Starting phenix.real_space_refine on Wed May 28 11:40:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8keg_37155/05_2025/8keg_37155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8keg_37155/05_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_37155/05_2025/8keg_37155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8keg_37155/05_2025/8keg_37155.map" model { file = "/net/cci-nas-00/data/ceres_data/8keg_37155/05_2025/8keg_37155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8keg_37155/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 16.96, per 1000 atoms: 0.55 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: 7.43 Conformation dependent library (CDL) restraints added in 3.4 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: 2.95 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: 8.83 Time building geometry restraints manager: 8.60 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: 2.170 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: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 59.660 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- 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 : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4433 time to fit residues: 958.0127 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 : 3.546 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059394 restraints weight = 147154.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.061019 restraints weight = 92709.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.062167 restraints weight = 66216.193| |-----------------------------------------------------------------------------| 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 : 3.355 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: 0.8903 (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: 0.8950 (p) cc_final: 0.8658 (p) REVERT: A 92 ASP cc_start: 0.8315 (p0) cc_final: 0.7933 (p0) REVERT: A 109 THR cc_start: 0.9648 (p) cc_final: 0.9281 (p) REVERT: A 112 LYS cc_start: 0.9405 (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: 0.9321 (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: 0.7870 (p0) cc_final: 0.7006 (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: 0.8741 (mm-30) cc_final: 0.8521 (tp30) REVERT: D 76 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8674 (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: 0.8689 (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: 0.8484 (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: 0.8012 (p0) cc_final: 0.7725 (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: 0.9100 (mt-10) cc_final: 0.8771 (mt-10) REVERT: F 92 ASP cc_start: 0.7596 (t70) cc_final: 0.7385 (t0) REVERT: F 106 GLU cc_start: 0.9425 (tp30) cc_final: 0.9130 (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: 0.8755 (mm-30) cc_final: 0.8042 (tp30) REVERT: G 92 ASP cc_start: 0.8688 (p0) cc_final: 0.8448 (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: 0.7439 (m-30) REVERT: H 17 ASN cc_start: 0.8905 (m110) cc_final: 0.8441 (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: 0.7653 (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: 0.8229 (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: 0.8692 (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: 0.8571 (tp40) REVERT: I 89 LYS cc_start: 0.9542 (ttpp) cc_final: 0.9224 (ttpp) REVERT: I 91 GLU cc_start: 0.8487 (pp20) cc_final: 0.8227 (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: 0.7972 (m110) REVERT: J 21 ASP cc_start: 0.8647 (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: 0.8545 (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: 0.8822 (ptmm) REVERT: K 116 ARG cc_start: 0.9251 (mmt-90) cc_final: 0.8841 (tpp80) REVERT: L 17 ASN cc_start: 0.9418 (m110) cc_final: 0.9076 (m-40) REVERT: L 21 ASP cc_start: 0.7494 (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: 0.8218 (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: 0.8007 (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: 0.9154 (m-30) cc_final: 0.8875 (m-30) REVERT: L 124 ASP cc_start: 0.8557 (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: 0.6793 (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: 0.7922 (tm-30) cc_final: 0.7571 (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: 0.8533 (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: 0.8851 (t80) REVERT: N 89 LYS cc_start: 0.8171 (ptmm) cc_final: 0.7640 (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: 0.9505 (t80) cc_final: 0.8974 (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: 0.8489 (OUTLIER) cc_final: 0.8281 (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: 0.8706 (p) REVERT: O 102 ASP cc_start: 0.9054 (m-30) cc_final: 0.8734 (m-30) REVERT: O 105 ASP cc_start: 0.9312 (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: 0.7767 (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: 0.7652 (tpt) cc_final: 0.6552 (tpt) REVERT: c 5 LYS cc_start: 0.7576 (mtmm) cc_final: 0.7049 (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: 0.8611 (mtmm) cc_final: 0.7910 (mtmm) REVERT: e 16 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.4932 (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: 0.8821 (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: 0.6630 (OUTLIER) cc_final: 0.5606 (tmm) REVERT: h 36 TYR cc_start: 0.8736 (m-80) cc_final: 0.8188 (m-10) REVERT: i 69 THR cc_start: 0.8492 (p) cc_final: 0.8286 (t) REVERT: j 13 ASP cc_start: 0.7216 (m-30) cc_final: 0.7005 (m-30) REVERT: j 48 ASN cc_start: 0.9139 (t0) cc_final: 0.8848 (t0) REVERT: j 50 GLU cc_start: 0.8404 (pm20) cc_final: 0.7596 (pm20) REVERT: k 58 ASN cc_start: 0.6846 (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: 0.8527 (OUTLIER) cc_final: 0.8097 (t70) REVERT: n 62 ASP cc_start: 0.9159 (t70) cc_final: 0.8803 (t0) REVERT: n 94 GLU cc_start: 0.8028 (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: 0.4369 time to fit residues: 889.3911 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 : 4.194 ------------------------------------------------------------------------------- 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: 9.9990 chunk 370 optimal weight: 6.9990 chunk 318 optimal weight: 0.8980 chunk 321 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 354 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN 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 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** ** n 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.072850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.058659 restraints weight = 148113.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.060328 restraints weight = 92138.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.061504 restraints weight = 65024.133| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31470 Z= 0.167 Angle : 0.757 14.054 42780 Z= 0.395 Chirality : 0.046 0.202 4995 Planarity : 0.005 0.071 5565 Dihedral : 7.610 84.006 4253 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.83 % Favored : 92.04 % Rotamer: Outliers : 5.73 % Allowed : 20.77 % Favored : 73.50 % 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: -1.06 (0.13), residues: 3795 helix: 0.66 (0.13), residues: 1603 sheet: -0.75 (0.20), residues: 615 loop : -2.15 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP o 16 HIS 0.015 0.001 HIS b 42 PHE 0.030 0.002 PHE J 49 TYR 0.041 0.002 TYR h 114 ARG 0.009 0.001 ARG d 9 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 1420) hydrogen bonds : angle 5.31345 ( 4086) covalent geometry : bond 0.00370 (31470) covalent geometry : angle 0.75725 (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 1368 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1166 time to evaluate : 3.362 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: 0.8922 (tp30) cc_final: 0.8437 (tp30) REVERT: A 38 MET cc_start: 0.9250 (tmm) cc_final: 0.8616 (tmm) REVERT: A 70 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8599 (tp30) REVERT: A 92 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8112 (p0) REVERT: A 99 TYR cc_start: 0.8781 (t80) cc_final: 0.8116 (t80) REVERT: A 112 LYS cc_start: 0.9414 (mttm) cc_final: 0.9176 (mmtm) REVERT: B 49 PHE cc_start: 0.9721 (t80) cc_final: 0.9498 (t80) REVERT: B 51 ASN cc_start: 0.9347 (m110) cc_final: 0.9033 (p0) REVERT: B 86 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8796 (tp-100) REVERT: B 89 LYS cc_start: 0.8728 (tppt) cc_final: 0.8429 (tppt) REVERT: B 105 ASP cc_start: 0.9254 (m-30) cc_final: 0.8953 (m-30) REVERT: B 106 GLU cc_start: 0.9256 (tp30) cc_final: 0.9006 (tp30) REVERT: B 131 ASP cc_start: 0.9286 (t0) cc_final: 0.8863 (t0) REVERT: C 13 GLU cc_start: 0.8866 (tp30) cc_final: 0.7656 (tp30) REVERT: C 17 ASN cc_start: 0.9376 (m-40) cc_final: 0.7987 (m-40) REVERT: C 19 PHE cc_start: 0.8794 (m-80) cc_final: 0.8543 (m-80) REVERT: C 30 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: C 38 MET cc_start: 0.9020 (tmm) cc_final: 0.8745 (tmm) REVERT: C 60 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8705 (mt-10) REVERT: C 70 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8830 (mm-30) REVERT: C 86 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8627 (tp40) REVERT: C 92 ASP cc_start: 0.7775 (p0) cc_final: 0.7126 (p0) REVERT: C 105 ASP cc_start: 0.9439 (m-30) cc_final: 0.9156 (m-30) REVERT: C 124 ASP cc_start: 0.7781 (t0) cc_final: 0.7466 (t0) REVERT: D 15 TYR cc_start: 0.8997 (t80) cc_final: 0.8680 (t80) REVERT: D 19 PHE cc_start: 0.9004 (m-80) cc_final: 0.8768 (m-80) REVERT: D 44 ARG cc_start: 0.8832 (ptm160) cc_final: 0.8413 (ptm160) REVERT: D 60 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8973 (mm-30) REVERT: D 106 GLU cc_start: 0.8979 (tp30) cc_final: 0.8688 (tp30) REVERT: D 113 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9161 (mtmt) REVERT: D 116 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8331 (tpp80) REVERT: E 44 ARG cc_start: 0.8279 (tpt-90) cc_final: 0.8017 (tpt-90) REVERT: E 46 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8577 (tm-30) REVERT: E 49 PHE cc_start: 0.9699 (t80) cc_final: 0.9260 (t80) REVERT: E 75 ASP cc_start: 0.8783 (t0) cc_final: 0.8467 (t0) REVERT: E 105 ASP cc_start: 0.9274 (m-30) cc_final: 0.9020 (m-30) REVERT: F 38 MET cc_start: 0.9221 (tmm) cc_final: 0.8939 (tmm) REVERT: F 39 CYS cc_start: 0.9422 (p) cc_final: 0.8994 (p) REVERT: F 60 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8749 (mt-10) REVERT: F 70 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8619 (mt-10) REVERT: F 110 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8310 (mm-30) REVERT: F 119 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9063 (mmmt) REVERT: F 127 TYR cc_start: 0.8898 (m-80) cc_final: 0.8642 (m-80) REVERT: G 29 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8499 (tm-30) REVERT: G 70 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8105 (tp30) REVERT: G 92 ASP cc_start: 0.8779 (p0) cc_final: 0.8502 (p0) REVERT: G 110 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9056 (mm-30) REVERT: H 17 ASN cc_start: 0.8903 (m110) cc_final: 0.8617 (m110) REVERT: H 21 ASP cc_start: 0.7562 (p0) cc_final: 0.6912 (p0) REVERT: H 44 ARG cc_start: 0.8867 (ptm-80) cc_final: 0.8223 (ttt180) REVERT: H 82 ILE cc_start: 0.9330 (tp) cc_final: 0.9036 (mt) REVERT: H 89 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8351 (ttmm) REVERT: H 92 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7390 (p0) REVERT: H 104 LYS cc_start: 0.9378 (mttm) cc_final: 0.9153 (mmtt) REVERT: H 105 ASP cc_start: 0.9114 (m-30) cc_final: 0.8874 (m-30) REVERT: H 124 ASP cc_start: 0.8904 (t0) cc_final: 0.8600 (t0) REVERT: I 13 GLU cc_start: 0.9219 (mt-10) cc_final: 0.9001 (mt-10) REVERT: I 21 ASP cc_start: 0.8420 (p0) cc_final: 0.8032 (p0) REVERT: I 38 MET cc_start: 0.9232 (tmm) cc_final: 0.8919 (tmm) REVERT: I 39 CYS cc_start: 0.9330 (p) cc_final: 0.8818 (p) REVERT: I 89 LYS cc_start: 0.9514 (ttpp) cc_final: 0.9241 (ttpp) REVERT: I 95 MET cc_start: 0.8883 (mmm) cc_final: 0.8676 (mmm) REVERT: I 99 TYR cc_start: 0.8382 (t80) cc_final: 0.8018 (t80) REVERT: I 102 ASP cc_start: 0.8916 (m-30) cc_final: 0.8682 (m-30) REVERT: I 106 GLU cc_start: 0.9355 (tp30) cc_final: 0.9085 (mm-30) REVERT: I 116 ARG cc_start: 0.8635 (mmm160) cc_final: 0.7928 (mmm160) REVERT: J 13 GLU cc_start: 0.8730 (tp30) cc_final: 0.8150 (tp30) REVERT: J 17 ASN cc_start: 0.8730 (m110) cc_final: 0.7897 (m110) REVERT: J 21 ASP cc_start: 0.8652 (p0) cc_final: 0.8306 (p0) REVERT: J 27 GLU cc_start: 0.7113 (mp0) cc_final: 0.6867 (mp0) REVERT: J 60 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8608 (mt-10) REVERT: J 79 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8856 (mtmm) REVERT: J 83 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7802 (pp20) REVERT: J 92 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8719 (p0) REVERT: J 110 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8555 (mm-30) REVERT: K 42 PHE cc_start: 0.9339 (m-10) cc_final: 0.8971 (m-10) REVERT: K 51 ASN cc_start: 0.9365 (m110) cc_final: 0.9140 (p0) REVERT: K 69 LYS cc_start: 0.9760 (tttp) cc_final: 0.9477 (ttmm) REVERT: K 86 GLN cc_start: 0.9147 (tp40) cc_final: 0.8801 (tp-100) REVERT: K 98 ASN cc_start: 0.8750 (p0) cc_final: 0.8457 (p0) REVERT: K 105 ASP cc_start: 0.9291 (m-30) cc_final: 0.8997 (m-30) REVERT: K 116 ARG cc_start: 0.9282 (mmt-90) cc_final: 0.8892 (tpp80) REVERT: L 21 ASP cc_start: 0.7592 (p0) cc_final: 0.7125 (p0) REVERT: L 26 SER cc_start: 0.7590 (t) cc_final: 0.6890 (p) REVERT: L 38 MET cc_start: 0.9122 (tmm) cc_final: 0.8839 (tmm) REVERT: L 39 CYS cc_start: 0.9253 (p) cc_final: 0.8715 (p) REVERT: L 83 GLU cc_start: 0.8294 (mp0) cc_final: 0.7904 (mp0) REVERT: L 86 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8807 (tp40) REVERT: L 124 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8310 (t0) REVERT: M 34 GLU cc_start: 0.9093 (tt0) cc_final: 0.8775 (tt0) REVERT: M 70 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: M 83 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7545 (pp20) REVERT: M 102 ASP cc_start: 0.9184 (m-30) cc_final: 0.8944 (m-30) REVERT: M 106 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8602 (mp0) REVERT: M 116 ARG cc_start: 0.8813 (tpp80) cc_final: 0.8513 (tpp80) REVERT: N 89 LYS cc_start: 0.8340 (ptmm) cc_final: 0.7623 (ptmm) REVERT: N 105 ASP cc_start: 0.9226 (m-30) cc_final: 0.8935 (m-30) REVERT: N 124 ASP cc_start: 0.8794 (t0) cc_final: 0.8452 (t0) REVERT: O 13 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8906 (mt-10) REVERT: O 21 ASP cc_start: 0.7503 (p0) cc_final: 0.7220 (p0) REVERT: O 38 MET cc_start: 0.8877 (tmm) cc_final: 0.8606 (tmm) REVERT: O 39 CYS cc_start: 0.9181 (p) cc_final: 0.8795 (p) REVERT: O 91 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: O 92 ASP cc_start: 0.6860 (t70) cc_final: 0.6337 (t0) REVERT: O 94 THR cc_start: 0.9190 (m) cc_final: 0.8827 (p) REVERT: O 95 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8215 (mtm) REVERT: O 99 TYR cc_start: 0.8426 (t80) cc_final: 0.7967 (t80) REVERT: O 102 ASP cc_start: 0.9097 (m-30) cc_final: 0.8704 (m-30) REVERT: O 105 ASP cc_start: 0.9332 (m-30) cc_final: 0.9040 (m-30) REVERT: O 116 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7500 (mmm160) REVERT: a 62 ASP cc_start: 0.7709 (t0) cc_final: 0.7304 (t0) REVERT: a 113 ASP cc_start: 0.9066 (t70) cc_final: 0.8716 (t0) REVERT: a 117 ASP cc_start: 0.9406 (m-30) cc_final: 0.9125 (m-30) REVERT: b 1 MET cc_start: 0.7786 (tpt) cc_final: 0.6653 (tpt) REVERT: b 55 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8131 (t) REVERT: b 91 VAL cc_start: 0.9592 (t) cc_final: 0.9363 (p) REVERT: c 5 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7233 (mtmm) REVERT: c 82 ASP cc_start: 0.7677 (t0) cc_final: 0.7410 (m-30) REVERT: d 17 ILE cc_start: 0.9069 (pt) cc_final: 0.8786 (mm) REVERT: d 29 THR cc_start: 0.8658 (m) cc_final: 0.8334 (p) REVERT: d 50 GLU cc_start: 0.7361 (tp30) cc_final: 0.7069 (tp30) REVERT: e 16 TRP cc_start: 0.7895 (OUTLIER) cc_final: 0.4975 (m100) REVERT: e 30 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7207 (p90) REVERT: f 3 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.8012 (ttp-110) REVERT: f 5 LYS cc_start: 0.8381 (mtmm) cc_final: 0.7265 (ptpp) REVERT: f 17 ILE cc_start: 0.8394 (mp) cc_final: 0.7960 (mm) REVERT: f 27 ASN cc_start: 0.8412 (m-40) cc_final: 0.7864 (m-40) REVERT: f 46 ASP cc_start: 0.8297 (p0) cc_final: 0.7917 (p0) REVERT: f 86 ASP cc_start: 0.8467 (p0) cc_final: 0.7839 (p0) REVERT: f 109 ASN cc_start: 0.8932 (m-40) cc_final: 0.8597 (m110) REVERT: g 14 GLN cc_start: 0.9172 (mp10) cc_final: 0.8897 (mm-40) REVERT: g 18 ASN cc_start: 0.9242 (p0) cc_final: 0.8888 (p0) REVERT: g 48 ASN cc_start: 0.9377 (t0) cc_final: 0.8850 (t0) REVERT: g 50 GLU cc_start: 0.8516 (mp0) cc_final: 0.7807 (mp0) REVERT: g 58 ASN cc_start: 0.7044 (OUTLIER) cc_final: 0.6418 (m-40) REVERT: g 68 LEU cc_start: 0.9548 (tt) cc_final: 0.9322 (tt) REVERT: h 1 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.5440 (tmm) REVERT: h 36 TYR cc_start: 0.8725 (m-80) cc_final: 0.8195 (m-10) REVERT: j 12 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.7312 (p0) REVERT: j 48 ASN cc_start: 0.9076 (t0) cc_final: 0.8703 (t0) REVERT: j 50 GLU cc_start: 0.8482 (pm20) cc_final: 0.7590 (pm20) REVERT: j 74 LYS cc_start: 0.6811 (tmtt) cc_final: 0.6594 (tmtt) REVERT: k 58 ASN cc_start: 0.6997 (OUTLIER) cc_final: 0.6402 (m-40) REVERT: l 14 GLN cc_start: 0.9204 (mp10) cc_final: 0.8833 (mp10) REVERT: l 110 TYR cc_start: 0.9110 (t80) cc_final: 0.8815 (t80) REVERT: m 29 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7384 (p) REVERT: m 48 ASN cc_start: 0.8954 (t0) cc_final: 0.8540 (t0) REVERT: m 50 GLU cc_start: 0.8212 (pm20) cc_final: 0.7512 (pm20) REVERT: n 13 ASP cc_start: 0.8507 (t0) cc_final: 0.8216 (t0) REVERT: n 42 HIS cc_start: 0.8673 (OUTLIER) cc_final: 0.8361 (t70) REVERT: n 111 LEU cc_start: 0.9462 (mm) cc_final: 0.9082 (pp) REVERT: o 1 MET cc_start: 0.7592 (ttm) cc_final: 0.7362 (ttp) REVERT: o 14 GLN cc_start: 0.9435 (mp10) cc_final: 0.9205 (mp10) REVERT: o 54 ASN cc_start: 0.7644 (p0) cc_final: 0.7226 (p0) REVERT: o 93 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8124 (tmt-80) outliers start: 202 outliers final: 120 residues processed: 1281 average time/residue: 0.4313 time to fit residues: 859.8567 Evaluate side-chains 1190 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1052 time to evaluate : 3.598 ------------------------------------------------------------------------------- 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 92 ASP 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 30 GLU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 92 ASP 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 118 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 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 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 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 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 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 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 23 LEU 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 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 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 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 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 34 ASN 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: 5.9990 chunk 359 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS E 17 ASN E 18 GLN E 51 ASN G 46 GLN G 98 ASN L 78 ASN O 18 GLN O 78 ASN a 18 ASN a 58 ASN a 73 ASN c 10 HIS ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 HIS i 73 ASN ** 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** o 47 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.055509 restraints weight = 149980.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057097 restraints weight = 93304.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058220 restraints weight = 66162.079| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31470 Z= 0.204 Angle : 0.766 11.934 42780 Z= 0.402 Chirality : 0.046 0.196 4995 Planarity : 0.005 0.052 5565 Dihedral : 7.486 76.490 4244 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.27 % Favored : 91.57 % Rotamer: Outliers : 6.47 % Allowed : 22.04 % Favored : 71.49 % 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: 0.53 (0.12), residues: 1615 sheet: -0.71 (0.20), residues: 621 loop : -2.22 (0.15), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP o 16 HIS 0.013 0.002 HIS b 42 PHE 0.026 0.002 PHE M 49 TYR 0.038 0.002 TYR h 114 ARG 0.009 0.001 ARG g 3 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 1420) hydrogen bonds : angle 5.27535 ( 4086) covalent geometry : bond 0.00450 (31470) covalent geometry : angle 0.76647 (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 1347 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 1119 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8843 (tp30) cc_final: 0.8339 (tp30) REVERT: A 17 ASN cc_start: 0.8968 (m110) cc_final: 0.8140 (m110) REVERT: A 29 GLU cc_start: 0.8978 (tp30) cc_final: 0.8755 (tp30) REVERT: A 30 GLU cc_start: 0.8687 (pm20) cc_final: 0.8290 (pm20) REVERT: A 38 MET cc_start: 0.9207 (tmm) cc_final: 0.8562 (tmm) REVERT: A 69 LYS cc_start: 0.9675 (tptm) cc_final: 0.9445 (tptm) REVERT: A 70 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8606 (tp30) REVERT: A 92 ASP cc_start: 0.8659 (p0) cc_final: 0.8415 (p0) REVERT: A 122 VAL cc_start: 0.9437 (p) cc_final: 0.9033 (p) REVERT: A 124 ASP cc_start: 0.9182 (t0) cc_final: 0.8903 (t0) REVERT: A 132 ASP cc_start: 0.8473 (m-30) cc_final: 0.7673 (t70) REVERT: B 49 PHE cc_start: 0.9734 (t80) cc_final: 0.9532 (t80) REVERT: B 51 ASN cc_start: 0.9362 (m110) cc_final: 0.9056 (p0) REVERT: B 86 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8777 (tp-100) REVERT: B 106 GLU cc_start: 0.9280 (tp30) cc_final: 0.8970 (tp30) REVERT: B 116 ARG cc_start: 0.9069 (tpp80) cc_final: 0.8787 (tpp80) REVERT: B 124 ASP cc_start: 0.8784 (t0) cc_final: 0.8353 (t0) REVERT: B 131 ASP cc_start: 0.9233 (t0) cc_final: 0.8805 (t0) REVERT: C 13 GLU cc_start: 0.8880 (tp30) cc_final: 0.7761 (tp30) REVERT: C 17 ASN cc_start: 0.9392 (m-40) cc_final: 0.8273 (m-40) REVERT: C 19 PHE cc_start: 0.8810 (m-80) cc_final: 0.8509 (m-80) REVERT: C 30 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: C 38 MET cc_start: 0.9052 (tmm) cc_final: 0.8647 (tmm) REVERT: C 39 CYS cc_start: 0.9354 (p) cc_final: 0.8926 (p) REVERT: C 60 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8697 (mt-10) REVERT: C 70 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8639 (mm-30) REVERT: C 86 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8641 (tp40) REVERT: C 102 ASP cc_start: 0.9157 (m-30) cc_final: 0.8878 (m-30) REVERT: C 105 ASP cc_start: 0.9435 (m-30) cc_final: 0.9206 (m-30) REVERT: C 116 ARG cc_start: 0.8530 (mmm160) cc_final: 0.8224 (mmm160) REVERT: D 60 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8958 (mm-30) REVERT: D 113 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9190 (mtmt) REVERT: E 17 ASN cc_start: 0.9443 (m-40) cc_final: 0.9070 (m110) REVERT: E 46 GLN cc_start: 0.9279 (tm-30) cc_final: 0.9009 (tm-30) REVERT: E 49 PHE cc_start: 0.9734 (t80) cc_final: 0.9432 (t80) REVERT: E 75 ASP cc_start: 0.8807 (t0) cc_final: 0.8545 (t0) REVERT: E 83 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8313 (tm-30) REVERT: E 89 LYS cc_start: 0.8933 (ptmm) cc_final: 0.8642 (ptmm) REVERT: E 92 ASP cc_start: 0.7687 (p0) cc_final: 0.7210 (p0) REVERT: E 105 ASP cc_start: 0.9260 (m-30) cc_final: 0.9019 (m-30) REVERT: E 116 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8781 (tpp80) REVERT: E 119 LYS cc_start: 0.9579 (mmtm) cc_final: 0.9331 (mmtm) REVERT: E 132 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: F 38 MET cc_start: 0.9254 (tmm) cc_final: 0.8968 (tmm) REVERT: F 39 CYS cc_start: 0.9355 (p) cc_final: 0.9050 (p) REVERT: F 70 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8676 (mt-10) REVERT: F 86 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8592 (tp40) REVERT: F 110 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8320 (mm-30) REVERT: G 60 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8752 (mt-10) REVERT: G 70 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8166 (tp30) REVERT: G 92 ASP cc_start: 0.8857 (p0) cc_final: 0.8552 (p0) REVERT: G 110 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9094 (mm-30) REVERT: G 116 ARG cc_start: 0.8900 (tpp80) cc_final: 0.8692 (tpp80) REVERT: G 132 ASP cc_start: 0.8598 (m-30) cc_final: 0.8275 (t70) REVERT: H 17 ASN cc_start: 0.8914 (m110) cc_final: 0.8676 (m110) REVERT: H 21 ASP cc_start: 0.7578 (p0) cc_final: 0.7239 (p0) REVERT: H 44 ARG cc_start: 0.8933 (ptm-80) cc_final: 0.8637 (ttt180) REVERT: H 53 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9089 (mm) REVERT: H 82 ILE cc_start: 0.9336 (tp) cc_final: 0.9066 (mt) REVERT: H 89 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8421 (ttmm) REVERT: H 95 MET cc_start: 0.8900 (mmm) cc_final: 0.8668 (mmm) REVERT: H 105 ASP cc_start: 0.9126 (m-30) cc_final: 0.8880 (m-30) REVERT: H 131 ASP cc_start: 0.9217 (p0) cc_final: 0.8908 (p0) REVERT: I 13 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8969 (mt-10) REVERT: I 21 ASP cc_start: 0.8376 (p0) cc_final: 0.8158 (p0) REVERT: I 38 MET cc_start: 0.9220 (tmm) cc_final: 0.8903 (tmm) REVERT: I 39 CYS cc_start: 0.9334 (p) cc_final: 0.8827 (p) REVERT: I 89 LYS cc_start: 0.9483 (ttpp) cc_final: 0.8579 (ttpp) REVERT: I 102 ASP cc_start: 0.8900 (m-30) cc_final: 0.8667 (m-30) REVERT: I 106 GLU cc_start: 0.9408 (tp30) cc_final: 0.9125 (mm-30) REVERT: I 116 ARG cc_start: 0.8681 (mmm160) cc_final: 0.7990 (mmm160) REVERT: J 13 GLU cc_start: 0.8730 (tp30) cc_final: 0.8122 (tp30) REVERT: J 17 ASN cc_start: 0.8690 (m110) cc_final: 0.7816 (m110) REVERT: J 21 ASP cc_start: 0.8616 (p0) cc_final: 0.8386 (p0) REVERT: J 27 GLU cc_start: 0.7129 (mp0) cc_final: 0.6914 (mp0) REVERT: J 60 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8665 (mt-10) REVERT: J 70 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8478 (mm-30) REVERT: J 92 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8157 (p0) REVERT: K 69 LYS cc_start: 0.9753 (tttp) cc_final: 0.9462 (ttmm) REVERT: K 86 GLN cc_start: 0.9182 (tp40) cc_final: 0.8743 (tp-100) REVERT: K 105 ASP cc_start: 0.9335 (m-30) cc_final: 0.9049 (m-30) REVERT: L 17 ASN cc_start: 0.9584 (m-40) cc_final: 0.9254 (m-40) REVERT: L 21 ASP cc_start: 0.7711 (p0) cc_final: 0.7469 (p0) REVERT: L 38 MET cc_start: 0.9229 (tmm) cc_final: 0.8949 (tmm) REVERT: L 39 CYS cc_start: 0.9212 (p) cc_final: 0.8681 (p) REVERT: L 76 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9075 (mmmm) REVERT: L 83 GLU cc_start: 0.8309 (mp0) cc_final: 0.8002 (mp0) REVERT: L 86 GLN cc_start: 0.9352 (mm-40) cc_final: 0.8887 (tp40) REVERT: L 124 ASP cc_start: 0.8732 (t70) cc_final: 0.8020 (t0) REVERT: M 17 ASN cc_start: 0.9491 (m-40) cc_final: 0.9286 (m110) REVERT: M 34 GLU cc_start: 0.9100 (tt0) cc_final: 0.8725 (tt0) REVERT: M 44 ARG cc_start: 0.8300 (ttt180) cc_final: 0.7590 (tpt170) REVERT: M 51 ASN cc_start: 0.9537 (OUTLIER) cc_final: 0.9323 (p0) REVERT: M 69 LYS cc_start: 0.9670 (OUTLIER) cc_final: 0.9467 (tptm) REVERT: M 75 ASP cc_start: 0.9037 (p0) cc_final: 0.8439 (p0) REVERT: M 83 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7576 (pp20) REVERT: M 86 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8569 (mm110) REVERT: M 102 ASP cc_start: 0.9224 (m-30) cc_final: 0.9005 (m-30) REVERT: M 106 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8637 (mp0) REVERT: M 116 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8464 (tpp80) REVERT: N 89 LYS cc_start: 0.8456 (ptmm) cc_final: 0.7665 (ptmm) REVERT: N 90 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8569 (m) REVERT: N 92 ASP cc_start: 0.7834 (p0) cc_final: 0.7189 (p0) REVERT: N 105 ASP cc_start: 0.9243 (m-30) cc_final: 0.8942 (m-30) REVERT: O 21 ASP cc_start: 0.7623 (p0) cc_final: 0.7312 (p0) REVERT: O 38 MET cc_start: 0.8907 (tmm) cc_final: 0.8613 (tmm) REVERT: O 39 CYS cc_start: 0.9179 (p) cc_final: 0.8792 (p) REVERT: O 92 ASP cc_start: 0.6985 (t70) cc_final: 0.6519 (t0) REVERT: O 94 THR cc_start: 0.9255 (m) cc_final: 0.8913 (p) REVERT: O 95 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (mtm) REVERT: O 102 ASP cc_start: 0.9087 (m-30) cc_final: 0.8724 (m-30) REVERT: O 105 ASP cc_start: 0.9383 (m-30) cc_final: 0.9182 (m-30) REVERT: a 62 ASP cc_start: 0.7883 (t0) cc_final: 0.7550 (t0) REVERT: a 101 ASP cc_start: 0.8976 (p0) cc_final: 0.8740 (p0) REVERT: a 108 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8999 (mm) REVERT: a 112 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9007 (mm-30) REVERT: a 113 ASP cc_start: 0.9126 (t70) cc_final: 0.8826 (t0) REVERT: a 117 ASP cc_start: 0.9428 (m-30) cc_final: 0.9169 (m-30) REVERT: b 1 MET cc_start: 0.8071 (tpt) cc_final: 0.6898 (tpt) REVERT: b 55 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8361 (t) REVERT: b 91 VAL cc_start: 0.9622 (t) cc_final: 0.9390 (p) REVERT: b 117 ASP cc_start: 0.8985 (m-30) cc_final: 0.8568 (t0) REVERT: c 103 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8579 (mm-30) REVERT: c 114 TYR cc_start: 0.9121 (t80) cc_final: 0.8914 (t80) REVERT: d 17 ILE cc_start: 0.9236 (pt) cc_final: 0.8943 (mm) REVERT: d 29 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8380 (p) REVERT: d 50 GLU cc_start: 0.7517 (tp30) cc_final: 0.7178 (tp30) REVERT: e 1 MET cc_start: 0.7719 (tpt) cc_final: 0.7271 (tpp) REVERT: e 5 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8225 (mtmm) REVERT: e 14 GLN cc_start: 0.8823 (mp10) cc_final: 0.8560 (mm-40) REVERT: e 30 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.6911 (p90) REVERT: e 108 LEU cc_start: 0.9175 (mt) cc_final: 0.8932 (mt) REVERT: f 3 ARG cc_start: 0.8633 (mtp-110) cc_final: 0.8228 (ttp-110) REVERT: f 27 ASN cc_start: 0.8635 (m-40) cc_final: 0.8224 (m-40) REVERT: f 82 ASP cc_start: 0.8078 (t0) cc_final: 0.7583 (m-30) REVERT: f 109 ASN cc_start: 0.8855 (m-40) cc_final: 0.8531 (m110) REVERT: g 14 GLN cc_start: 0.9141 (mp10) cc_final: 0.8922 (mm-40) REVERT: g 48 ASN cc_start: 0.9403 (t0) cc_final: 0.8856 (t0) REVERT: g 50 GLU cc_start: 0.8333 (mp0) cc_final: 0.7710 (mp0) REVERT: h 1 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.5666 (ttp) REVERT: h 36 TYR cc_start: 0.8770 (m-80) cc_final: 0.8227 (m-10) REVERT: i 74 LYS cc_start: 0.7767 (tmtt) cc_final: 0.7549 (tptp) REVERT: j 48 ASN cc_start: 0.9107 (t0) cc_final: 0.8708 (t0) REVERT: j 50 GLU cc_start: 0.8486 (pm20) cc_final: 0.7550 (pm20) REVERT: j 82 ASP cc_start: 0.8823 (m-30) cc_final: 0.8620 (m-30) REVERT: m 29 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7508 (p) REVERT: m 48 ASN cc_start: 0.9063 (t0) cc_final: 0.8647 (t0) REVERT: m 50 GLU cc_start: 0.8302 (pm20) cc_final: 0.8014 (mp0) REVERT: n 13 ASP cc_start: 0.8427 (t0) cc_final: 0.8086 (t0) REVERT: n 42 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8436 (t70) REVERT: n 94 GLU cc_start: 0.7920 (pm20) cc_final: 0.7715 (pm20) REVERT: n 111 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9105 (pp) REVERT: o 54 ASN cc_start: 0.7625 (p0) cc_final: 0.7322 (p0) REVERT: o 93 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8255 (tmt-80) outliers start: 228 outliers final: 148 residues processed: 1252 average time/residue: 0.4480 time to fit residues: 871.0577 Evaluate side-chains 1202 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1036 time to evaluate : 3.405 ------------------------------------------------------------------------------- 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 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 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 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 40 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 56 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 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 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 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 51 ASN 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 90 VAL Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 130 TYR 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 95 MET Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 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 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 91 VAL Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR 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 13 ASP Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 26 ILE Chi-restraints excluded: chain h residue 121 ASN Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 68 LEU Chi-restraints excluded: chain i residue 80 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 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 23 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 38 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 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 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 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 47 GLN Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 93 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 103 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 374 optimal weight: 20.0000 chunk 241 optimal weight: 0.0980 chunk 337 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 78 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN O 78 ASN a 58 ASN ** f 10 HIS ** 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** ** 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 = 0.3416 r_free = 0.3416 target = 0.068403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054483 restraints weight = 149347.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056076 restraints weight = 93071.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057183 restraints weight = 65844.765| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31470 Z= 0.184 Angle : 0.766 13.759 42780 Z= 0.401 Chirality : 0.046 0.220 4995 Planarity : 0.005 0.065 5565 Dihedral : 7.221 62.168 4227 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.17 % Favored : 91.70 % Rotamer: Outliers : 6.72 % Allowed : 23.55 % Favored : 69.73 % 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: -1.15 (0.13), residues: 3795 helix: 0.54 (0.12), residues: 1615 sheet: -0.64 (0.20), residues: 599 loop : -2.22 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 16 HIS 0.011 0.001 HIS b 42 PHE 0.024 0.002 PHE F 42 TYR 0.041 0.002 TYR m 110 ARG 0.007 0.001 ARG J 44 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 1420) hydrogen bonds : angle 5.17246 ( 4086) covalent geometry : bond 0.00408 (31470) covalent geometry : angle 0.76599 (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 1363 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 1126 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8839 (tp30) cc_final: 0.8310 (tp30) REVERT: A 17 ASN cc_start: 0.8983 (m110) cc_final: 0.8149 (m110) REVERT: A 29 GLU cc_start: 0.8984 (tp30) cc_final: 0.8559 (tp30) REVERT: A 30 GLU cc_start: 0.8710 (pm20) cc_final: 0.7967 (pm20) REVERT: A 38 MET cc_start: 0.9252 (tmm) cc_final: 0.8686 (tmm) REVERT: A 70 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8414 (tp30) REVERT: A 92 ASP cc_start: 0.8811 (p0) cc_final: 0.8589 (p0) REVERT: B 49 PHE cc_start: 0.9738 (t80) cc_final: 0.9441 (t80) REVERT: B 86 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8782 (tp-100) REVERT: B 105 ASP cc_start: 0.9255 (m-30) cc_final: 0.9032 (m-30) REVERT: B 106 GLU cc_start: 0.9315 (tp30) cc_final: 0.8982 (tp30) REVERT: B 124 ASP cc_start: 0.8787 (t0) cc_final: 0.8424 (t0) REVERT: B 131 ASP cc_start: 0.9301 (t0) cc_final: 0.8871 (t0) REVERT: C 13 GLU cc_start: 0.8919 (tp30) cc_final: 0.7815 (tp30) REVERT: C 17 ASN cc_start: 0.9408 (m-40) cc_final: 0.8364 (m-40) REVERT: C 19 PHE cc_start: 0.8828 (m-80) cc_final: 0.8488 (m-80) REVERT: C 30 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8253 (pt0) REVERT: C 38 MET cc_start: 0.9065 (tmm) cc_final: 0.8681 (tmm) REVERT: C 60 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8705 (mt-10) REVERT: C 70 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8644 (mm-30) REVERT: C 86 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8590 (tp40) REVERT: C 102 ASP cc_start: 0.9169 (m-30) cc_final: 0.8879 (m-30) REVERT: C 105 ASP cc_start: 0.9449 (m-30) cc_final: 0.9214 (m-30) REVERT: C 112 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9383 (mttp) REVERT: C 116 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8209 (mmm160) REVERT: D 60 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8932 (mm-30) REVERT: D 69 LYS cc_start: 0.9661 (ttmm) cc_final: 0.9357 (ttpp) REVERT: D 70 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8648 (mm-30) REVERT: D 112 LYS cc_start: 0.9442 (mtmm) cc_final: 0.8988 (mtmm) REVERT: D 113 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9182 (mtmt) REVERT: D 132 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7426 (t0) REVERT: E 17 ASN cc_start: 0.9507 (m-40) cc_final: 0.9246 (m110) REVERT: E 89 LYS cc_start: 0.8952 (ptmm) cc_final: 0.8189 (ptmm) REVERT: E 92 ASP cc_start: 0.7784 (p0) cc_final: 0.7256 (p0) REVERT: E 105 ASP cc_start: 0.9279 (m-30) cc_final: 0.9013 (m-30) REVERT: E 132 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: F 38 MET cc_start: 0.9270 (tmm) cc_final: 0.8954 (tmm) REVERT: F 39 CYS cc_start: 0.9354 (p) cc_final: 0.9044 (p) REVERT: F 86 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8541 (tp40) REVERT: F 92 ASP cc_start: 0.7618 (t0) cc_final: 0.7000 (t0) REVERT: F 97 MET cc_start: 0.8745 (mmm) cc_final: 0.8403 (mmt) REVERT: F 110 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8379 (mm-30) REVERT: G 34 GLU cc_start: 0.8751 (tt0) cc_final: 0.8251 (tt0) REVERT: G 44 ARG cc_start: 0.8763 (ptm160) cc_final: 0.7625 (ttm170) REVERT: G 70 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8461 (mm-30) REVERT: G 92 ASP cc_start: 0.8849 (p0) cc_final: 0.8538 (p0) REVERT: H 21 ASP cc_start: 0.7667 (p0) cc_final: 0.7288 (p0) REVERT: H 44 ARG cc_start: 0.9050 (ptm-80) cc_final: 0.8526 (ttt90) REVERT: H 82 ILE cc_start: 0.9320 (tp) cc_final: 0.9051 (mt) REVERT: H 95 MET cc_start: 0.8891 (mmm) cc_final: 0.8658 (mmm) REVERT: H 105 ASP cc_start: 0.9138 (m-30) cc_final: 0.8896 (m-30) REVERT: I 13 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8988 (mt-10) REVERT: I 35 PHE cc_start: 0.9627 (t80) cc_final: 0.8954 (t80) REVERT: I 38 MET cc_start: 0.9223 (tmm) cc_final: 0.8894 (tmm) REVERT: I 39 CYS cc_start: 0.9356 (p) cc_final: 0.8722 (p) REVERT: I 60 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8832 (mt-10) REVERT: I 90 VAL cc_start: 0.9053 (t) cc_final: 0.8638 (p) REVERT: I 99 TYR cc_start: 0.8432 (t80) cc_final: 0.8094 (t80) REVERT: I 102 ASP cc_start: 0.8938 (m-30) cc_final: 0.8737 (m-30) REVERT: I 116 ARG cc_start: 0.8628 (mmm160) cc_final: 0.8176 (mmm160) REVERT: J 13 GLU cc_start: 0.8752 (tp30) cc_final: 0.8359 (tp30) REVERT: J 21 ASP cc_start: 0.8689 (p0) cc_final: 0.8313 (p0) REVERT: J 27 GLU cc_start: 0.7152 (mp0) cc_final: 0.6924 (mp0) REVERT: J 60 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8711 (mt-10) REVERT: J 70 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8270 (tp30) REVERT: J 79 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8850 (mtmm) REVERT: J 83 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8052 (pp20) REVERT: J 92 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8472 (p0) REVERT: K 69 LYS cc_start: 0.9759 (tttp) cc_final: 0.9449 (ttmm) REVERT: K 86 GLN cc_start: 0.9133 (tp40) cc_final: 0.8698 (tp-100) REVERT: K 105 ASP cc_start: 0.9324 (m-30) cc_final: 0.9065 (m-30) REVERT: L 38 MET cc_start: 0.9226 (tmm) cc_final: 0.8928 (tmm) REVERT: L 39 CYS cc_start: 0.9249 (p) cc_final: 0.8668 (p) REVERT: L 76 LYS cc_start: 0.9382 (mmmm) cc_final: 0.9080 (mmmm) REVERT: L 83 GLU cc_start: 0.8271 (mp0) cc_final: 0.7667 (mp0) REVERT: L 86 GLN cc_start: 0.9341 (mm-40) cc_final: 0.8848 (tp40) REVERT: L 124 ASP cc_start: 0.8805 (t70) cc_final: 0.8147 (t0) REVERT: M 17 ASN cc_start: 0.9529 (m-40) cc_final: 0.9287 (m110) REVERT: M 70 GLU cc_start: 0.9030 (tp30) cc_final: 0.8196 (tp30) REVERT: M 73 ARG cc_start: 0.9334 (tmm-80) cc_final: 0.8661 (ttp80) REVERT: M 83 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7520 (pp20) REVERT: M 86 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8533 (mm110) REVERT: M 102 ASP cc_start: 0.9224 (m-30) cc_final: 0.9009 (m-30) REVERT: M 106 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8632 (mp0) REVERT: M 116 ARG cc_start: 0.8890 (tpp80) cc_final: 0.8409 (tpp80) REVERT: M 131 ASP cc_start: 0.8964 (t0) cc_final: 0.8650 (t0) REVERT: N 89 LYS cc_start: 0.8561 (ptmm) cc_final: 0.7705 (ptmm) REVERT: N 92 ASP cc_start: 0.7784 (p0) cc_final: 0.7102 (p0) REVERT: N 105 ASP cc_start: 0.9228 (m-30) cc_final: 0.8927 (m-30) REVERT: O 13 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8936 (mt-10) REVERT: O 21 ASP cc_start: 0.7642 (p0) cc_final: 0.7276 (p0) REVERT: O 38 MET cc_start: 0.8922 (tmm) cc_final: 0.8592 (tmm) REVERT: O 39 CYS cc_start: 0.9161 (p) cc_final: 0.8776 (p) REVERT: O 70 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8609 (mt-10) REVERT: O 92 ASP cc_start: 0.7206 (t70) cc_final: 0.6719 (t0) REVERT: O 99 TYR cc_start: 0.8440 (t80) cc_final: 0.8100 (t80) REVERT: O 102 ASP cc_start: 0.9109 (m-30) cc_final: 0.8757 (m-30) REVERT: O 105 ASP cc_start: 0.9404 (m-30) cc_final: 0.9168 (m-30) REVERT: a 62 ASP cc_start: 0.7925 (t0) cc_final: 0.7615 (t0) REVERT: a 108 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9007 (mm) REVERT: a 112 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8926 (mm-30) REVERT: a 113 ASP cc_start: 0.9162 (t70) cc_final: 0.8813 (t0) REVERT: a 117 ASP cc_start: 0.9443 (m-30) cc_final: 0.9169 (m-30) REVERT: b 1 MET cc_start: 0.8149 (tpt) cc_final: 0.7230 (tpt) REVERT: b 55 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8444 (t) REVERT: b 91 VAL cc_start: 0.9628 (t) cc_final: 0.9398 (p) REVERT: b 117 ASP cc_start: 0.8999 (m-30) cc_final: 0.8632 (t0) REVERT: c 3 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7859 (ttp80) REVERT: c 50 GLU cc_start: 0.7703 (tp30) cc_final: 0.7374 (tp30) REVERT: c 103 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8721 (mm-30) REVERT: c 114 TYR cc_start: 0.9192 (t80) cc_final: 0.8932 (t80) REVERT: d 17 ILE cc_start: 0.9326 (pt) cc_final: 0.9035 (mm) REVERT: d 29 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (p) REVERT: d 50 GLU cc_start: 0.7431 (tp30) cc_final: 0.7157 (tp30) REVERT: d 58 ASN cc_start: 0.6904 (t0) cc_final: 0.6682 (t0) REVERT: e 1 MET cc_start: 0.8006 (tpt) cc_final: 0.7719 (tpp) REVERT: e 14 GLN cc_start: 0.8901 (mp10) cc_final: 0.8585 (mm-40) REVERT: e 30 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.6832 (p90) REVERT: e 108 LEU cc_start: 0.9168 (mt) cc_final: 0.8911 (mt) REVERT: f 5 LYS cc_start: 0.8646 (mtmm) cc_final: 0.7998 (mtmm) REVERT: f 27 ASN cc_start: 0.8622 (m-40) cc_final: 0.8320 (m-40) REVERT: f 50 GLU cc_start: 0.8039 (tp30) cc_final: 0.7703 (tp30) REVERT: f 86 ASP cc_start: 0.8499 (p0) cc_final: 0.8297 (p0) REVERT: f 109 ASN cc_start: 0.8883 (m-40) cc_final: 0.8538 (m110) REVERT: g 48 ASN cc_start: 0.9426 (t0) cc_final: 0.8969 (t0) REVERT: g 50 GLU cc_start: 0.8387 (mp0) cc_final: 0.7690 (pm20) REVERT: h 1 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.5576 (ttp) REVERT: h 36 TYR cc_start: 0.8779 (m-80) cc_final: 0.8412 (m-10) REVERT: i 62 ASP cc_start: 0.7949 (m-30) cc_final: 0.7745 (m-30) REVERT: k 67 ILE cc_start: 0.8291 (mp) cc_final: 0.7905 (mp) REVERT: m 29 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7536 (p) REVERT: m 48 ASN cc_start: 0.9104 (t0) cc_final: 0.8670 (t0) REVERT: m 50 GLU cc_start: 0.8414 (pm20) cc_final: 0.7815 (pm20) REVERT: n 42 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8494 (t70) REVERT: n 111 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9170 (pp) REVERT: o 1 MET cc_start: 0.7849 (ttp) cc_final: 0.7077 (tmm) REVERT: o 54 ASN cc_start: 0.7977 (p0) cc_final: 0.7573 (p0) REVERT: o 65 TYR cc_start: 0.6486 (OUTLIER) cc_final: 0.5490 (t80) REVERT: o 77 SER cc_start: 0.9468 (p) cc_final: 0.8976 (p) outliers start: 237 outliers final: 153 residues processed: 1268 average time/residue: 0.4384 time to fit residues: 859.6379 Evaluate side-chains 1214 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1044 time to evaluate : 3.684 ------------------------------------------------------------------------------- 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 9 THR 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 112 LYS 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 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 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain 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 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 98 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 120 LEU Chi-restraints excluded: chain H residue 130 TYR 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 118 LEU Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 123 LEU 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 118 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 129 SER Chi-restraints excluded: chain O residue 132 ASP Chi-restraints excluded: chain O residue 133 VAL Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain a residue 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 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 3 ARG Chi-restraints excluded: chain c residue 69 THR 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 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 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 52 VAL Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 70 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 13 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 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 80 VAL Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 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 23 LEU Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 38 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 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 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 47 GLN Chi-restraints excluded: chain o residue 52 VAL 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: 5.9990 chunk 30 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN D 17 ASN ** 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** H 78 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN a 48 ASN a 58 ASN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 GLN ** 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** o 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.064966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.051484 restraints weight = 152124.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053005 restraints weight = 93870.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054059 restraints weight = 66205.857| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 31470 Z= 0.257 Angle : 0.821 12.329 42780 Z= 0.435 Chirality : 0.047 0.232 4995 Planarity : 0.005 0.065 5565 Dihedral : 7.400 63.316 4225 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.93 % Favored : 90.91 % Rotamer: Outliers : 6.87 % Allowed : 25.19 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.13), residues: 3795 helix: 0.41 (0.12), residues: 1611 sheet: -0.64 (0.20), residues: 602 loop : -2.30 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP o 16 HIS 0.011 0.002 HIS b 42 PHE 0.021 0.002 PHE F 19 TYR 0.044 0.002 TYR m 110 ARG 0.017 0.001 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1420) hydrogen bonds : angle 5.33969 ( 4086) covalent geometry : bond 0.00566 (31470) covalent geometry : angle 0.82114 (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 1302 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 1060 time to evaluate : 3.910 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: A 13 GLU cc_start: 0.8910 (tp30) cc_final: 0.8447 (tp30) REVERT: A 29 GLU cc_start: 0.9011 (tp30) cc_final: 0.8487 (tp30) REVERT: A 30 GLU cc_start: 0.8785 (pm20) cc_final: 0.8017 (pm20) REVERT: A 38 MET cc_start: 0.9301 (tmm) cc_final: 0.8772 (tmm) REVERT: A 49 PHE cc_start: 0.9531 (t80) cc_final: 0.9312 (t80) REVERT: A 70 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8218 (tp30) REVERT: A 73 ARG cc_start: 0.9002 (ttp80) cc_final: 0.8651 (ttp80) REVERT: A 92 ASP cc_start: 0.8849 (p0) cc_final: 0.8571 (p0) REVERT: A 112 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9164 (mmtm) REVERT: A 124 ASP cc_start: 0.9196 (t0) cc_final: 0.8919 (t0) REVERT: B 86 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8896 (tp-100) REVERT: B 91 GLU cc_start: 0.8227 (pp20) cc_final: 0.7388 (pp20) REVERT: B 105 ASP cc_start: 0.9284 (m-30) cc_final: 0.9075 (m-30) REVERT: B 116 ARG cc_start: 0.9142 (tpp80) cc_final: 0.8750 (tpp80) REVERT: B 124 ASP cc_start: 0.8940 (t0) cc_final: 0.8627 (t0) REVERT: B 131 ASP cc_start: 0.9293 (t0) cc_final: 0.8891 (t0) REVERT: C 13 GLU cc_start: 0.8950 (tp30) cc_final: 0.7978 (tp30) REVERT: C 17 ASN cc_start: 0.9406 (m-40) cc_final: 0.8527 (m-40) REVERT: C 19 PHE cc_start: 0.8781 (m-80) cc_final: 0.8424 (m-80) REVERT: C 30 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (pt0) REVERT: C 38 MET cc_start: 0.9175 (tmm) cc_final: 0.8633 (tmm) REVERT: C 39 CYS cc_start: 0.9294 (p) cc_final: 0.8824 (p) REVERT: C 70 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8574 (mm-30) REVERT: C 83 GLU cc_start: 0.8039 (mp0) cc_final: 0.7620 (mp0) REVERT: C 86 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8686 (tp40) REVERT: C 102 ASP cc_start: 0.9173 (m-30) cc_final: 0.8858 (m-30) REVERT: C 105 ASP cc_start: 0.9455 (m-30) cc_final: 0.9205 (m-30) REVERT: C 116 ARG cc_start: 0.8662 (mmm160) cc_final: 0.8279 (mmm160) REVERT: D 21 ASP cc_start: 0.7607 (p0) cc_final: 0.7295 (p0) REVERT: D 44 ARG cc_start: 0.8763 (ptm160) cc_final: 0.8248 (ptm160) REVERT: D 60 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8927 (mm-30) REVERT: D 69 LYS cc_start: 0.9660 (ttmm) cc_final: 0.9367 (ttpp) REVERT: D 106 GLU cc_start: 0.8982 (tp30) cc_final: 0.8680 (tp30) REVERT: D 112 LYS cc_start: 0.9426 (mtmm) cc_final: 0.8981 (mtmm) REVERT: D 113 LYS cc_start: 0.9449 (mtpt) cc_final: 0.9197 (mtmt) REVERT: D 132 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7567 (t0) REVERT: E 17 ASN cc_start: 0.9499 (m-40) cc_final: 0.9197 (m-40) REVERT: E 46 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8706 (tp-100) REVERT: E 92 ASP cc_start: 0.7937 (p0) cc_final: 0.7310 (p0) REVERT: E 105 ASP cc_start: 0.9282 (m-30) cc_final: 0.9019 (m-30) REVERT: E 132 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: F 38 MET cc_start: 0.9313 (tmm) cc_final: 0.9040 (tmm) REVERT: F 39 CYS cc_start: 0.9331 (p) cc_final: 0.9017 (p) REVERT: F 86 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8597 (tp40) REVERT: F 110 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8457 (mm-30) REVERT: F 119 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9193 (mmmt) REVERT: G 29 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8741 (tm-30) REVERT: G 34 GLU cc_start: 0.8799 (tt0) cc_final: 0.8257 (tt0) REVERT: G 70 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8346 (mm-30) REVERT: G 79 LYS cc_start: 0.9507 (mppt) cc_final: 0.9160 (mtmm) REVERT: G 92 ASP cc_start: 0.8924 (p0) cc_final: 0.8466 (p0) REVERT: G 112 LYS cc_start: 0.9301 (mttp) cc_final: 0.8985 (mttp) REVERT: H 21 ASP cc_start: 0.7756 (p0) cc_final: 0.7360 (p0) REVERT: H 44 ARG cc_start: 0.9094 (ptm-80) cc_final: 0.8594 (ttt180) REVERT: H 92 ASP cc_start: 0.8366 (p0) cc_final: 0.7538 (p0) REVERT: H 105 ASP cc_start: 0.9173 (m-30) cc_final: 0.8929 (m-30) REVERT: I 21 ASP cc_start: 0.8440 (p0) cc_final: 0.8186 (p0) REVERT: I 35 PHE cc_start: 0.9640 (t80) cc_final: 0.9181 (t80) REVERT: I 38 MET cc_start: 0.9269 (tmm) cc_final: 0.9043 (tmm) REVERT: I 39 CYS cc_start: 0.9374 (p) cc_final: 0.8912 (p) REVERT: I 70 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8635 (tt0) REVERT: I 116 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8296 (mmm160) REVERT: J 13 GLU cc_start: 0.8807 (tp30) cc_final: 0.8434 (tp30) REVERT: J 21 ASP cc_start: 0.8707 (p0) cc_final: 0.8311 (p0) REVERT: J 27 GLU cc_start: 0.7325 (mp0) cc_final: 0.7054 (mp0) REVERT: J 34 GLU cc_start: 0.9079 (tt0) cc_final: 0.8588 (tt0) REVERT: J 60 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8766 (mt-10) REVERT: J 70 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8299 (tp30) REVERT: K 46 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8905 (mp10) REVERT: K 69 LYS cc_start: 0.9767 (tttp) cc_final: 0.9454 (ttmm) REVERT: K 86 GLN cc_start: 0.9152 (tp40) cc_final: 0.8708 (tp-100) REVERT: K 105 ASP cc_start: 0.9354 (m-30) cc_final: 0.9078 (m-30) REVERT: L 39 CYS cc_start: 0.9237 (p) cc_final: 0.8825 (p) REVERT: L 46 GLN cc_start: 0.9001 (mt0) cc_final: 0.8765 (mt0) REVERT: L 76 LYS cc_start: 0.9418 (mmmm) cc_final: 0.9075 (mmmm) REVERT: L 83 GLU cc_start: 0.8307 (mp0) cc_final: 0.7710 (mp0) REVERT: L 86 GLN cc_start: 0.9392 (mm-40) cc_final: 0.8963 (tp40) REVERT: L 110 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8877 (tp30) REVERT: L 124 ASP cc_start: 0.8763 (t70) cc_final: 0.8215 (t0) REVERT: M 17 ASN cc_start: 0.9532 (m-40) cc_final: 0.9277 (m-40) REVERT: M 34 GLU cc_start: 0.8992 (tt0) cc_final: 0.8693 (tt0) REVERT: M 69 LYS cc_start: 0.9641 (ttpp) cc_final: 0.9433 (ttpp) REVERT: M 73 ARG cc_start: 0.9367 (tmm-80) cc_final: 0.8722 (ttp80) REVERT: M 75 ASP cc_start: 0.8970 (p0) cc_final: 0.8398 (p0) REVERT: M 76 LYS cc_start: 0.9160 (mppt) cc_final: 0.8883 (mmtm) REVERT: M 83 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7602 (pp20) REVERT: M 86 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8531 (mm110) REVERT: M 102 ASP cc_start: 0.9256 (m-30) cc_final: 0.9027 (m-30) REVERT: M 106 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8677 (mp0) REVERT: M 116 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8453 (tpp80) REVERT: M 131 ASP cc_start: 0.9024 (t0) cc_final: 0.8641 (t0) REVERT: M 132 ASP cc_start: 0.8812 (m-30) cc_final: 0.8235 (m-30) REVERT: N 35 PHE cc_start: 0.9520 (t80) cc_final: 0.9079 (t80) REVERT: N 39 CYS cc_start: 0.9674 (m) cc_final: 0.9386 (m) REVERT: N 44 ARG cc_start: 0.8554 (tpt170) cc_final: 0.8114 (tpt170) REVERT: N 86 GLN cc_start: 0.8738 (mp10) cc_final: 0.8108 (mp10) REVERT: N 89 LYS cc_start: 0.8647 (ptmm) cc_final: 0.7847 (ptmm) REVERT: N 92 ASP cc_start: 0.7757 (p0) cc_final: 0.7186 (p0) REVERT: N 97 MET cc_start: 0.9202 (mmm) cc_final: 0.8706 (mmm) REVERT: N 105 ASP cc_start: 0.9258 (m-30) cc_final: 0.8967 (m-30) REVERT: O 13 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8983 (mt-10) REVERT: O 21 ASP cc_start: 0.7718 (p0) cc_final: 0.7369 (p0) REVERT: O 38 MET cc_start: 0.8970 (tmm) cc_final: 0.8622 (tmm) REVERT: O 39 CYS cc_start: 0.9191 (p) cc_final: 0.8811 (p) REVERT: O 70 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8681 (mt-10) REVERT: O 92 ASP cc_start: 0.7308 (t70) cc_final: 0.6837 (t0) REVERT: O 99 TYR cc_start: 0.8552 (t80) cc_final: 0.8210 (t80) REVERT: O 102 ASP cc_start: 0.9103 (m-30) cc_final: 0.8779 (m-30) REVERT: O 105 ASP cc_start: 0.9431 (m-30) cc_final: 0.9192 (m-30) REVERT: O 112 LYS cc_start: 0.9537 (mttp) cc_final: 0.9174 (mtmm) REVERT: a 62 ASP cc_start: 0.8108 (t0) cc_final: 0.7849 (t0) REVERT: a 112 GLU cc_start: 0.9354 (mm-30) cc_final: 0.8898 (mm-30) REVERT: a 113 ASP cc_start: 0.9162 (t70) cc_final: 0.8792 (t0) REVERT: a 117 ASP cc_start: 0.9452 (m-30) cc_final: 0.9193 (m-30) REVERT: b 1 MET cc_start: 0.8597 (tpt) cc_final: 0.8202 (tpt) REVERT: b 55 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8671 (t) REVERT: b 112 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7855 (pp20) REVERT: b 117 ASP cc_start: 0.8984 (m-30) cc_final: 0.8565 (t0) REVERT: c 3 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: c 103 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8911 (mm-30) REVERT: c 114 TYR cc_start: 0.9232 (t80) cc_final: 0.8814 (t80) REVERT: d 13 ASP cc_start: 0.8577 (m-30) cc_final: 0.8372 (m-30) REVERT: d 17 ILE cc_start: 0.9369 (pt) cc_final: 0.9120 (mm) REVERT: d 29 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8615 (p) REVERT: d 50 GLU cc_start: 0.7693 (tp30) cc_final: 0.7451 (tp30) REVERT: d 58 ASN cc_start: 0.7173 (t0) cc_final: 0.6962 (t0) REVERT: e 14 GLN cc_start: 0.8893 (mp10) cc_final: 0.8614 (mm-40) REVERT: e 30 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.6958 (p90) REVERT: f 5 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8145 (mtmm) REVERT: f 27 ASN cc_start: 0.8784 (m-40) cc_final: 0.8447 (m-40) REVERT: f 50 GLU cc_start: 0.8139 (tp30) cc_final: 0.7919 (tp30) REVERT: f 59 VAL cc_start: 0.7874 (m) cc_final: 0.7215 (p) REVERT: f 82 ASP cc_start: 0.8571 (t0) cc_final: 0.8280 (m-30) REVERT: f 86 ASP cc_start: 0.8425 (p0) cc_final: 0.8111 (p0) REVERT: f 113 ASP cc_start: 0.9190 (m-30) cc_final: 0.8668 (p0) REVERT: g 1 MET cc_start: 0.8721 (tpp) cc_final: 0.8392 (tmm) REVERT: g 48 ASN cc_start: 0.9368 (t0) cc_final: 0.8890 (t0) REVERT: g 50 GLU cc_start: 0.8272 (mp0) cc_final: 0.7732 (mp0) REVERT: h 1 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.5600 (ttp) REVERT: h 36 TYR cc_start: 0.8754 (m-80) cc_final: 0.8536 (m-10) REVERT: h 74 LYS cc_start: 0.9390 (mmtp) cc_final: 0.9116 (mmmm) REVERT: j 18 ASN cc_start: 0.9109 (p0) cc_final: 0.8905 (p0) REVERT: j 44 LYS cc_start: 0.9255 (tppp) cc_final: 0.8806 (tppt) REVERT: j 48 ASN cc_start: 0.8890 (t0) cc_final: 0.8486 (t0) REVERT: j 50 GLU cc_start: 0.8309 (pm20) cc_final: 0.8023 (pm20) REVERT: k 17 ILE cc_start: 0.9647 (OUTLIER) cc_final: 0.9440 (mm) REVERT: k 67 ILE cc_start: 0.8564 (mp) cc_final: 0.8329 (mp) REVERT: l 123 GLN cc_start: 0.8357 (mm110) cc_final: 0.7574 (tp40) REVERT: m 9 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7480 (tpp80) REVERT: m 29 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7901 (p) REVERT: m 44 LYS cc_start: 0.9586 (ttmm) cc_final: 0.9377 (mtpp) REVERT: m 48 ASN cc_start: 0.9268 (t0) cc_final: 0.8821 (t0) REVERT: m 50 GLU cc_start: 0.8429 (pm20) cc_final: 0.7779 (pm20) REVERT: n 111 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9177 (pp) REVERT: o 1 MET cc_start: 0.7860 (ttp) cc_final: 0.7335 (tmm) REVERT: o 54 ASN cc_start: 0.8059 (p0) cc_final: 0.7619 (p0) REVERT: o 65 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5546 (t80) REVERT: o 77 SER cc_start: 0.9481 (p) cc_final: 0.8963 (p) outliers start: 242 outliers final: 171 residues processed: 1203 average time/residue: 0.4425 time to fit residues: 820.6988 Evaluate side-chains 1198 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1013 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 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 33 ILE 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 C residue 20 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 122 VAL 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 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 132 ASP 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 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 47 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 118 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 90 VAL Chi-restraints excluded: chain J residue 94 THR 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 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 L residue 134 GLU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain 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 80 GLU Chi-restraints excluded: chain N residue 130 TYR 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 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 85 SER Chi-restraints excluded: chain a residue 94 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 3 ARG Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain c residue 107 VAL 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 52 VAL 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 31 ASN Chi-restraints excluded: chain e residue 87 ILE Chi-restraints excluded: chain e residue 91 VAL Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 110 TYR Chi-restraints excluded: chain e residue 113 ASP Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 104 TYR Chi-restraints excluded: chain g residue 70 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 13 ASP Chi-restraints excluded: chain h residue 24 THR 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 h residue 114 TYR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 80 VAL 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 38 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 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 n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain n residue 115 ILE Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain o residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 81 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 373 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 140 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 GLN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** o 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.064129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.050797 restraints weight = 150805.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052306 restraints weight = 93737.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053346 restraints weight = 66142.163| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31470 Z= 0.211 Angle : 0.820 12.023 42780 Z= 0.431 Chirality : 0.047 0.220 4995 Planarity : 0.005 0.074 5565 Dihedral : 7.277 58.784 4218 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.38 % Favored : 91.54 % Rotamer: Outliers : 6.44 % Allowed : 26.30 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.13), residues: 3795 helix: 0.36 (0.12), residues: 1611 sheet: -0.56 (0.20), residues: 616 loop : -2.29 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP o 16 HIS 0.009 0.001 HIS b 42 PHE 0.019 0.002 PHE F 19 TYR 0.039 0.002 TYR h 114 ARG 0.011 0.001 ARG c 93 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 1420) hydrogen bonds : angle 5.25647 ( 4086) covalent geometry : bond 0.00470 (31470) covalent geometry : angle 0.82009 (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 1337 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1110 time to evaluate : 3.836 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: A 13 GLU cc_start: 0.8933 (tp30) cc_final: 0.8386 (tp30) REVERT: A 17 ASN cc_start: 0.9031 (m110) cc_final: 0.8194 (m110) REVERT: A 29 GLU cc_start: 0.9033 (tp30) cc_final: 0.8431 (tp30) REVERT: A 30 GLU cc_start: 0.8719 (pm20) cc_final: 0.8014 (pm20) REVERT: A 38 MET cc_start: 0.9326 (tmm) cc_final: 0.8762 (tmm) REVERT: A 53 LEU cc_start: 0.9273 (mm) cc_final: 0.9043 (mm) REVERT: A 70 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8303 (tp30) REVERT: A 73 ARG cc_start: 0.8945 (ttp80) cc_final: 0.8628 (ttp80) REVERT: A 92 ASP cc_start: 0.8914 (p0) cc_final: 0.8589 (p0) REVERT: A 124 ASP cc_start: 0.9256 (t0) cc_final: 0.8859 (t0) REVERT: A 132 ASP cc_start: 0.8758 (m-30) cc_final: 0.7971 (t70) REVERT: B 38 MET cc_start: 0.9217 (mtm) cc_final: 0.8987 (ttm) REVERT: B 86 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8862 (tp-100) REVERT: B 91 GLU cc_start: 0.8294 (pp20) cc_final: 0.7607 (pp20) REVERT: B 105 ASP cc_start: 0.9298 (m-30) cc_final: 0.9079 (m-30) REVERT: B 116 ARG cc_start: 0.9148 (tpp80) cc_final: 0.8718 (tpp80) REVERT: B 124 ASP cc_start: 0.8983 (t0) cc_final: 0.8701 (t0) REVERT: B 131 ASP cc_start: 0.9281 (t0) cc_final: 0.9062 (t0) REVERT: C 13 GLU cc_start: 0.8986 (tp30) cc_final: 0.7938 (tp30) REVERT: C 17 ASN cc_start: 0.9407 (m-40) cc_final: 0.8458 (m-40) REVERT: C 19 PHE cc_start: 0.8753 (m-80) cc_final: 0.8464 (m-80) REVERT: C 38 MET cc_start: 0.9206 (tmm) cc_final: 0.8738 (tmm) REVERT: C 39 CYS cc_start: 0.9286 (p) cc_final: 0.8799 (p) REVERT: C 70 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8572 (mm-30) REVERT: C 83 GLU cc_start: 0.8020 (mp0) cc_final: 0.7712 (mp0) REVERT: C 86 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8573 (tp40) REVERT: C 102 ASP cc_start: 0.9179 (m-30) cc_final: 0.8876 (m-30) REVERT: C 105 ASP cc_start: 0.9446 (m-30) cc_final: 0.9193 (m-30) REVERT: C 113 LYS cc_start: 0.9615 (mtpt) cc_final: 0.9287 (ttmm) REVERT: C 116 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8340 (mmm160) REVERT: D 21 ASP cc_start: 0.7738 (p0) cc_final: 0.7383 (p0) REVERT: D 44 ARG cc_start: 0.8774 (ptm160) cc_final: 0.8236 (ptm160) REVERT: D 60 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8920 (mm-30) REVERT: D 69 LYS cc_start: 0.9666 (OUTLIER) cc_final: 0.9389 (ttpp) REVERT: D 106 GLU cc_start: 0.8994 (tp30) cc_final: 0.8693 (tp30) REVERT: D 113 LYS cc_start: 0.9460 (mtpt) cc_final: 0.9229 (mtmt) REVERT: D 132 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7465 (t0) REVERT: E 17 ASN cc_start: 0.9503 (m-40) cc_final: 0.9247 (m-40) REVERT: E 44 ARG cc_start: 0.8489 (tpt-90) cc_final: 0.8215 (tpt-90) REVERT: E 46 GLN cc_start: 0.9262 (tp-100) cc_final: 0.8653 (tp-100) REVERT: E 92 ASP cc_start: 0.7811 (p0) cc_final: 0.7192 (p0) REVERT: E 105 ASP cc_start: 0.9283 (m-30) cc_final: 0.9012 (m-30) REVERT: E 132 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: F 13 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8929 (pt0) REVERT: F 38 MET cc_start: 0.9339 (tmm) cc_final: 0.9071 (tmm) REVERT: F 39 CYS cc_start: 0.9286 (p) cc_final: 0.9063 (p) REVERT: F 86 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8550 (tp40) REVERT: F 110 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8432 (mm-30) REVERT: G 21 ASP cc_start: 0.8517 (p0) cc_final: 0.8072 (p0) REVERT: G 29 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8719 (tm-30) REVERT: G 44 ARG cc_start: 0.8628 (ptm160) cc_final: 0.7461 (ttm170) REVERT: G 70 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8406 (mm-30) REVERT: G 79 LYS cc_start: 0.9489 (mppt) cc_final: 0.9157 (mppt) REVERT: G 86 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8676 (mm-40) REVERT: G 92 ASP cc_start: 0.8927 (p0) cc_final: 0.8570 (p0) REVERT: G 112 LYS cc_start: 0.9337 (mttp) cc_final: 0.9042 (mttp) REVERT: H 44 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8505 (ttt90) REVERT: H 92 ASP cc_start: 0.8322 (p0) cc_final: 0.7439 (p0) REVERT: H 105 ASP cc_start: 0.9169 (m-30) cc_final: 0.8927 (m-30) REVERT: H 116 ARG cc_start: 0.9020 (tpp80) cc_final: 0.8708 (tpp80) REVERT: I 35 PHE cc_start: 0.9623 (t80) cc_final: 0.9176 (t80) REVERT: I 38 MET cc_start: 0.9279 (tmm) cc_final: 0.9074 (tmm) REVERT: I 39 CYS cc_start: 0.9388 (p) cc_final: 0.8913 (p) REVERT: I 70 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8572 (mt-10) REVERT: I 95 MET cc_start: 0.8982 (mmm) cc_final: 0.8768 (mmm) REVERT: I 116 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8200 (mmm160) REVERT: I 124 ASP cc_start: 0.8840 (t70) cc_final: 0.8578 (t70) REVERT: J 13 GLU cc_start: 0.8816 (tp30) cc_final: 0.8462 (tp30) REVERT: J 21 ASP cc_start: 0.8632 (p0) cc_final: 0.8232 (p0) REVERT: J 27 GLU cc_start: 0.7336 (mp0) cc_final: 0.7058 (mp0) REVERT: J 30 GLU cc_start: 0.8560 (pm20) cc_final: 0.8158 (pm20) REVERT: J 34 GLU cc_start: 0.9066 (tt0) cc_final: 0.8569 (tt0) REVERT: J 60 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8755 (mt-10) REVERT: J 70 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8507 (mm-30) REVERT: J 79 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8922 (mtmm) REVERT: J 83 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8017 (pp20) REVERT: J 92 ASP cc_start: 0.8987 (p0) cc_final: 0.8496 (p0) REVERT: J 116 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8868 (tpp80) REVERT: K 46 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8924 (mp10) REVERT: K 69 LYS cc_start: 0.9758 (tttp) cc_final: 0.9437 (ttmm) REVERT: K 86 GLN cc_start: 0.9118 (tp40) cc_final: 0.8651 (tp-100) REVERT: K 102 ASP cc_start: 0.9288 (p0) cc_final: 0.9017 (p0) REVERT: K 104 LYS cc_start: 0.9499 (mmtp) cc_final: 0.9276 (mmtt) REVERT: K 105 ASP cc_start: 0.9357 (m-30) cc_final: 0.9061 (m-30) REVERT: L 39 CYS cc_start: 0.9216 (p) cc_final: 0.8814 (p) REVERT: L 46 GLN cc_start: 0.9021 (mt0) cc_final: 0.8693 (mt0) REVERT: L 76 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9062 (mmmm) REVERT: L 83 GLU cc_start: 0.8274 (mp0) cc_final: 0.7841 (mp0) REVERT: L 86 GLN cc_start: 0.9357 (mm-40) cc_final: 0.8946 (tp40) REVERT: L 110 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8865 (tp30) REVERT: L 124 ASP cc_start: 0.8778 (t70) cc_final: 0.8386 (t0) REVERT: M 17 ASN cc_start: 0.9552 (m-40) cc_final: 0.9271 (m-40) REVERT: M 44 ARG cc_start: 0.9034 (mmm-85) cc_final: 0.8702 (tpp80) REVERT: M 73 ARG cc_start: 0.9371 (tmm-80) cc_final: 0.8872 (ttp80) REVERT: M 75 ASP cc_start: 0.8927 (p0) cc_final: 0.8702 (p0) REVERT: M 83 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7564 (pp20) REVERT: M 86 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8511 (mm110) REVERT: M 106 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8696 (mt-10) REVERT: M 112 LYS cc_start: 0.9565 (ttmm) cc_final: 0.9090 (mttp) REVERT: M 116 ARG cc_start: 0.8863 (tpp80) cc_final: 0.8514 (tpp80) REVERT: M 131 ASP cc_start: 0.9029 (t0) cc_final: 0.8689 (t0) REVERT: M 132 ASP cc_start: 0.8764 (m-30) cc_final: 0.8146 (m-30) REVERT: N 39 CYS cc_start: 0.9658 (m) cc_final: 0.9298 (m) REVERT: N 86 GLN cc_start: 0.8746 (mp10) cc_final: 0.8058 (mp10) REVERT: N 89 LYS cc_start: 0.8716 (ptmm) cc_final: 0.7922 (ptmm) REVERT: N 92 ASP cc_start: 0.7732 (p0) cc_final: 0.7065 (p0) REVERT: N 98 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8649 (p0) REVERT: N 105 ASP cc_start: 0.9272 (m-30) cc_final: 0.8972 (m-30) REVERT: O 13 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8918 (mt-10) REVERT: O 21 ASP cc_start: 0.7698 (p0) cc_final: 0.7342 (p0) REVERT: O 38 MET cc_start: 0.8976 (tmm) cc_final: 0.8610 (tmm) REVERT: O 39 CYS cc_start: 0.9201 (p) cc_final: 0.8827 (p) REVERT: O 70 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8630 (mt-10) REVERT: O 76 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9071 (mmtm) REVERT: O 92 ASP cc_start: 0.7197 (t70) cc_final: 0.6716 (t0) REVERT: O 99 TYR cc_start: 0.8525 (t80) cc_final: 0.8224 (t80) REVERT: O 102 ASP cc_start: 0.9074 (m-30) cc_final: 0.8750 (m-30) REVERT: O 105 ASP cc_start: 0.9435 (m-30) cc_final: 0.9191 (m-30) REVERT: a 62 ASP cc_start: 0.8116 (t0) cc_final: 0.7839 (t0) REVERT: a 75 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8057 (mmmt) REVERT: a 103 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6550 (pm20) REVERT: a 108 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9104 (mm) REVERT: a 112 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8895 (mm-30) REVERT: a 113 ASP cc_start: 0.9163 (t70) cc_final: 0.8787 (t0) REVERT: a 117 ASP cc_start: 0.9463 (m-30) cc_final: 0.9203 (m-30) REVERT: b 1 MET cc_start: 0.8696 (tpt) cc_final: 0.8228 (tpt) REVERT: b 55 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8715 (t) REVERT: b 91 VAL cc_start: 0.9679 (t) cc_final: 0.9440 (p) REVERT: b 117 ASP cc_start: 0.9071 (m-30) cc_final: 0.8667 (t0) REVERT: c 5 LYS cc_start: 0.8958 (ptpp) cc_final: 0.8467 (ptpp) REVERT: c 7 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.8285 (m) REVERT: c 94 GLU cc_start: 0.8469 (tt0) cc_final: 0.8263 (tt0) REVERT: c 103 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8779 (mm-30) REVERT: c 114 TYR cc_start: 0.9226 (t80) cc_final: 0.8952 (t80) REVERT: d 29 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8657 (p) REVERT: d 50 GLU cc_start: 0.7760 (tp30) cc_final: 0.7466 (tp30) REVERT: d 58 ASN cc_start: 0.7237 (t0) cc_final: 0.7026 (t0) REVERT: e 14 GLN cc_start: 0.8956 (mp10) cc_final: 0.8582 (mp10) REVERT: e 30 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.6969 (p90) REVERT: e 77 SER cc_start: 0.9371 (m) cc_final: 0.8936 (t) REVERT: f 3 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8053 (ttp80) REVERT: f 5 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8335 (ptpp) REVERT: f 27 ASN cc_start: 0.8850 (m-40) cc_final: 0.8492 (m-40) REVERT: f 50 GLU cc_start: 0.8152 (tp30) cc_final: 0.7845 (tp30) REVERT: f 59 VAL cc_start: 0.8125 (m) cc_final: 0.7706 (p) REVERT: f 82 ASP cc_start: 0.8628 (t0) cc_final: 0.8358 (m-30) REVERT: f 86 ASP cc_start: 0.8387 (p0) cc_final: 0.8085 (p0) REVERT: f 109 ASN cc_start: 0.8911 (m-40) cc_final: 0.8605 (m110) REVERT: g 1 MET cc_start: 0.8778 (tpp) cc_final: 0.8386 (tmm) REVERT: g 48 ASN cc_start: 0.9413 (t0) cc_final: 0.8913 (t0) REVERT: g 50 GLU cc_start: 0.8228 (mp0) cc_final: 0.7644 (mp0) REVERT: h 1 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.5813 (tmm) REVERT: i 74 LYS cc_start: 0.8169 (tmtt) cc_final: 0.7883 (tptp) REVERT: i 113 ASP cc_start: 0.8874 (m-30) cc_final: 0.8494 (m-30) REVERT: j 48 ASN cc_start: 0.8949 (t0) cc_final: 0.8468 (t0) REVERT: j 50 GLU cc_start: 0.8363 (pm20) cc_final: 0.7959 (pm20) REVERT: j 101 ASP cc_start: 0.8511 (p0) cc_final: 0.8219 (p0) REVERT: j 112 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8807 (tm-30) REVERT: k 17 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9453 (mm) REVERT: m 12 ASP cc_start: 0.7631 (p0) cc_final: 0.7029 (p0) REVERT: m 29 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7986 (p) REVERT: m 48 ASN cc_start: 0.9268 (t0) cc_final: 0.8750 (t0) REVERT: m 50 GLU cc_start: 0.8527 (pm20) cc_final: 0.7780 (pm20) REVERT: m 54 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7032 (p0) REVERT: n 107 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8018 (m) REVERT: n 111 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9196 (pp) REVERT: o 54 ASN cc_start: 0.8247 (p0) cc_final: 0.7872 (p0) REVERT: o 65 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5510 (t80) REVERT: o 77 SER cc_start: 0.9452 (p) cc_final: 0.8824 (p) outliers start: 227 outliers final: 168 residues processed: 1244 average time/residue: 0.4417 time to fit residues: 850.7156 Evaluate side-chains 1214 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1025 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 69 LYS 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 59 ILE 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 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 D residue 94 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 130 TYR Chi-restraints excluded: chain 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 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 132 ASP 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 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 81 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 118 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 75 ASP Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 94 THR 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 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 L residue 134 GLU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain 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 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN 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 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 85 SER Chi-restraints excluded: chain a residue 94 GLU Chi-restraints excluded: chain a residue 98 ILE Chi-restraints excluded: chain a residue 103 GLU 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 7 THR 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 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 67 ILE 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 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 73 ASN Chi-restraints excluded: chain f residue 104 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 106 ASN Chi-restraints excluded: chain h residue 107 VAL Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 80 VAL Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 23 LEU Chi-restraints excluded: chain k residue 27 ASN Chi-restraints excluded: chain k residue 30 PHE Chi-restraints excluded: chain k residue 38 ILE 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 42 HIS Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain 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 21 LEU Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 93 ARG Chi-restraints excluded: chain o residue 104 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 63 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 247 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051850 restraints weight = 150609.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.053388 restraints weight = 91901.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.054494 restraints weight = 64463.132| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 31470 Z= 0.177 Angle : 0.844 12.892 42780 Z= 0.438 Chirality : 0.048 0.207 4995 Planarity : 0.005 0.067 5565 Dihedral : 7.195 61.441 4214 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.72 % Favored : 91.17 % Rotamer: Outliers : 5.96 % Allowed : 27.72 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.42 (0.13), residues: 1602 sheet: -0.43 (0.21), residues: 608 loop : -2.26 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 16 HIS 0.009 0.001 HIS b 42 PHE 0.021 0.002 PHE D 35 TYR 0.041 0.002 TYR h 114 ARG 0.009 0.001 ARG B 44 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 1420) hydrogen bonds : angle 5.19156 ( 4086) covalent geometry : bond 0.00399 (31470) covalent geometry : angle 0.84440 (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 1327 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1117 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8937 (tp30) cc_final: 0.8502 (tp30) REVERT: A 29 GLU cc_start: 0.9048 (tp30) cc_final: 0.8216 (tp30) REVERT: A 30 GLU cc_start: 0.8689 (pm20) cc_final: 0.8035 (pm20) REVERT: A 38 MET cc_start: 0.9314 (tmm) cc_final: 0.8713 (tmm) REVERT: A 46 GLN cc_start: 0.8921 (pt0) cc_final: 0.8678 (pt0) REVERT: A 70 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8542 (mm-30) REVERT: A 92 ASP cc_start: 0.8858 (p0) cc_final: 0.8459 (p0) REVERT: A 112 LYS cc_start: 0.9395 (mtmm) cc_final: 0.9116 (mtmm) REVERT: A 132 ASP cc_start: 0.8735 (m-30) cc_final: 0.8440 (m-30) REVERT: B 51 ASN cc_start: 0.9512 (m110) cc_final: 0.9292 (p0) REVERT: B 86 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8724 (tp-100) REVERT: B 105 ASP cc_start: 0.9270 (m-30) cc_final: 0.9058 (m-30) REVERT: B 124 ASP cc_start: 0.8930 (t0) cc_final: 0.8730 (t0) REVERT: B 131 ASP cc_start: 0.9406 (t0) cc_final: 0.8852 (t0) REVERT: C 13 GLU cc_start: 0.8989 (tp30) cc_final: 0.7890 (tp30) REVERT: C 17 ASN cc_start: 0.9412 (m-40) cc_final: 0.8341 (m-40) REVERT: C 19 PHE cc_start: 0.8815 (m-80) cc_final: 0.8559 (m-80) REVERT: C 38 MET cc_start: 0.9177 (tmm) cc_final: 0.8779 (tmm) REVERT: C 70 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8569 (mm-30) REVERT: C 83 GLU cc_start: 0.8058 (mp0) cc_final: 0.7752 (mp0) REVERT: C 86 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8411 (tp40) REVERT: C 102 ASP cc_start: 0.9157 (m-30) cc_final: 0.8857 (m-30) REVERT: C 105 ASP cc_start: 0.9440 (m-30) cc_final: 0.9222 (m-30) REVERT: C 116 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8378 (mmm160) REVERT: D 21 ASP cc_start: 0.7708 (p0) cc_final: 0.7334 (p0) REVERT: D 44 ARG cc_start: 0.8764 (ptm160) cc_final: 0.8236 (ptm160) REVERT: D 60 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8919 (mm-30) REVERT: D 69 LYS cc_start: 0.9657 (OUTLIER) cc_final: 0.9422 (ttpp) REVERT: D 106 GLU cc_start: 0.8993 (tp30) cc_final: 0.8694 (tp30) REVERT: D 112 LYS cc_start: 0.9440 (mtmm) cc_final: 0.9081 (mtmm) REVERT: D 113 LYS cc_start: 0.9436 (mtpt) cc_final: 0.9200 (mtmt) REVERT: D 132 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7386 (t0) REVERT: E 17 ASN cc_start: 0.9505 (m-40) cc_final: 0.9190 (m110) REVERT: E 46 GLN cc_start: 0.9326 (tp-100) cc_final: 0.8746 (tp-100) REVERT: E 59 ILE cc_start: 0.9733 (mm) cc_final: 0.9432 (pt) REVERT: E 92 ASP cc_start: 0.7737 (p0) cc_final: 0.7158 (p0) REVERT: E 132 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: F 38 MET cc_start: 0.9404 (tmm) cc_final: 0.9124 (tmm) REVERT: F 39 CYS cc_start: 0.9487 (p) cc_final: 0.9083 (p) REVERT: F 70 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8490 (tt0) REVERT: F 86 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8565 (tp40) REVERT: F 110 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8503 (mm-30) REVERT: G 21 ASP cc_start: 0.8534 (p0) cc_final: 0.8080 (p0) REVERT: G 29 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8475 (tm-30) REVERT: G 34 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8773 (mp0) REVERT: G 44 ARG cc_start: 0.8527 (ptm160) cc_final: 0.7079 (ttm170) REVERT: G 70 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8365 (mm-30) REVERT: G 79 LYS cc_start: 0.9506 (mppt) cc_final: 0.9146 (mppt) REVERT: G 92 ASP cc_start: 0.8931 (p0) cc_final: 0.8455 (p0) REVERT: H 21 ASP cc_start: 0.8082 (p0) cc_final: 0.7441 (p0) REVERT: H 44 ARG cc_start: 0.9052 (ptm-80) cc_final: 0.8494 (ttt90) REVERT: H 105 ASP cc_start: 0.9211 (m-30) cc_final: 0.8943 (m-30) REVERT: H 116 ARG cc_start: 0.9013 (tpp80) cc_final: 0.8661 (tpp80) REVERT: I 35 PHE cc_start: 0.9590 (t80) cc_final: 0.9178 (t80) REVERT: I 38 MET cc_start: 0.9271 (tmm) cc_final: 0.9045 (tmm) REVERT: I 39 CYS cc_start: 0.9385 (p) cc_final: 0.8897 (p) REVERT: I 70 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8420 (mt-10) REVERT: I 89 LYS cc_start: 0.9511 (ttpp) cc_final: 0.8689 (ttpp) REVERT: I 99 TYR cc_start: 0.8588 (t80) cc_final: 0.8179 (t80) REVERT: I 116 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8211 (mmm160) REVERT: J 13 GLU cc_start: 0.8792 (tp30) cc_final: 0.8402 (tp30) REVERT: J 21 ASP cc_start: 0.8550 (p0) cc_final: 0.8141 (p0) REVERT: J 27 GLU cc_start: 0.7344 (mp0) cc_final: 0.7035 (mp0) REVERT: J 34 GLU cc_start: 0.9080 (tt0) cc_final: 0.8597 (tt0) REVERT: J 60 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8789 (mt-10) REVERT: J 70 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8449 (mm-30) REVERT: J 79 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8914 (mtmm) REVERT: J 83 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7993 (pp20) REVERT: J 92 ASP cc_start: 0.8996 (OUTLIER) cc_final: 0.8459 (p0) REVERT: J 116 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8777 (tpp80) REVERT: K 46 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8863 (mp10) REVERT: K 69 LYS cc_start: 0.9737 (tttp) cc_final: 0.9408 (ttmm) REVERT: K 75 ASP cc_start: 0.9061 (t0) cc_final: 0.8845 (t0) REVERT: K 86 GLN cc_start: 0.9108 (tp40) cc_final: 0.8677 (tp-100) REVERT: K 102 ASP cc_start: 0.9277 (p0) cc_final: 0.8979 (p0) REVERT: K 105 ASP cc_start: 0.9336 (m-30) cc_final: 0.9044 (m-30) REVERT: K 116 ARG cc_start: 0.9272 (mmp80) cc_final: 0.8782 (tpp80) REVERT: L 39 CYS cc_start: 0.9259 (p) cc_final: 0.8898 (p) REVERT: L 46 GLN cc_start: 0.8950 (mt0) cc_final: 0.8596 (mt0) REVERT: L 60 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8777 (mt-10) REVERT: L 76 LYS cc_start: 0.9424 (mmmm) cc_final: 0.9061 (mmmm) REVERT: L 83 GLU cc_start: 0.8226 (mp0) cc_final: 0.7792 (mp0) REVERT: L 86 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8881 (tp40) REVERT: M 17 ASN cc_start: 0.9564 (m-40) cc_final: 0.9311 (m-40) REVERT: M 44 ARG cc_start: 0.9042 (mmm-85) cc_final: 0.8737 (tpp80) REVERT: M 73 ARG cc_start: 0.9350 (tmm-80) cc_final: 0.8826 (ttp80) REVERT: M 75 ASP cc_start: 0.8925 (p0) cc_final: 0.8559 (p0) REVERT: M 83 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7497 (pp20) REVERT: M 86 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8524 (mm110) REVERT: M 106 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8647 (mp0) REVERT: M 112 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9084 (mttp) REVERT: M 116 ARG cc_start: 0.8859 (tpp80) cc_final: 0.8649 (tpp80) REVERT: M 131 ASP cc_start: 0.9030 (t0) cc_final: 0.8693 (t0) REVERT: M 132 ASP cc_start: 0.8759 (m-30) cc_final: 0.8122 (m-30) REVERT: N 28 LEU cc_start: 0.9472 (mm) cc_final: 0.9202 (mm) REVERT: N 39 CYS cc_start: 0.9643 (m) cc_final: 0.9188 (m) REVERT: N 44 ARG cc_start: 0.8544 (tpt170) cc_final: 0.8314 (tpp80) REVERT: N 86 GLN cc_start: 0.8736 (mp10) cc_final: 0.8015 (mp10) REVERT: N 89 LYS cc_start: 0.8761 (ptmm) cc_final: 0.7950 (ptmm) REVERT: N 92 ASP cc_start: 0.7671 (p0) cc_final: 0.6965 (p0) REVERT: N 98 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8653 (p0) REVERT: N 105 ASP cc_start: 0.9263 (m-30) cc_final: 0.8964 (m-30) REVERT: O 21 ASP cc_start: 0.7637 (p0) cc_final: 0.7294 (p0) REVERT: O 38 MET cc_start: 0.8937 (tmm) cc_final: 0.8590 (tmm) REVERT: O 39 CYS cc_start: 0.9190 (p) cc_final: 0.8743 (p) REVERT: O 99 TYR cc_start: 0.8493 (t80) cc_final: 0.8232 (t80) REVERT: O 102 ASP cc_start: 0.9056 (m-30) cc_final: 0.8711 (m-30) REVERT: O 105 ASP cc_start: 0.9421 (m-30) cc_final: 0.9187 (m-30) REVERT: a 62 ASP cc_start: 0.8066 (t0) cc_final: 0.7766 (t0) REVERT: a 75 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7899 (mmmt) REVERT: a 103 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: a 108 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9265 (mm) REVERT: a 112 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9165 (mm-30) REVERT: a 113 ASP cc_start: 0.9180 (t70) cc_final: 0.8829 (t0) REVERT: a 117 ASP cc_start: 0.9484 (m-30) cc_final: 0.9225 (m-30) REVERT: b 1 MET cc_start: 0.8640 (tpt) cc_final: 0.8173 (tpt) REVERT: b 55 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8766 (t) REVERT: b 91 VAL cc_start: 0.9677 (t) cc_final: 0.9441 (p) REVERT: b 117 ASP cc_start: 0.9021 (m-30) cc_final: 0.8592 (t0) REVERT: c 74 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7559 (tptp) REVERT: c 89 PHE cc_start: 0.9198 (t80) cc_final: 0.8825 (t80) REVERT: c 94 GLU cc_start: 0.8568 (tt0) cc_final: 0.8314 (tt0) REVERT: c 103 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8713 (mm-30) REVERT: d 14 GLN cc_start: 0.8889 (mp10) cc_final: 0.8620 (pm20) REVERT: d 29 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8703 (p) REVERT: d 50 GLU cc_start: 0.7934 (tp30) cc_final: 0.7733 (tp30) REVERT: d 56 VAL cc_start: 0.9643 (t) cc_final: 0.9436 (t) REVERT: e 14 GLN cc_start: 0.8952 (mp10) cc_final: 0.8583 (mm-40) REVERT: e 30 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.6950 (p90) REVERT: f 3 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8227 (ttp80) REVERT: f 5 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8468 (ptpp) REVERT: f 27 ASN cc_start: 0.8752 (m-40) cc_final: 0.8353 (m-40) REVERT: f 50 GLU cc_start: 0.8158 (tp30) cc_final: 0.7872 (tp30) REVERT: f 59 VAL cc_start: 0.8086 (m) cc_final: 0.7217 (p) REVERT: f 82 ASP cc_start: 0.8599 (t0) cc_final: 0.8297 (m-30) REVERT: f 86 ASP cc_start: 0.8440 (p0) cc_final: 0.8208 (p0) REVERT: f 113 ASP cc_start: 0.9208 (m-30) cc_final: 0.8659 (p0) REVERT: g 1 MET cc_start: 0.8866 (tpp) cc_final: 0.8296 (tmm) REVERT: g 50 GLU cc_start: 0.8284 (mp0) cc_final: 0.7985 (pm20) REVERT: h 1 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6284 (tmm) REVERT: i 46 ASP cc_start: 0.8798 (p0) cc_final: 0.8251 (p0) REVERT: i 48 ASN cc_start: 0.9523 (m-40) cc_final: 0.8860 (p0) REVERT: j 44 LYS cc_start: 0.9524 (tppp) cc_final: 0.9153 (tppt) REVERT: j 48 ASN cc_start: 0.9005 (t0) cc_final: 0.8448 (t0) REVERT: j 50 GLU cc_start: 0.8386 (pm20) cc_final: 0.7953 (pm20) REVERT: j 101 ASP cc_start: 0.8542 (p0) cc_final: 0.8239 (p0) REVERT: j 112 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8847 (tm-30) REVERT: k 17 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9479 (mm) REVERT: l 93 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8279 (tpt170) REVERT: m 12 ASP cc_start: 0.7415 (p0) cc_final: 0.6841 (p0) REVERT: m 29 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (p) REVERT: m 48 ASN cc_start: 0.9308 (t0) cc_final: 0.8760 (t0) REVERT: m 50 GLU cc_start: 0.8626 (pm20) cc_final: 0.7897 (pm20) REVERT: m 54 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.6881 (p0) REVERT: n 13 ASP cc_start: 0.8602 (m-30) cc_final: 0.8252 (m-30) REVERT: n 107 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7990 (m) REVERT: n 111 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9191 (pp) REVERT: o 14 GLN cc_start: 0.9467 (mp10) cc_final: 0.9159 (mp10) REVERT: o 50 GLU cc_start: 0.7933 (tp30) cc_final: 0.7237 (tp30) REVERT: o 54 ASN cc_start: 0.8579 (p0) cc_final: 0.7943 (p0) REVERT: o 65 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5530 (t80) REVERT: o 77 SER cc_start: 0.9439 (p) cc_final: 0.8899 (p) REVERT: o 103 GLU cc_start: 0.8012 (tp30) cc_final: 0.7635 (tm-30) outliers start: 210 outliers final: 155 residues processed: 1229 average time/residue: 0.4349 time to fit residues: 823.9092 Evaluate side-chains 1242 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 1064 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 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 20 LEU 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 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 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 34 GLU 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 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 129 SER 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 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 46 GLN 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 L residue 134 GLU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain N residue 130 TYR Chi-restraints excluded: chain O residue 44 ARG 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 10 HIS Chi-restraints excluded: chain a residue 23 LEU 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 103 GLU 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 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 70 THR Chi-restraints excluded: chain d residue 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 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 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 107 VAL Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 52 VAL Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 80 VAL Chi-restraints excluded: chain i residue 92 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 17 ILE Chi-restraints excluded: chain k residue 23 LEU 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 86 ASP Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 42 HIS Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 70 THR Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 38 ILE Chi-restraints excluded: chain n residue 42 HIS Chi-restraints excluded: chain n residue 107 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 113 ASP Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 59 VAL 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 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 30 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 277 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 ASN f 109 ASN g 48 ASN ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 58 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053133 restraints weight = 148001.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.054742 restraints weight = 90574.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055837 restraints weight = 63281.457| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31470 Z= 0.161 Angle : 0.876 14.858 42780 Z= 0.451 Chirality : 0.048 0.311 4995 Planarity : 0.005 0.077 5565 Dihedral : 7.030 63.847 4210 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.86 % Rotamer: Outliers : 4.88 % Allowed : 29.45 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.11 (0.13), residues: 3795 helix: 0.38 (0.13), residues: 1581 sheet: -0.20 (0.21), residues: 608 loop : -2.13 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 16 HIS 0.007 0.001 HIS b 42 PHE 0.020 0.002 PHE L 19 TYR 0.040 0.002 TYR h 114 ARG 0.014 0.001 ARG c 93 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 1420) hydrogen bonds : angle 5.09307 ( 4086) covalent geometry : bond 0.00355 (31470) covalent geometry : angle 0.87605 (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 1360 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1188 time to evaluate : 3.611 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: A 13 GLU cc_start: 0.8901 (tp30) cc_final: 0.8434 (tp30) REVERT: A 38 MET cc_start: 0.9280 (tmm) cc_final: 0.8714 (tmm) REVERT: A 92 ASP cc_start: 0.8816 (p0) cc_final: 0.8448 (p0) REVERT: A 124 ASP cc_start: 0.9253 (t0) cc_final: 0.9033 (t0) REVERT: A 132 ASP cc_start: 0.8670 (m-30) cc_final: 0.8050 (t70) REVERT: B 51 ASN cc_start: 0.9516 (m110) cc_final: 0.9279 (p0) REVERT: B 76 LYS cc_start: 0.9402 (tppt) cc_final: 0.9050 (mmmm) REVERT: B 86 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8616 (tp-100) REVERT: B 116 ARG cc_start: 0.9179 (tpp80) cc_final: 0.8958 (tpp80) REVERT: B 131 ASP cc_start: 0.9311 (t0) cc_final: 0.8885 (t0) REVERT: C 13 GLU cc_start: 0.8935 (tp30) cc_final: 0.7756 (tp30) REVERT: C 17 ASN cc_start: 0.9473 (m-40) cc_final: 0.8306 (m-40) REVERT: C 19 PHE cc_start: 0.8770 (m-80) cc_final: 0.8551 (m-80) REVERT: C 38 MET cc_start: 0.9117 (tmm) cc_final: 0.8755 (tmm) REVERT: C 60 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8694 (mt-10) REVERT: C 70 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8616 (mm-30) REVERT: C 86 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8233 (tp40) REVERT: C 102 ASP cc_start: 0.9131 (m-30) cc_final: 0.8887 (m-30) REVERT: C 105 ASP cc_start: 0.9425 (m-30) cc_final: 0.9214 (m-30) REVERT: C 116 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8363 (mmm160) REVERT: C 124 ASP cc_start: 0.7985 (t0) cc_final: 0.7708 (t0) REVERT: D 21 ASP cc_start: 0.7788 (p0) cc_final: 0.7284 (p0) REVERT: D 34 GLU cc_start: 0.8864 (tt0) cc_final: 0.8417 (mt-10) REVERT: D 44 ARG cc_start: 0.8777 (ptm160) cc_final: 0.8309 (ptm160) REVERT: D 60 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8950 (mm-30) REVERT: D 69 LYS cc_start: 0.9651 (ttmm) cc_final: 0.9403 (ttpp) REVERT: D 89 LYS cc_start: 0.9267 (ptmm) cc_final: 0.8899 (ptmm) REVERT: D 106 GLU cc_start: 0.8977 (tp30) cc_final: 0.8535 (tp30) REVERT: D 116 ARG cc_start: 0.8747 (tpp80) cc_final: 0.8490 (tpp80) REVERT: D 132 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7242 (t0) REVERT: E 17 ASN cc_start: 0.9496 (m-40) cc_final: 0.9274 (m-40) REVERT: E 46 GLN cc_start: 0.9395 (tp-100) cc_final: 0.8901 (tp-100) REVERT: E 53 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9251 (mm) REVERT: E 59 ILE cc_start: 0.9756 (mm) cc_final: 0.9479 (pt) REVERT: E 92 ASP cc_start: 0.7644 (p0) cc_final: 0.7165 (t70) REVERT: E 132 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: F 34 GLU cc_start: 0.9309 (tt0) cc_final: 0.8987 (tt0) REVERT: F 35 PHE cc_start: 0.9619 (t80) cc_final: 0.8897 (t80) REVERT: F 38 MET cc_start: 0.9423 (tmm) cc_final: 0.9116 (tmm) REVERT: F 39 CYS cc_start: 0.9547 (p) cc_final: 0.8948 (p) REVERT: F 86 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8459 (tp40) REVERT: F 104 LYS cc_start: 0.9376 (mmmt) cc_final: 0.9162 (mmtt) REVERT: F 110 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8476 (mm-30) REVERT: G 21 ASP cc_start: 0.8518 (p0) cc_final: 0.8236 (p0) REVERT: G 29 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8489 (tm-30) REVERT: G 44 ARG cc_start: 0.8464 (ptm160) cc_final: 0.7397 (ttm170) REVERT: G 70 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8016 (tp30) REVERT: G 79 LYS cc_start: 0.9484 (mppt) cc_final: 0.9137 (mtmm) REVERT: G 92 ASP cc_start: 0.8884 (p0) cc_final: 0.8506 (p0) REVERT: H 38 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8664 (mtt) REVERT: H 44 ARG cc_start: 0.8987 (ptm-80) cc_final: 0.8435 (ttt180) REVERT: H 82 ILE cc_start: 0.9331 (tp) cc_final: 0.9020 (mt) REVERT: H 102 ASP cc_start: 0.9255 (p0) cc_final: 0.9054 (p0) REVERT: H 105 ASP cc_start: 0.9186 (m-30) cc_final: 0.8893 (m-30) REVERT: I 13 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8856 (pt0) REVERT: I 35 PHE cc_start: 0.9553 (t80) cc_final: 0.9038 (t80) REVERT: I 38 MET cc_start: 0.9270 (tmm) cc_final: 0.8968 (tmm) REVERT: I 39 CYS cc_start: 0.9375 (p) cc_final: 0.8652 (p) REVERT: I 49 PHE cc_start: 0.9483 (t80) cc_final: 0.9236 (t80) REVERT: I 53 LEU cc_start: 0.9521 (tm) cc_final: 0.9314 (pp) REVERT: I 70 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8467 (mt-10) REVERT: I 89 LYS cc_start: 0.9485 (ttpp) cc_final: 0.8688 (ttpp) REVERT: I 95 MET cc_start: 0.8927 (mmm) cc_final: 0.8661 (mmm) REVERT: I 99 TYR cc_start: 0.8573 (t80) cc_final: 0.8258 (t80) REVERT: I 124 ASP cc_start: 0.8724 (t70) cc_final: 0.8426 (t70) REVERT: J 21 ASP cc_start: 0.8527 (p0) cc_final: 0.7981 (p0) REVERT: J 34 GLU cc_start: 0.9087 (tt0) cc_final: 0.8541 (tt0) REVERT: J 60 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8802 (mt-10) REVERT: J 70 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8278 (tp30) REVERT: J 79 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8880 (mtmm) REVERT: J 83 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7923 (pp20) REVERT: J 90 VAL cc_start: 0.9343 (p) cc_final: 0.8399 (p) REVERT: J 92 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8379 (p0) REVERT: K 46 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8793 (mp10) REVERT: K 86 GLN cc_start: 0.9052 (tp40) cc_final: 0.8665 (tp-100) REVERT: K 102 ASP cc_start: 0.9242 (p0) cc_final: 0.8841 (p0) REVERT: K 105 ASP cc_start: 0.9369 (m-30) cc_final: 0.9030 (m-30) REVERT: K 116 ARG cc_start: 0.9218 (mmp80) cc_final: 0.8758 (tpp80) REVERT: L 35 PHE cc_start: 0.9605 (t80) cc_final: 0.9144 (t80) REVERT: L 39 CYS cc_start: 0.9231 (p) cc_final: 0.8828 (p) REVERT: L 75 ASP cc_start: 0.9009 (t0) cc_final: 0.8748 (t0) REVERT: L 76 LYS cc_start: 0.9413 (mmmm) cc_final: 0.9047 (mmmm) REVERT: L 79 LYS cc_start: 0.9367 (mmmm) cc_final: 0.8717 (mmtm) REVERT: L 83 GLU cc_start: 0.8165 (mp0) cc_final: 0.7628 (mp0) REVERT: L 86 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8919 (tp40) REVERT: M 17 ASN cc_start: 0.9542 (m-40) cc_final: 0.9281 (m110) REVERT: M 44 ARG cc_start: 0.8955 (mmm-85) cc_final: 0.8703 (tpp80) REVERT: M 73 ARG cc_start: 0.9352 (tmm-80) cc_final: 0.8365 (ttp80) REVERT: M 75 ASP cc_start: 0.8827 (p0) cc_final: 0.8452 (p0) REVERT: M 83 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7443 (pp20) REVERT: M 86 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8524 (mm110) REVERT: M 106 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8640 (mt-10) REVERT: M 112 LYS cc_start: 0.9536 (ttmm) cc_final: 0.9029 (mttp) REVERT: M 131 ASP cc_start: 0.9084 (t0) cc_final: 0.8757 (t0) REVERT: M 132 ASP cc_start: 0.8805 (m-30) cc_final: 0.8259 (m-30) REVERT: N 28 LEU cc_start: 0.9475 (mm) cc_final: 0.9189 (mm) REVERT: N 35 PHE cc_start: 0.9525 (t80) cc_final: 0.8972 (t80) REVERT: N 39 CYS cc_start: 0.9560 (m) cc_final: 0.9121 (m) REVERT: N 44 ARG cc_start: 0.8533 (tpt170) cc_final: 0.8317 (tpp80) REVERT: N 75 ASP cc_start: 0.8933 (t0) cc_final: 0.8731 (t0) REVERT: N 86 GLN cc_start: 0.8733 (mp10) cc_final: 0.7999 (mp10) REVERT: N 89 LYS cc_start: 0.8963 (ptmm) cc_final: 0.8402 (ptmm) REVERT: N 92 ASP cc_start: 0.7613 (p0) cc_final: 0.6986 (p0) REVERT: N 98 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8612 (p0) REVERT: N 105 ASP cc_start: 0.9280 (m-30) cc_final: 0.8979 (m-30) REVERT: O 13 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8964 (mt-10) REVERT: O 21 ASP cc_start: 0.7611 (p0) cc_final: 0.7283 (p0) REVERT: O 38 MET cc_start: 0.8852 (tmm) cc_final: 0.8492 (tmm) REVERT: O 39 CYS cc_start: 0.9180 (p) cc_final: 0.8728 (p) REVERT: O 44 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8666 (tpt-90) REVERT: O 92 ASP cc_start: 0.8284 (t0) cc_final: 0.7806 (t0) REVERT: O 94 THR cc_start: 0.9269 (m) cc_final: 0.9039 (p) REVERT: O 99 TYR cc_start: 0.8373 (t80) cc_final: 0.8131 (t80) REVERT: O 102 ASP cc_start: 0.9002 (m-30) cc_final: 0.8598 (m-30) REVERT: O 105 ASP cc_start: 0.9377 (m-30) cc_final: 0.9077 (m-30) REVERT: a 62 ASP cc_start: 0.8030 (t0) cc_final: 0.7803 (t0) REVERT: a 103 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6462 (pm20) REVERT: a 108 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9099 (mm) REVERT: a 112 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8877 (mm-30) REVERT: a 113 ASP cc_start: 0.9173 (t70) cc_final: 0.8829 (t0) REVERT: a 117 ASP cc_start: 0.9484 (m-30) cc_final: 0.9227 (m-30) REVERT: b 1 MET cc_start: 0.8576 (tpt) cc_final: 0.7940 (tpt) REVERT: b 13 ASP cc_start: 0.8307 (m-30) cc_final: 0.7337 (t0) REVERT: b 55 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8705 (t) REVERT: b 91 VAL cc_start: 0.9647 (t) cc_final: 0.9407 (p) REVERT: b 117 ASP cc_start: 0.9037 (m-30) cc_final: 0.8657 (t0) REVERT: c 94 GLU cc_start: 0.8336 (tt0) cc_final: 0.8084 (tt0) REVERT: c 103 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8438 (mm-30) REVERT: d 14 GLN cc_start: 0.8708 (mp10) cc_final: 0.8439 (pm20) REVERT: d 29 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8577 (p) REVERT: e 14 GLN cc_start: 0.9011 (mp10) cc_final: 0.8629 (mm-40) REVERT: e 30 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.6845 (p90) REVERT: f 3 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.7997 (ttp-110) REVERT: f 5 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8017 (mtmm) REVERT: f 27 ASN cc_start: 0.8803 (m-40) cc_final: 0.8408 (m-40) REVERT: f 50 GLU cc_start: 0.8103 (tp30) cc_final: 0.7792 (tp30) REVERT: f 59 VAL cc_start: 0.7993 (m) cc_final: 0.7445 (p) REVERT: f 82 ASP cc_start: 0.8523 (t0) cc_final: 0.8306 (m-30) REVERT: f 86 ASP cc_start: 0.8481 (p0) cc_final: 0.7973 (p0) REVERT: f 88 GLU cc_start: 0.8006 (tp30) cc_final: 0.7756 (tm-30) REVERT: f 109 ASN cc_start: 0.8842 (m110) cc_final: 0.8585 (m110) REVERT: f 113 ASP cc_start: 0.9184 (m-30) cc_final: 0.8659 (p0) REVERT: h 1 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6422 (tmm) REVERT: i 73 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8424 (t0) REVERT: i 74 LYS cc_start: 0.8335 (tmtt) cc_final: 0.8099 (tptp) REVERT: i 114 TYR cc_start: 0.8898 (t80) cc_final: 0.8554 (t80) REVERT: j 44 LYS cc_start: 0.9476 (tppp) cc_final: 0.9160 (tppt) REVERT: j 47 GLN cc_start: 0.9458 (pp30) cc_final: 0.9148 (pp30) REVERT: j 48 ASN cc_start: 0.8936 (t0) cc_final: 0.8365 (t0) REVERT: j 50 GLU cc_start: 0.8352 (pm20) cc_final: 0.7875 (pm20) REVERT: j 101 ASP cc_start: 0.8561 (p0) cc_final: 0.8296 (p0) REVERT: j 112 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8731 (tm-30) REVERT: k 14 GLN cc_start: 0.9026 (mp-120) cc_final: 0.8675 (mm-40) REVERT: l 27 ASN cc_start: 0.8731 (m-40) cc_final: 0.8472 (m-40) REVERT: m 12 ASP cc_start: 0.7594 (p0) cc_final: 0.7126 (p0) REVERT: m 29 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7753 (p) REVERT: m 48 ASN cc_start: 0.9285 (t0) cc_final: 0.8727 (t0) REVERT: m 50 GLU cc_start: 0.8654 (pm20) cc_final: 0.7857 (pm20) REVERT: m 54 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7337 (p0) REVERT: m 66 TYR cc_start: 0.7456 (m-80) cc_final: 0.7170 (m-80) REVERT: n 8 ILE cc_start: 0.9371 (mm) cc_final: 0.9129 (mm) REVERT: n 13 ASP cc_start: 0.8482 (m-30) cc_final: 0.8162 (m-30) REVERT: n 36 TYR cc_start: 0.8993 (m-80) cc_final: 0.8502 (m-10) REVERT: n 111 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9173 (pp) REVERT: o 14 GLN cc_start: 0.9461 (mp10) cc_final: 0.9135 (mp10) REVERT: o 50 GLU cc_start: 0.7883 (tp30) cc_final: 0.7055 (tp30) REVERT: o 54 ASN cc_start: 0.8468 (p0) cc_final: 0.7986 (p0) REVERT: o 65 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.5599 (t80) REVERT: o 77 SER cc_start: 0.9401 (p) cc_final: 0.8879 (p) REVERT: o 103 GLU cc_start: 0.7907 (tp30) cc_final: 0.7593 (tm-30) outliers start: 172 outliers final: 119 residues processed: 1282 average time/residue: 0.4357 time to fit residues: 867.5878 Evaluate side-chains 1226 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1085 time to evaluate : 3.521 ------------------------------------------------------------------------------- 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 122 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain D residue 9 THR 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 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 122 VAL 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 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 12 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 MET 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 81 SER Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 46 GLN Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 130 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 134 GLU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 98 ASN Chi-restraints excluded: chain O residue 44 ARG 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 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 103 GLU Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain b residue 38 ILE Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 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 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 i residue 11 LEU 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 80 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain k residue 23 LEU 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 86 ASP Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 54 ASN Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain 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 n residue 115 ILE Chi-restraints excluded: chain o residue 21 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 65 TYR Chi-restraints excluded: chain o residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 47 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 208 optimal weight: 0.0270 chunk 214 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 355 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 48 ASN ** c 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 ASN ** f 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 48 ASN ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 73 ASN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 47 GLN l 109 ASN n 73 ASN ** 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 = 0.3306 r_free = 0.3306 target = 0.063663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050651 restraints weight = 152145.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052171 restraints weight = 92884.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053221 restraints weight = 65002.085| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31470 Z= 0.233 Angle : 0.925 12.813 42780 Z= 0.483 Chirality : 0.050 0.237 4995 Planarity : 0.006 0.116 5565 Dihedral : 7.074 58.377 4203 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.72 % Favored : 91.12 % Rotamer: Outliers : 4.62 % Allowed : 30.98 % Favored : 64.40 % 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: -1.33 (0.13), residues: 3795 helix: 0.11 (0.12), residues: 1605 sheet: -0.30 (0.20), residues: 614 loop : -2.18 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 16 HIS 0.010 0.002 HIS b 42 PHE 0.052 0.002 PHE c 89 TYR 0.045 0.002 TYR h 114 ARG 0.014 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 1420) hydrogen bonds : angle 5.32969 ( 4086) covalent geometry : bond 0.00525 (31470) covalent geometry : angle 0.92547 (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 1267 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1104 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8975 (tp30) cc_final: 0.8420 (tp30) REVERT: A 17 ASN cc_start: 0.9126 (m110) cc_final: 0.8339 (m110) REVERT: A 38 MET cc_start: 0.9282 (tmm) cc_final: 0.8733 (tmm) REVERT: A 124 ASP cc_start: 0.9247 (t0) cc_final: 0.8846 (t0) REVERT: A 132 ASP cc_start: 0.8741 (m-30) cc_final: 0.7848 (t70) REVERT: B 44 ARG cc_start: 0.8643 (ttm170) cc_final: 0.8385 (ttm170) REVERT: B 51 ASN cc_start: 0.9504 (m110) cc_final: 0.9282 (p0) REVERT: B 86 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8745 (tp-100) REVERT: B 89 LYS cc_start: 0.8917 (tppt) cc_final: 0.8485 (mmmt) REVERT: B 105 ASP cc_start: 0.9317 (m-30) cc_final: 0.9099 (m-30) REVERT: B 116 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8758 (tpp80) REVERT: B 124 ASP cc_start: 0.9028 (t0) cc_final: 0.8735 (t0) REVERT: B 131 ASP cc_start: 0.9310 (t0) cc_final: 0.8865 (t0) REVERT: C 13 GLU cc_start: 0.8982 (tp30) cc_final: 0.7902 (tp30) REVERT: C 17 ASN cc_start: 0.9479 (m-40) cc_final: 0.8594 (m-40) REVERT: C 19 PHE cc_start: 0.8795 (m-80) cc_final: 0.8528 (m-80) REVERT: C 38 MET cc_start: 0.9164 (tmm) cc_final: 0.8761 (tmm) REVERT: C 39 CYS cc_start: 0.9254 (p) cc_final: 0.8862 (p) REVERT: C 70 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8616 (mm-30) REVERT: C 83 GLU cc_start: 0.8119 (mp0) cc_final: 0.7788 (mp0) REVERT: C 86 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8432 (tp40) REVERT: C 92 ASP cc_start: 0.7991 (p0) cc_final: 0.7637 (t0) REVERT: C 102 ASP cc_start: 0.9149 (m-30) cc_final: 0.8827 (m-30) REVERT: C 105 ASP cc_start: 0.9444 (m-30) cc_final: 0.9199 (m-30) REVERT: C 116 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8361 (mmm160) REVERT: D 21 ASP cc_start: 0.7798 (p0) cc_final: 0.7289 (p0) REVERT: D 34 GLU cc_start: 0.8876 (tt0) cc_final: 0.7912 (tm-30) REVERT: D 44 ARG cc_start: 0.8865 (ptm160) cc_final: 0.8405 (ptm160) REVERT: D 60 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8990 (mm-30) REVERT: D 69 LYS cc_start: 0.9651 (ttmm) cc_final: 0.9421 (ttpp) REVERT: D 106 GLU cc_start: 0.9032 (tp30) cc_final: 0.8617 (tp30) REVERT: D 112 LYS cc_start: 0.9431 (mtmm) cc_final: 0.9108 (mtmm) REVERT: E 17 ASN cc_start: 0.9504 (m-40) cc_final: 0.9221 (m-40) REVERT: E 44 ARG cc_start: 0.8507 (tpt-90) cc_final: 0.8042 (tpp80) REVERT: E 46 GLN cc_start: 0.9357 (tp-100) cc_final: 0.8765 (tp-100) REVERT: E 53 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9316 (mm) REVERT: E 92 ASP cc_start: 0.7720 (p0) cc_final: 0.7165 (t70) REVERT: E 105 ASP cc_start: 0.9363 (m-30) cc_final: 0.9103 (p0) REVERT: E 132 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6969 (m-30) REVERT: F 38 MET cc_start: 0.9438 (tmm) cc_final: 0.9161 (tmm) REVERT: F 86 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8601 (tp40) REVERT: G 21 ASP cc_start: 0.8543 (p0) cc_final: 0.8048 (p0) REVERT: G 29 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8512 (tm-30) REVERT: G 44 ARG cc_start: 0.8423 (ptm160) cc_final: 0.7197 (ttm170) REVERT: G 70 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8166 (mm-30) REVERT: G 79 LYS cc_start: 0.9529 (mppt) cc_final: 0.9184 (mtmm) REVERT: G 92 ASP cc_start: 0.8887 (p0) cc_final: 0.8493 (p0) REVERT: H 21 ASP cc_start: 0.8676 (p0) cc_final: 0.7859 (p0) REVERT: H 38 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8803 (mtt) REVERT: H 44 ARG cc_start: 0.9026 (ptm-80) cc_final: 0.8408 (ttt180) REVERT: H 105 ASP cc_start: 0.9161 (m-30) cc_final: 0.8863 (m-30) REVERT: I 13 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8906 (pt0) REVERT: I 21 ASP cc_start: 0.8386 (p0) cc_final: 0.7995 (p0) REVERT: I 35 PHE cc_start: 0.9561 (t80) cc_final: 0.9024 (t80) REVERT: I 38 MET cc_start: 0.9269 (tmm) cc_final: 0.8934 (tmm) REVERT: I 39 CYS cc_start: 0.9440 (p) cc_final: 0.8781 (p) REVERT: I 70 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8526 (mt-10) REVERT: I 89 LYS cc_start: 0.9467 (ttpp) cc_final: 0.8697 (ttpp) REVERT: I 136 ARG cc_start: 0.7852 (ttp-170) cc_final: 0.7538 (ttt-90) REVERT: J 21 ASP cc_start: 0.8547 (p0) cc_final: 0.8131 (p0) REVERT: J 34 GLU cc_start: 0.9100 (tt0) cc_final: 0.8551 (tt0) REVERT: J 60 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8752 (mt-10) REVERT: J 70 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8354 (tp30) REVERT: J 79 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8847 (mtmm) REVERT: J 83 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7925 (pp20) REVERT: J 92 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8382 (p0) REVERT: K 46 GLN cc_start: 0.9177 (mp10) cc_final: 0.8827 (mp10) REVERT: K 69 LYS cc_start: 0.9711 (ttmm) cc_final: 0.9343 (ttmm) REVERT: K 86 GLN cc_start: 0.9087 (tp40) cc_final: 0.8651 (tp-100) REVERT: K 92 ASP cc_start: 0.8336 (p0) cc_final: 0.7987 (p0) REVERT: K 102 ASP cc_start: 0.9317 (p0) cc_final: 0.8967 (p0) REVERT: K 105 ASP cc_start: 0.9357 (m-30) cc_final: 0.9069 (m-30) REVERT: L 39 CYS cc_start: 0.9244 (p) cc_final: 0.8903 (p) REVERT: L 76 LYS cc_start: 0.9448 (mmmm) cc_final: 0.9089 (mmmm) REVERT: L 79 LYS cc_start: 0.9408 (mmmm) cc_final: 0.9055 (mmtm) REVERT: L 83 GLU cc_start: 0.8215 (mp0) cc_final: 0.7960 (mp0) REVERT: L 86 GLN cc_start: 0.9331 (mm-40) cc_final: 0.8898 (tp40) REVERT: L 110 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8908 (tp30) REVERT: M 17 ASN cc_start: 0.9584 (m-40) cc_final: 0.9333 (m110) REVERT: M 38 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9026 (tpp) REVERT: M 86 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8536 (mm110) REVERT: M 106 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8720 (mt-10) REVERT: M 112 LYS cc_start: 0.9578 (ttmm) cc_final: 0.9096 (mttp) REVERT: M 131 ASP cc_start: 0.9095 (t0) cc_final: 0.8769 (t0) REVERT: M 132 ASP cc_start: 0.8832 (m-30) cc_final: 0.8204 (m-30) REVERT: N 28 LEU cc_start: 0.9446 (mm) cc_final: 0.9176 (mm) REVERT: N 39 CYS cc_start: 0.9612 (m) cc_final: 0.9141 (m) REVERT: N 44 ARG cc_start: 0.8561 (tpt170) cc_final: 0.8304 (tpp80) REVERT: N 86 GLN cc_start: 0.8688 (mp10) cc_final: 0.7962 (mp10) REVERT: N 89 LYS cc_start: 0.8924 (ptmm) cc_final: 0.8514 (ptmm) REVERT: N 92 ASP cc_start: 0.7740 (p0) cc_final: 0.7015 (p0) REVERT: N 105 ASP cc_start: 0.9254 (m-30) cc_final: 0.8977 (m-30) REVERT: O 13 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8985 (mt-10) REVERT: O 21 ASP cc_start: 0.7787 (p0) cc_final: 0.7440 (p0) REVERT: O 35 PHE cc_start: 0.9622 (t80) cc_final: 0.8957 (t80) REVERT: O 38 MET cc_start: 0.8880 (tmm) cc_final: 0.8548 (tmm) REVERT: O 39 CYS cc_start: 0.9207 (p) cc_final: 0.8802 (p) REVERT: O 92 ASP cc_start: 0.8162 (t0) cc_final: 0.7828 (t0) REVERT: O 94 THR cc_start: 0.9254 (m) cc_final: 0.9012 (p) REVERT: O 99 TYR cc_start: 0.8581 (t80) cc_final: 0.8358 (t80) REVERT: O 102 ASP cc_start: 0.9005 (m-30) cc_final: 0.8680 (m-30) REVERT: O 105 ASP cc_start: 0.9386 (m-30) cc_final: 0.9135 (m-30) REVERT: a 62 ASP cc_start: 0.8145 (t0) cc_final: 0.7844 (t0) REVERT: a 108 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9242 (mm) REVERT: a 113 ASP cc_start: 0.9169 (t70) cc_final: 0.8866 (t0) REVERT: a 117 ASP cc_start: 0.9467 (m-30) cc_final: 0.9232 (m-30) REVERT: b 1 MET cc_start: 0.8660 (tpt) cc_final: 0.7782 (tpt) REVERT: b 55 VAL cc_start: 0.9187 (OUTLIER) cc_final: 0.8699 (t) REVERT: b 91 VAL cc_start: 0.9694 (t) cc_final: 0.9461 (p) REVERT: b 117 ASP cc_start: 0.9061 (m-30) cc_final: 0.8679 (t0) REVERT: c 5 LYS cc_start: 0.8710 (ptpp) cc_final: 0.8154 (ptpp) REVERT: c 75 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8953 (mptt) REVERT: c 103 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8351 (mm-30) REVERT: c 109 ASN cc_start: 0.9204 (m-40) cc_final: 0.8828 (m110) REVERT: d 29 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8749 (p) REVERT: d 86 ASP cc_start: 0.8707 (t0) cc_final: 0.8349 (t0) REVERT: e 14 GLN cc_start: 0.8900 (mp10) cc_final: 0.8352 (mm-40) REVERT: e 30 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7080 (p90) REVERT: f 3 ARG cc_start: 0.8674 (mtp-110) cc_final: 0.7980 (ttp80) REVERT: f 5 LYS cc_start: 0.8852 (mtmm) cc_final: 0.7734 (pttm) REVERT: f 27 ASN cc_start: 0.8818 (m-40) cc_final: 0.8600 (m-40) REVERT: f 50 GLU cc_start: 0.8252 (tp30) cc_final: 0.7931 (tp30) REVERT: f 59 VAL cc_start: 0.8358 (m) cc_final: 0.7579 (p) REVERT: f 82 ASP cc_start: 0.8715 (t0) cc_final: 0.8398 (m-30) REVERT: f 86 ASP cc_start: 0.8526 (p0) cc_final: 0.7906 (p0) REVERT: f 109 ASN cc_start: 0.8951 (m110) cc_final: 0.8674 (m110) REVERT: h 1 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6573 (tmm) REVERT: h 74 LYS cc_start: 0.9472 (mmtp) cc_final: 0.9227 (mmmm) REVERT: i 114 TYR cc_start: 0.9015 (t80) cc_final: 0.8666 (t80) REVERT: j 44 LYS cc_start: 0.9520 (tppp) cc_final: 0.9241 (tppt) REVERT: j 48 ASN cc_start: 0.8890 (t0) cc_final: 0.8382 (t0) REVERT: j 50 GLU cc_start: 0.8178 (pm20) cc_final: 0.7721 (pm20) REVERT: j 101 ASP cc_start: 0.8710 (p0) cc_final: 0.8382 (p0) REVERT: j 112 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8813 (tm-30) REVERT: l 44 LYS cc_start: 0.9236 (mmtp) cc_final: 0.9014 (tppt) REVERT: m 12 ASP cc_start: 0.7591 (p0) cc_final: 0.7128 (p0) REVERT: m 48 ASN cc_start: 0.9388 (t0) cc_final: 0.9046 (t0) REVERT: m 66 TYR cc_start: 0.7599 (m-80) cc_final: 0.7176 (m-80) REVERT: n 13 ASP cc_start: 0.8627 (m-30) cc_final: 0.8217 (m-30) REVERT: n 36 TYR cc_start: 0.8984 (m-80) cc_final: 0.8450 (m-80) REVERT: n 73 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8045 (p0) REVERT: n 111 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9185 (pp) REVERT: o 50 GLU cc_start: 0.7964 (tp30) cc_final: 0.7216 (tp30) REVERT: o 54 ASN cc_start: 0.8447 (p0) cc_final: 0.7888 (p0) REVERT: o 65 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.5529 (t80) REVERT: o 77 SER cc_start: 0.9407 (p) cc_final: 0.8857 (p) outliers start: 163 outliers final: 122 residues processed: 1193 average time/residue: 0.4348 time to fit residues: 802.7881 Evaluate side-chains 1210 residues out of total 3525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1071 time to evaluate : 3.388 ------------------------------------------------------------------------------- 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 122 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain D residue 9 THR 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 E residue 9 THR 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 122 VAL 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 86 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 132 ASP 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 38 MET Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 130 TYR Chi-restraints excluded: chain I residue 45 SER Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 132 ASP Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 79 LYS Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 124 ASP Chi-restraints excluded: chain K residue 130 TYR Chi-restraints excluded: chain L residue 47 ASN Chi-restraints excluded: chain L residue 93 ILE 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 L residue 134 GLU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 59 ILE Chi-restraints excluded: chain M residue 93 ILE Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain O residue 44 ARG 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 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 48 ASN Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 75 LYS Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 42 HIS Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain e residue 11 LEU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain e residue 30 PHE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain e residue 110 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 42 HIS Chi-restraints excluded: chain g residue 48 ASN 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 114 TYR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 80 VAL Chi-restraints excluded: chain i residue 117 ASP Chi-restraints excluded: chain i residue 121 ASN Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 65 TYR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 113 ASP Chi-restraints excluded: chain j residue 114 TYR Chi-restraints excluded: chain k residue 108 LEU Chi-restraints excluded: chain k residue 121 ASN Chi-restraints excluded: chain l residue 86 ASP Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 109 ASN 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 73 ASN 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 21 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 7 optimal weight: 9.9990 chunk 357 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN ** O 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 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** ** l 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 54 ASN ** l 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 GLN ** n 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 73 ASN ** o 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.063266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050336 restraints weight = 151837.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051849 restraints weight = 92599.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.052894 restraints weight = 64767.270| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 31470 Z= 0.231 Angle : 0.937 13.052 42780 Z= 0.489 Chirality : 0.050 0.251 4995 Planarity : 0.006 0.103 5565 Dihedral : 7.094 59.060 4203 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.91 % Favored : 90.94 % Rotamer: Outliers : 4.40 % Allowed : 31.94 % Favored : 63.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.40 (0.13), residues: 3795 helix: 0.03 (0.12), residues: 1605 sheet: -0.30 (0.20), residues: 618 loop : -2.22 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 16 HIS 0.009 0.001 HIS b 42 PHE 0.048 0.002 PHE c 89 TYR 0.043 0.002 TYR h 114 ARG 0.017 0.001 ARG N 136 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 1420) hydrogen bonds : angle 5.32891 ( 4086) covalent geometry : bond 0.00521 (31470) covalent geometry : angle 0.93651 (42780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14686.86 seconds wall clock time: 256 minutes 3.27 seconds (15363.27 seconds total)