Favored : 91.44 % Rotamer: Outliers : 5.16 % Allowed : 28.94 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3795 helix: 0.31 (0.13), residues: 1611 sheet: -0.37 (0.21), residues: 603 loop : -2.18 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 16 HIS 0.007 0.001 HIS I 10 PHE 0.029 0.002 PHE A 49 TYR 0.038 0.002 TYR h 114 ARG 0.011 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 1420) hydrogen bonds : angle 5.16274 ( 4086) covalent geometry : bond 0.00384 (31470) covalent geometry : angle 0.86068 (42780) *********************** 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 1307 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1125 time to evaluate : 3.474 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: A 13 GLU cc_start: 0.8909 (tp30) cc_final: 0.8468 (tp30) REVERT: A 29 GLU cc_start: 0.9067 (tp30) cc_final: 0.8115 (tp30) REVERT: A 30 GLU cc_start: 0.8782 (pm20) cc_final: 0.8050 (pm20) REVERT: A 38 MET cc_start: 0.9285 (tmm) cc_final: 0.8730 (tmm) REVERT: A 70 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8249 (tp30) REVERT: A 73 ARG cc_start: 0.8852 (ttp80) cc_final: 0.8484 (ttp80) REVERT: A 92 ASP cc_start: 0.8778 (p0) cc_final: 0.8392 (p0) REVERT: A 132 ASP cc_start: 0.8761 (m-30) cc_final: 0.8109 (t70) REVERT: B 51 ASN cc_start: 0.9513 (m110) cc_final: 0.9283 (p0) REVERT: B 76 LYS cc_start: 0.9426 (tppt) cc_final: 0.9072 (mmmm) REVERT: B 86 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8718 (tp-100) REVERT: B 102 ASP cc_start: 0.9197 (p0) cc_final: 0.8851 (p0) REVERT: B 105 ASP cc_start: 0.9311 (m-30) cc_final: 0.9091 (m-30) REVERT: B 116 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8965 (tpp80) REVERT: B 124 ASP cc_start: 0.8904 (t0) cc_final: 0.8486 (t0) REVERT: B 131 ASP cc_start: 0.9382 (t0) cc_final: 0.8801 (t0) REVERT: C 13 GLU cc_start: 0.8935 (tp30) cc_final: 0.8257 (tp30) REVERT: C 19 PHE cc_start: 0.8808 (m-80) cc_final: 0.8588 (m-80) REVERT: C 30 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: C 38 MET cc_start: 0.9173 (tmm) cc_final: 0.8805 (tmm) REVERT: C 70 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8627 (mm-30) REVERT: C 83 GLU cc_start: 0.7938 (mp0) cc_final: 0.7646 (mp0) REVERT: C 86 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8427 (tp40) REVERT: C 92 ASP cc_start: 0.8187 (p0) cc_final: 0.7202 (p0) REVERT: C 102 ASP cc_start: 0.9151 (m-30) cc_final: 0.8887 (m-30) REVERT: C 105 ASP cc_start: 0.9441 (m-30) cc_final: 0.9218 (m-30) REVERT: C 116 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8263 (mmm160) REVERT: C 124 ASP cc_start: 0.7933 (t0) cc_final: 0.7573 (t0) REVERT: D 21 ASP cc_start: 0.7743 (p0) cc_final: 0.7252 (p0) REVERT: D 44 ARG cc_start: 0.8785 (ptm160) cc_final: 0.8264 (ptm160) REVERT: D 60 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8895 (mm-30) REVERT: D 69 LYS cc_start: 0.9653 (ttmm) cc_final: 0.9428 (ttpp) REVERT: D 79 LYS cc_start: 0.9353 (mppt) cc_final: 0.9148 (mmtm) REVERT: D 106 GLU cc_start: 0.9032 (tp30) cc_final: 0.8580 (tp30) REVERT: D 116 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8380 (tpp80) REVERT: D 132 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7308 (t0) REVERT: E 17 ASN cc_start: 0.9500 (m-40) cc_final: 0.9185 (m-40) REVERT: E 46 GLN cc_start: 0.9391 (tp-100) cc_final: 0.8895 (tp-100) REVERT: E 92 ASP cc_start: 0.7756 (p0) cc_final: 0.7193 (p0) REVERT: E 105 ASP cc_start: 0.9320 (m-30) cc_final: 0.9105 (p0) REVERT: E 116 ARG cc_start: 0.9255 (tpp80) cc_final: 0.8914 (tpp80) REVERT: E 132 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: F 38 MET cc_start: 0.9222 (tmm) cc_final: 0.8905 (tmm) REVERT: F 86 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8536 (tp40) REVERT: F 110 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8469 (mm-30) REVERT: F 116 ARG cc_start: 0.8532 (mmp80) cc_final: 0.8271 (mmp80) REVERT: G 21 ASP cc_start: 0.8547 (p0) cc_final: 0.8095 (p0) REVERT: G 44 ARG cc_start: 0.8628 (ptm160) cc_final: 0.7466 (ttm170) REVERT: G 70 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8304 (mm-30) REVERT: G 79 LYS cc_start: 0.9500 (mppt) cc_final: 0.9101 (mtmm) REVERT: G 92 ASP cc_start: 0.8873 (p0) cc_final: 0.8457 (p0) REVERT: H 21 ASP cc_start: 0.8008 (p0) cc_final: 0.7434 (p0) REVERT: H 38 MET cc_start: 0.9323 (ttp) cc_final: 0.9065 (ttm) REVERT: H 44 ARG cc_start: 0.9056 (ptm-80) cc_final: 0.8624 (ttt180) REVERT: H 82 ILE cc_start: 0.9228 (tp) cc_final: 0.9001 (mt) REVERT: H 92 ASP cc_start: 0.8371 (p0) cc_final: 0.7445 (p0) REVERT: H 102 ASP cc_start: 0.9233 (p0) cc_final: 0.8979 (p0) REVERT: H 105 ASP cc_start: 0.9140 (m-30) cc_final: 0.8859 (m-30) REVERT: H 116 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8736 (tpp80) REVERT: I 13 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8967 (pt0) REVERT: I 35 PHE cc_start: 0.9577 (t80) cc_final: 0.8968 (t80) REVERT: I 38 MET cc_start: 0.9270 (tmm) cc_final: 0.8933 (tmm) REVERT: I 39 CYS cc_start: 0.9409 (p) cc_final: 0.8782 (p) REVERT: I 60 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8698 (mt-10) REVERT: I 90 VAL cc_start: 0.9156 (t) cc_final: 0.8921 (p) REVERT: I 99 TYR cc_start: 0.8371 (t80) cc_final: 0.8022 (t80) REVERT: J 21 ASP cc_start: 0.8571 (p0) cc_final: 0.7960 (p0) REVERT: J 27 GLU cc_start: 0.7301 (mp0) cc_final: 0.7001 (mp0) REVERT: J 34 GLU cc_start: 0.9041 (tt0) cc_final: 0.8483 (tt0) REVERT: J 60 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8784 (mt-10) REVERT: J 69 LYS cc_start: 0.9607 (OUTLIER) cc_final: 0.9387 (ttpp) REVERT: J 70 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8197 (tp30) REVERT: J 74 LEU cc_start: 0.9756 (mp) cc_final: 0.8913 (mt) REVERT: J 83 GLU cc_start: 0.7955 (pp20) cc_final: 0.7677 (pp20) REVERT: J 92 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8643 (p0) REVERT: K 44 ARG cc_start: 0.8746 (tpp80) cc_final: 0.8513 (tpp80) REVERT: K 69 LYS cc_start: 0.9760 (tttp) cc_final: 0.9357 (ttmm) REVERT: K 86 GLN cc_start: 0.9046 (tp40) cc_final: 0.8638 (tp-100) REVERT: K 93 ILE cc_start: 0.9161 (pt) cc_final: 0.8887 (mp) REVERT: K 105 ASP cc_start: 0.9325 (m-30) cc_final: 0.9012 (m-30) REVERT: L 13 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8918 (mt-10) REVERT: L 39 CYS cc_start: 0.9239 (p) cc_final: 0.8767 (p) REVERT: L 76 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9031 (mmmm) REVERT: L 79 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9075 (mmmm) REVERT: L 83 GLU cc_start: 0.8250 (mp0) cc_final: 0.7826 (mp0) REVERT: L 86 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8920 (tp40) REVERT: M 17 ASN cc_start: 0.9564 (m-40) cc_final: 0.9316 (m110) REVERT: M 69 LYS cc_start: 0.9621 (ttpp) cc_final: 0.9404 (ttpp) REVERT: M 70 GLU cc_start: 0.8975 (tp30) cc_final: 0.8311 (tp30) REVERT: M 73 ARG cc_start: 0.9318 (tmm-80) cc_final: 0.8706 (ttp80) REVERT: M 83 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7473 (pp20) REVERT: M 106 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8681 (mt-10) REVERT: M 112 LYS cc_start: 0.9559 (ttmm) cc_final: 0.9077 (mttp) REVERT: M 116 ARG cc_start: 0.8841 (tpp80) cc_final: 0.8560 (tpp80) REVERT: M 131 ASP cc_start: 0.9067 (t0) cc_final: 0.8740 (t0) REVERT: M 132 ASP cc_start: 0.8737 (m-30) cc_final: 0.8097 (m-30) REVERT: N 35 PHE cc_start: 0.9514 (t80) cc_final: 0.8960 (t80) REVERT: N 36 VAL cc_start: 0.9721 (t) cc_final: 0.9496 (p) REVERT: N 39 CYS cc_start: 0.9648 (m) cc_final: 0.9270 (m) REVERT: N 89 LYS cc_start: 0.8773 (ptmm) cc_final: 0.7987 (ptmm) REVERT: N 92 ASP cc_start: 0.7667 (p0) cc_final: 0.6945 (p0) REVERT: N 105 ASP cc_start: 0.9251 (m-30) cc_final: 0.8956 (m-30) REVERT: O 13 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9062 (mt-10) REVERT: O 15 TYR cc_start: 0.8694 (t80) cc_final: 0.8303 (t80) REVERT: O 21 ASP cc_start: 0.7555 (p0) cc_final: 0.7201 (p0) REVERT: O 35 PHE cc_start: 0.9619 (t80) cc_final: 0.8967 (t80) REVERT: O 38 MET cc_start: 0.8895 (tmm) cc_final: 0.8546 (tmm) REVERT: O 39 CYS cc_start: 0.9121 (p) cc_final: 0.8741 (p) REVERT: O 102 ASP cc_start: 0.9011 (m-30) cc_final: 0.8681 (m-30) REVERT: O 105 ASP cc_start: 0.9423 (m-30) cc_final: 0.9186 (m-30) REVERT: a 62 ASP cc_start: 0.8038 (t0) cc_final: 0.7729 (t0) REVERT: a 108 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9219 (mm) REVERT: a 112 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9074 (mm-30) REVERT: a 113 ASP cc_start: 0.9180 (t70) cc_final: 0.8821 (t0) REVERT: a 117 ASP cc_start: 0.9468 (m-30) cc_final: 0.9188 (m-30) REVERT: b 1 MET cc_start: 0.8650 (tpt) cc_final: 0.8190 (tpt) REVERT: b 23 LEU cc_start: 0.9229 (tp) cc_final: 0.9028 (tp) REVERT: b 55 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8758 (t) REVERT: b 91 VAL cc_start: 0.9665 (t) cc_final: 0.9428 (p) REVERT: b 117 ASP cc_start: 0.9020 (m-30) cc_final: 0.8634 (t0) REVERT: c 3 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.7928 (ttp80) REVERT: c 50 GLU cc_start: 0.8069 (tp30) cc_final: 0.7602 (tp30) REVERT: c 88 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7282 (tm-30) REVERT: c 103 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8429 (mm-30) REVERT: d 14 GLN cc_start: 0.9029 (mp10) cc_final: 0.8699 (mp10) REVERT: d 17 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9144 (mm) REVERT: d 29 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8586 (p) REVERT: d 86 ASP cc_start: 0.8661 (m-30) cc_final: 0.8331 (t0) REVERT: e 14 GLN cc_start: 0.8906 (mp10) cc_final: 0.8360 (mm-40) REVERT: e 30 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.6934 (p90) REVERT: f 109 ASN cc_start: 0.8879 (m110) cc_final: 0.8626 (m110) REVERT: f 113 ASP cc_start: 0.9204 (m-30) cc_final: 0.8641 (p0) REVERT: g 1 MET cc_start: 0.8756 (tpp) cc_final: 0.8404 (tpt) REVERT: g 68 LEU cc_start: 0.9619 (tt) cc_final: 0.9369 (tt) REVERT: g 86 ASP cc_start: 0.8982 (m-30) cc_final: 0.8675 (t0) REVERT: h 1 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.5967 (tmm) REVERT: i 73 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8434 (t0) REVERT: i 74 LYS cc_start: 0.8195 (tmtt) cc_final: 0.7950 (tptp) REVERT: i 114 TYR cc_start: 0.8883 (t80) cc_final: 0.8337 (t80) REVERT: j 1 MET cc_start: 0.6923 (tpt) cc_final: 0.6322 (tmm) REVERT: j 12 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8369 (p0) REVERT: j 44 LYS cc_start: 0.9551 (mmmm) cc_final: 0.9171 (tppt) REVERT: j 47 GLN cc_start: 0.9487 (pp30) cc_final: 0.9189 (pp30) REVERT: j 48 ASN cc_start: 0.9059 (t0) cc_final: 0.8616 (t0) REVERT: j 50 GLU cc_start: 0.8226 (pm20) cc_final: 0.7630 (pm20) REVERT: j 74 LYS cc_start: 0.7366 (tmtt) cc_final: 0.6940 (tmtt) REVERT: j 101 ASP cc_start: 0.8504 (p0) cc_final: 0.8271 (p0) REVERT: j 112 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8821 (tm-30) REVERT: l 14 GLN cc_start: 0.9225 (mp10) cc_final: 0.9006 (mm110) REVERT: l 123 GLN cc_start: 0.8116 (mp10) cc_final: 0.7831 (tp40) REVERT: m 12 ASP cc_start: 0.7957 (p0) cc_final: 0.7462 (p0) REVERT: m 13 ASP cc_start: 0.8115 (m-30) cc_final: 0.7882 (m-30) REVERT: m 29 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7905 (p) REVERT: m 48 ASN cc_start: 0.9402 (t0) cc_final: 0.8777 (t0) REVERT: m 50 GLU cc_start: 0.8693 (pm20) cc_final: 0.7868 (pm20) REVERT: n 107 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7948 (m) REVERT: n 111 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9185 (pp) REVERT: o 14 GLN cc_start: 0.9456 (mp10) cc_final: 0.9171 (mp10) REVERT: o 50 GLU cc_start: 0.7888 (tp30) cc_final: 0.7031 (tp30) REVERT: o 54 ASN cc_start: 0.8355 (p0) cc_final: 0.7900 (p0) REVERT: o 65 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.4912 (t80) REVERT: o 103 GLU cc_start: 0.7809 (tp30) cc_final: 0.7598 (tp30) outliers start: 182 outliers final: 133 residues processed: 1236 average time/residue: 0.4422 time to fit residues: 847.4551 Evaluate side-chains 1216 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1064 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR 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 86 GLN 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 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 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 132 ASP 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 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 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 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 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 90 VAL 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 46 GLN 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 130 TYR Chi-restraints excluded: chain L residue 47 ASN 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 132 ASP Chi-restraints excluded: chain L residue 133 VAL 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 18 GLN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 58 THR 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 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 17 ILE 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 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 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 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 1 MET 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 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 42 HIS 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 87 ILE Chi-restraints excluded: chain k residue 108 LEU 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 91 VAL 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 Chi-restraints excluded: chain o residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 47 optimal weight: 8.9990 chunk 254 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 355 optimal weight: 20.0000 chunk 364 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 18 GLN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 48 ASN i 47 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 109 ASN n 58 ASN ** o 34 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 = 0.3354 r_free = 0.3354 target = 0.065783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052357 restraints weight = 150197.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053931 restraints weight = 91260.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055039 restraints weight = 63898.656| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.6122 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= 0.169 Angle : 0.893 15.367 42780 Z= 0.462 Chirality : 0.048 0.256 4995 Planarity : 0.005 0.064 5565 Dihedral : 6.952 61.964 4204 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 4.17 % Allowed : 30.67 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 3795 helix: 0.20 (0.12), residues: 1617 sheet: -0.17 (0.21), residues: 602 loop : -2.19 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 16 HIS 0.005 0.001 HIS j 10 PHE 0.035 0.002 PHE A 49 TYR 0.048 0.002 TYR l 104 ARG 0.019 0.001 ARG c 93 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 1420) hydrogen bonds : angle 5.18836 ( 4086) covalent geometry : bond 0.00377 (31470) covalent geometry : angle 0.89332 (42780) ********************** 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 1278 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1131 time to evaluate : 3.570 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: A 13 GLU cc_start: 0.8928 (tp30) cc_final: 0.8469 (tp30) REVERT: A 38 MET cc_start: 0.9260 (tmm) cc_final: 0.8681 (tmm) REVERT: A 79 LYS cc_start: 0.9420 (mtmm) cc_final: 0.8975 (mppt) REVERT: A 116 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7984 (tpp80) REVERT: A 124 ASP cc_start: 0.9226 (t0) cc_final: 0.8877 (t0) REVERT: A 132 ASP cc_start: 0.8736 (m-30) cc_final: 0.8096 (t70) REVERT: B 51 ASN cc_start: 0.9509 (m110) cc_final: 0.9294 (p0) REVERT: B 76 LYS cc_start: 0.9419 (tppt) cc_final: 0.9058 (mmmm) REVERT: B 86 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8655 (tp-100) REVERT: B 89 LYS cc_start: 0.8874 (tppt) cc_final: 0.8504 (mmmt) REVERT: B 102 ASP cc_start: 0.9195 (p0) cc_final: 0.8849 (p0) REVERT: B 105 ASP cc_start: 0.9321 (m-30) cc_final: 0.9120 (m-30) REVERT: B 116 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8813 (tpp80) REVERT: B 124 ASP cc_start: 0.8883 (t0) cc_final: 0.8183 (t0) REVERT: B 131 ASP cc_start: 0.9282 (t0) cc_final: 0.8835 (t0) REVERT: C 13 GLU cc_start: 0.8919 (tp30) cc_final: 0.7789 (tp30) REVERT: C 17 ASN cc_start: 0.9457 (m-40) cc_final: 0.8472 (m-40) REVERT: C 19 PHE cc_start: 0.8763 (m-80) cc_final: 0.8560 (m-80) REVERT: C 38 MET cc_start: 0.9119 (tmm) cc_final: 0.8753 (tmm) REVERT: C 70 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8637 (mm-30) REVERT: C 83 GLU cc_start: 0.7868 (mp0) cc_final: 0.7552 (mp0) REVERT: C 86 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8386 (tp40) REVERT: C 92 ASP cc_start: 0.8080 (p0) cc_final: 0.7335 (p0) REVERT: C 102 ASP cc_start: 0.9113 (m-30) cc_final: 0.8847 (m-30) REVERT: C 105 ASP cc_start: 0.9413 (m-30) cc_final: 0.9148 (m-30) REVERT: C 116 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8160 (mmm160) REVERT: D 21 ASP cc_start: 0.7821 (p0) cc_final: 0.7281 (p0) REVERT: D 34 GLU cc_start: 0.8937 (tt0) cc_final: 0.8081 (tm-30) REVERT: D 44 ARG cc_start: 0.8803 (ptm160) cc_final: 0.8297 (ptm160) REVERT: D 60 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8909 (mm-30) REVERT: D 69 LYS cc_start: 0.9648 (ttmm) cc_final: 0.9425 (ttpp) REVERT: D 79 LYS cc_start: 0.9357 (mppt) cc_final: 0.9136 (mmtm) REVERT: D 106 GLU cc_start: 0.9029 (tp30) cc_final: 0.8549 (tp30) REVERT: D 132 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7263 (t0) REVERT: E 44 ARG cc_start: 0.8409 (tpt-90) cc_final: 0.8117 (tpp80) REVERT: E 46 GLN cc_start: 0.9409 (tp-100) cc_final: 0.8882 (tp-100) REVERT: E 92 ASP cc_start: 0.7736 (p0) cc_final: 0.7251 (t70) REVERT: E 116 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8923 (tpp80) REVERT: E 132 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: F 34 GLU cc_start: 0.9305 (tt0) cc_final: 0.9015 (tt0) REVERT: F 38 MET cc_start: 0.9209 (tmm) cc_final: 0.8867 (tmm) REVERT: F 86 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8531 (tp40) REVERT: F 110 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8412 (mm-30) REVERT: F 116 ARG cc_start: 0.8534 (mmp80) cc_final: 0.8322 (mmp80) REVERT: G 21 ASP cc_start: 0.8536 (p0) cc_final: 0.8069 (p0) REVERT: G 29 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8607 (tm-30) REVERT: G 44 ARG cc_start: 0.8498 (ptm160) cc_final: 0.7467 (ttm170) REVERT: G 70 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8127 (mm-30) REVERT: G 79 LYS cc_start: 0.9509 (mppt) cc_final: 0.9118 (mppt) REVERT: G 90 VAL cc_start: 0.9073 (m) cc_final: 0.8170 (m) REVERT: G 92 ASP cc_start: 0.8881 (p0) cc_final: 0.8484 (p0) REVERT: H 21 ASP cc_start: 0.8234 (p0) cc_final: 0.7655 (p0) REVERT: H 38 MET cc_start: 0.9295 (ttp) cc_final: 0.9046 (ttm) REVERT: H 44 ARG cc_start: 0.9045 (ptm-80) cc_final: 0.8541 (ttt180) REVERT: H 82 ILE cc_start: 0.9111 (tp) cc_final: 0.8898 (mt) REVERT: H 89 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8662 (mmmt) REVERT: H 92 ASP cc_start: 0.8315 (p0) cc_final: 0.7215 (p0) REVERT: H 102 ASP cc_start: 0.9230 (p0) cc_final: 0.8950 (p0) REVERT: H 105 ASP cc_start: 0.9140 (m-30) cc_final: 0.8854 (m-30) REVERT: H 116 ARG cc_start: 0.9058 (tpp80) cc_final: 0.8827 (tpp80) REVERT: I 13 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8930 (pt0) REVERT: I 35 PHE cc_start: 0.9538 (t80) cc_final: 0.8911 (t80) REVERT: I 38 MET cc_start: 0.9303 (tmm) cc_final: 0.8992 (tmm) REVERT: I 39 CYS cc_start: 0.9417 (p) cc_final: 0.8806 (p) REVERT: I 53 LEU cc_start: 0.9359 (tt) cc_final: 0.9108 (pp) REVERT: I 60 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8720 (mt-10) REVERT: I 76 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9189 (mmmm) REVERT: I 90 VAL cc_start: 0.9175 (t) cc_final: 0.8744 (p) REVERT: I 99 TYR cc_start: 0.8319 (t80) cc_final: 0.8039 (t80) REVERT: I 124 ASP cc_start: 0.8681 (t70) cc_final: 0.8103 (t70) REVERT: J 21 ASP cc_start: 0.8525 (p0) cc_final: 0.7937 (p0) REVERT: J 34 GLU cc_start: 0.9038 (tt0) cc_final: 0.8478 (tt0) REVERT: J 60 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8747 (mt-10) REVERT: J 69 LYS cc_start: 0.9599 (OUTLIER) cc_final: 0.9396 (ttpp) REVERT: J 70 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8195 (tp30) REVERT: J 74 LEU cc_start: 0.9750 (mp) cc_final: 0.8884 (mt) REVERT: J 79 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9059 (mtmm) REVERT: J 83 GLU cc_start: 0.7921 (pp20) cc_final: 0.7586 (pp20) REVERT: J 92 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8499 (p0) REVERT: K 44 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8573 (tpp80) REVERT: K 69 LYS cc_start: 0.9758 (tttp) cc_final: 0.9403 (ttmm) REVERT: K 86 GLN cc_start: 0.9032 (tp40) cc_final: 0.8672 (tp-100) REVERT: K 92 ASP cc_start: 0.8360 (p0) cc_final: 0.7739 (p0) REVERT: K 93 ILE cc_start: 0.9119 (pt) cc_final: 0.8899 (mp) REVERT: K 102 ASP cc_start: 0.9236 (p0) cc_final: 0.8932 (p0) REVERT: K 105 ASP cc_start: 0.9306 (m-30) cc_final: 0.8947 (m-30) REVERT: K 116 ARG cc_start: 0.9225 (mmp80) cc_final: 0.8737 (tpp80) REVERT: L 13 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8835 (mt-10) REVERT: L 39 CYS cc_start: 0.9179 (p) cc_final: 0.8726 (p) REVERT: L 76 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9021 (mmmm) REVERT: L 79 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9140 (mmmm) REVERT: L 83 GLU cc_start: 0.8199 (mp0) cc_final: 0.7745 (mp0) REVERT: L 86 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8952 (tp40) REVERT: M 17 ASN cc_start: 0.9559 (m-40) cc_final: 0.9290 (m110) REVERT: M 35 PHE cc_start: 0.9554 (t80) cc_final: 0.9250 (t80) REVERT: M 70 GLU cc_start: 0.8948 (tp30) cc_final: 0.8286 (tp30) REVERT: M 73 ARG cc_start: 0.9315 (tmm-80) cc_final: 0.8751 (ttp80) REVERT: M 83 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7429 (pp20) REVERT: M 106 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8781 (mt-10) REVERT: M 112 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9063 (mttp) REVERT: M 116 ARG cc_start: 0.8835 (tpp80) cc_final: 0.8629 (tpp80) REVERT: M 131 ASP cc_start: 0.9069 (t0) cc_final: 0.8754 (t0) REVERT: M 132 ASP cc_start: 0.8740 (m-30) cc_final: 0.8170 (m-30) REVERT: N 35 PHE cc_start: 0.9480 (t80) cc_final: 0.8924 (t80) REVERT: N 36 VAL cc_start: 0.9717 (t) cc_final: 0.9490 (p) REVERT: N 39 CYS cc_start: 0.9586 (m) cc_final: 0.9170 (m) REVERT: N 75 ASP cc_start: 0.8951 (t0) cc_final: 0.8731 (t0) REVERT: N 89 LYS cc_start: 0.8943 (ptmm) cc_final: 0.8554 (ptmm) REVERT: N 92 ASP cc_start: 0.7604 (p0) cc_final: 0.6978 (p0) REVERT: N 105 ASP cc_start: 0.9282 (m-30) cc_final: 0.8974 (m-30) REVERT: O 21 ASP cc_start: 0.7547 (p0) cc_final: 0.7204 (p0) REVERT: O 35 PHE cc_start: 0.9622 (t80) cc_final: 0.8911 (t80) REVERT: O 38 MET cc_start: 0.8848 (tmm) cc_final: 0.8501 (tmm) REVERT: O 39 CYS cc_start: 0.9152 (p) cc_final: 0.8712 (p) REVERT: O 69 LYS cc_start: 0.9317 (ttpp) cc_final: 0.9117 (ttmm) REVERT: O 92 ASP cc_start: 0.8226 (t0) cc_final: 0.7953 (t0) REVERT: O 94 THR cc_start: 0.9320 (m) cc_final: 0.9111 (p) REVERT: O 102 ASP cc_start: 0.9013 (m-30) cc_final: 0.8649 (m-30) REVERT: O 105 ASP cc_start: 0.9390 (m-30) cc_final: 0.9105 (m-30) REVERT: a 62 ASP cc_start: 0.8019 (t0) cc_final: 0.7716 (t0) REVERT: a 108 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9203 (mm) REVERT: a 113 ASP cc_start: 0.9169 (t70) cc_final: 0.8856 (t0) REVERT: a 117 ASP cc_start: 0.9474 (m-30) cc_final: 0.9220 (m-30) REVERT: b 1 MET cc_start: 0.8623 (tpt) cc_final: 0.7900 (tpt) REVERT: b 23 LEU cc_start: 0.9237 (tp) cc_final: 0.9035 (tp) REVERT: b 55 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8724 (t) REVERT: b 91 VAL cc_start: 0.9649 (t) cc_final: 0.9412 (p) REVERT: b 117 ASP cc_start: 0.9032 (m-30) cc_final: 0.8654 (t0) REVERT: c 3 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8002 (ttp80) REVERT: c 50 GLU cc_start: 0.8124 (tp30) cc_final: 0.7612 (tp30) REVERT: c 75 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8865 (mptt) REVERT: c 88 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7168 (tm-30) REVERT: c 103 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8148 (mm-30) REVERT: c 109 ASN cc_start: 0.9132 (m-40) cc_final: 0.8781 (m110) REVERT: d 14 GLN cc_start: 0.9005 (mp10) cc_final: 0.8694 (mp10) REVERT: d 17 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9152 (mm) REVERT: d 29 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8529 (p) REVERT: d 50 GLU cc_start: 0.7535 (tp30) cc_final: 0.7306 (tp30) REVERT: d 86 ASP cc_start: 0.8649 (m-30) cc_final: 0.8320 (t0) REVERT: e 14 GLN cc_start: 0.9003 (mp10) cc_final: 0.8538 (mm-40) REVERT: e 30 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.6995 (p90) REVERT: f 3 ARG cc_start: 0.8644 (mtp-110) cc_final: 0.8161 (ttp-110) REVERT: f 109 ASN cc_start: 0.8864 (m110) cc_final: 0.8586 (m110) REVERT: f 113 ASP cc_start: 0.9206 (m-30) cc_final: 0.8646 (p0) REVERT: g 68 LEU cc_start: 0.9601 (tt) cc_final: 0.9349 (tt) REVERT: g 86 ASP cc_start: 0.8977 (m-30) cc_final: 0.8731 (t0) REVERT: h 1 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.5854 (tmm) REVERT: i 73 ASN cc_start: 0.9212 (OUTLIER) cc_final: 0.8430 (t0) REVERT: i 74 LYS cc_start: 0.8340 (tmtt) cc_final: 0.8102 (tptp) REVERT: j 1 MET cc_start: 0.6971 (tpt) cc_final: 0.6431 (tmm) REVERT: j 12 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8353 (p0) REVERT: j 44 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9152 (tppt) REVERT: j 47 GLN cc_start: 0.9450 (pp30) cc_final: 0.9144 (pp30) REVERT: j 48 ASN cc_start: 0.9034 (t0) cc_final: 0.8621 (t0) REVERT: j 50 GLU cc_start: 0.8135 (pm20) cc_final: 0.7568 (pm20) REVERT: j 101 ASP cc_start: 0.8583 (p0) cc_final: 0.8283 (p0) REVERT: j 112 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8834 (tm-30) REVERT: l 14 GLN cc_start: 0.9247 (mp10) cc_final: 0.9035 (mm110) REVERT: l 123 GLN cc_start: 0.8156 (mp10) cc_final: 0.7909 (tp40) REVERT: m 12 ASP cc_start: 0.7981 (p0) cc_final: 0.7535 (p0) REVERT: m 13 ASP cc_start: 0.8066 (m-30) cc_final: 0.7760 (m-30) REVERT: m 29 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7866 (p) REVERT: m 48 ASN cc_start: 0.9400 (t0) cc_final: 0.8753 (t0) REVERT: m 50 GLU cc_start: 0.8687 (pm20) cc_final: 0.7878 (pm20) REVERT: m 66 TYR cc_start: 0.7373 (m-80) cc_final: 0.7048 (m-80) REVERT: n 111 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9162 (pp) REVERT: o 14 GLN cc_start: 0.9444 (mp10) cc_final: 0.9151 (mp10) REVERT: o 50 GLU cc_start: 0.7967 (tp30) cc_final: 0.7423 (tp30) REVERT: o 54 ASN cc_start: 0.8363 (p0) cc_final: 0.7918 (p0) REVERT: o 65 TYR cc_start: 0.6271 (OUTLIER) cc_final: 0.4952 (t80) outliers start: 147 outliers final: 118 residues processed: 1218 average time/residue: 0.4471 time to fit residues: 846.1816 Evaluate side-chains 1219 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1082 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 86 GLN 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 81 SER Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR 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 122 VAL Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain E residue 132 ASP 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 133 VAL 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 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 118 LEU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN 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 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 79 LYS Chi-restraints excluded: chain J residue 90 VAL 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 28 LEU Chi-restraints excluded: chain K residue 46 GLN Chi-restraints excluded: chain K residue 53 LEU 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 58 THR 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 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain O residue 44 ARG Chi-restraints excluded: chain O residue 58 THR 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 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 17 ILE 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 16 TRP Chi-restraints excluded: chain e residue 19 VAL 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 48 ASN 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 i residue 52 VAL 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 12 ASP Chi-restraints excluded: chain j residue 23 LEU Chi-restraints excluded: chain j residue 42 HIS 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 l residue 107 VAL Chi-restraints excluded: chain l residue 109 ASN Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 91 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 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 7 optimal weight: 0.9980 chunk 357 optimal weight: 7.9990 chunk 293 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN e 121 ASN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 47 GLN l 109 ASN ** n 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.063383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.050333 restraints weight = 151691.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051824 restraints weight = 92657.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052871 restraints weight = 65301.794| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31470 Z= 0.231 Angle : 0.916 15.421 42780 Z= 0.479 Chirality : 0.049 0.303 4995 Planarity : 0.005 0.067 5565 Dihedral : 6.961 59.826 4200 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.88 % Favored : 91.01 % Rotamer: Outliers : 4.60 % Allowed : 31.12 % Favored : 64.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3795 helix: 0.10 (0.12), residues: 1618 sheet: -0.27 (0.21), residues: 615 loop : -2.22 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 16 HIS 0.010 0.002 HIS e 76 PHE 0.053 0.002 PHE H 49 TYR 0.049 0.002 TYR h 114 ARG 0.016 0.001 ARG c 93 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 1420) hydrogen bonds : angle 5.35476 ( 4086) covalent geometry : bond 0.00518 (31470) covalent geometry : angle 0.91648 (42780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16031.88 seconds wall clock time: 277 minutes 58.35 seconds (16678.35 seconds total)