Starting phenix.real_space_refine on Mon Aug 25 13:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu3_48618/08_2025/9mu3_48618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu3_48618/08_2025/9mu3_48618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mu3_48618/08_2025/9mu3_48618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu3_48618/08_2025/9mu3_48618.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu3_48618/08_2025/9mu3_48618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu3_48618/08_2025/9mu3_48618.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.018 sd= 0.257 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 114 5.16 5 C 18216 2.51 5 N 4776 2.21 5 O 5826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28932 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "D" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "M" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "Q" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "S" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "T" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "U" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "V" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "W" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "X" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "Y" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "Z" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "0" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "1" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "2" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "3" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "4" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "5" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "6" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "7" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "8" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "9" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 5.45, per 1000 atoms: 0.19 Number of scatterers: 28932 At special positions: 0 Unit cell: (115.71, 118.37, 167.58, 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 114 16.00 O 5826 8.00 N 4776 7.00 C 18216 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: 2.04 Conformation dependent library (CDL) restraints added in 746.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 30.4% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.325A pdb=" N VAL A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.642A pdb=" N GLU A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 62 removed outlier: 4.271A pdb=" N ILE A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 removed outlier: 4.151A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.096A pdb=" N VAL B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 3.653A pdb=" N GLU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 48 through 63 removed outlier: 4.185A pdb=" N ILE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 removed outlier: 4.186A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 70 through 86 removed outlier: 3.661A pdb=" N HIS D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.720A pdb=" N VAL E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'G' and resid 3 through 11 removed outlier: 4.325A pdb=" N VAL G 7 " --> pdb=" O THR G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 37 removed outlier: 3.642A pdb=" N GLU G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 48 through 62 removed outlier: 4.271A pdb=" N ILE G 52 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 97 removed outlier: 4.151A pdb=" N ALA G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 removed outlier: 4.096A pdb=" N VAL H 7 " --> pdb=" O THR H 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.653A pdb=" N GLU H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 48 through 63 removed outlier: 4.185A pdb=" N ILE H 52 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 4.186A pdb=" N ALA H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 70 through 86 removed outlier: 3.661A pdb=" N HIS J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 8 No H-bonds generated for 'chain 'K' and resid 6 through 8' Processing helix chain 'K' and resid 71 through 83 removed outlier: 3.719A pdb=" N VAL K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 152 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'M' and resid 3 through 11 removed outlier: 4.325A pdb=" N VAL M 7 " --> pdb=" O THR M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 37 removed outlier: 3.642A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 48 through 62 removed outlier: 4.271A pdb=" N ILE M 52 " --> pdb=" O PHE M 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS M 53 " --> pdb=" O SER M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 97 removed outlier: 4.151A pdb=" N ALA M 90 " --> pdb=" O LYS M 86 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE M 91 " --> pdb=" O GLU M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 11 removed outlier: 4.095A pdb=" N VAL N 7 " --> pdb=" O THR N 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 37 removed outlier: 3.653A pdb=" N GLU N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 47 No H-bonds generated for 'chain 'N' and resid 45 through 47' Processing helix chain 'N' and resid 48 through 63 removed outlier: 4.186A pdb=" N ILE N 52 " --> pdb=" O PHE N 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS N 53 " --> pdb=" O SER N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 97 removed outlier: 4.186A pdb=" N ALA N 90 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE N 91 " --> pdb=" O GLU N 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 16 Processing helix chain 'P' and resid 70 through 86 removed outlier: 3.660A pdb=" N HIS P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 8 No H-bonds generated for 'chain 'Q' and resid 6 through 8' Processing helix chain 'Q' and resid 71 through 83 removed outlier: 3.719A pdb=" N VAL Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 152 Processing helix chain 'R' and resid 165 through 169 Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.325A pdb=" N VAL S 7 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 37 removed outlier: 3.642A pdb=" N GLU S 24 " --> pdb=" O GLU S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 47 No H-bonds generated for 'chain 'S' and resid 45 through 47' Processing helix chain 'S' and resid 48 through 62 removed outlier: 4.271A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 97 removed outlier: 4.151A pdb=" N ALA S 90 " --> pdb=" O LYS S 86 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.096A pdb=" N VAL T 7 " --> pdb=" O THR T 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 37 removed outlier: 3.653A pdb=" N GLU T 24 " --> pdb=" O GLU T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 47 No H-bonds generated for 'chain 'T' and resid 45 through 47' Processing helix chain 'T' and resid 48 through 63 removed outlier: 4.185A pdb=" N ILE T 52 " --> pdb=" O PHE T 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS T 53 " --> pdb=" O SER T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 97 removed outlier: 4.186A pdb=" N ALA T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE T 91 " --> pdb=" O GLU T 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 16 Processing helix chain 'V' and resid 70 through 86 removed outlier: 3.661A pdb=" N HIS V 74 " --> pdb=" O ASP V 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 8 No H-bonds generated for 'chain 'W' and resid 6 through 8' Processing helix chain 'W' and resid 71 through 83 removed outlier: 3.720A pdb=" N VAL W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 152 Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'Y' and resid 3 through 11 removed outlier: 4.325A pdb=" N VAL Y 7 " --> pdb=" O THR Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 37 removed outlier: 3.642A pdb=" N GLU Y 24 " --> pdb=" O GLU Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'Y' and resid 48 through 62 removed outlier: 4.270A pdb=" N ILE Y 52 " --> pdb=" O PHE Y 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 97 removed outlier: 4.151A pdb=" N ALA Y 90 " --> pdb=" O LYS Y 86 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE Y 91 " --> pdb=" O GLU Y 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 11 removed outlier: 4.096A pdb=" N VAL Z 7 " --> pdb=" O THR Z 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Z 10 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 37 removed outlier: 3.653A pdb=" N GLU Z 24 " --> pdb=" O GLU Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 47 No H-bonds generated for 'chain 'Z' and resid 45 through 47' Processing helix chain 'Z' and resid 48 through 63 removed outlier: 4.185A pdb=" N ILE Z 52 " --> pdb=" O PHE Z 48 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 97 removed outlier: 4.186A pdb=" N ALA Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE Z 91 " --> pdb=" O GLU Z 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN Z 94 " --> pdb=" O ALA Z 90 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 16 Processing helix chain '1' and resid 70 through 86 removed outlier: 3.661A pdb=" N HIS 1 74 " --> pdb=" O ASP 1 70 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 8 No H-bonds generated for 'chain '2' and resid 6 through 8' Processing helix chain '2' and resid 71 through 83 removed outlier: 3.719A pdb=" N VAL 2 81 " --> pdb=" O GLU 2 77 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 152 Processing helix chain '3' and resid 165 through 169 Processing helix chain '4' and resid 3 through 11 removed outlier: 4.325A pdb=" N VAL 4 7 " --> pdb=" O THR 4 3 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 37 removed outlier: 3.642A pdb=" N GLU 4 24 " --> pdb=" O GLU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 47 No H-bonds generated for 'chain '4' and resid 45 through 47' Processing helix chain '4' and resid 48 through 62 removed outlier: 4.271A pdb=" N ILE 4 52 " --> pdb=" O PHE 4 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS 4 53 " --> pdb=" O SER 4 49 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 97 removed outlier: 4.151A pdb=" N ALA 4 90 " --> pdb=" O LYS 4 86 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE 4 91 " --> pdb=" O GLU 4 87 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 11 removed outlier: 4.095A pdb=" N VAL 5 7 " --> pdb=" O THR 5 3 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG 5 10 " --> pdb=" O ASP 5 6 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 37 removed outlier: 3.653A pdb=" N GLU 5 24 " --> pdb=" O GLU 5 20 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 47 No H-bonds generated for 'chain '5' and resid 45 through 47' Processing helix chain '5' and resid 48 through 63 removed outlier: 4.186A pdb=" N ILE 5 52 " --> pdb=" O PHE 5 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS 5 53 " --> pdb=" O SER 5 49 " (cutoff:3.500A) Processing helix chain '5' and resid 85 through 97 removed outlier: 4.186A pdb=" N ALA 5 90 " --> pdb=" O LYS 5 86 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE 5 91 " --> pdb=" O GLU 5 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN 5 94 " --> pdb=" O ALA 5 90 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 70 through 86 removed outlier: 3.660A pdb=" N HIS 7 74 " --> pdb=" O ASP 7 70 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 8 No H-bonds generated for 'chain '8' and resid 6 through 8' Processing helix chain '8' and resid 71 through 83 removed outlier: 3.719A pdb=" N VAL 8 81 " --> pdb=" O GLU 8 77 " (cutoff:3.500A) Processing helix chain '8' and resid 147 through 152 Processing helix chain '9' and resid 165 through 169 Processing sheet with id=1, first strand: chain 'A' and resid 70 through 73 removed outlier: 6.729A pdb=" N SER A 77 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU B 71 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 79 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.419A pdb=" N ILE C 82 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU C 97 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS C 63 " --> pdb=" O PRO C 35 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=4, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL D 61 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN D 59 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER D 44 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP D 57 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL D 61 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN D 59 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER D 44 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP D 57 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU D 115 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL D 107 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS D 117 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN D 105 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER D 119 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE D 103 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR D 121 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR D 101 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER D 123 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS E 106 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU E 132 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE E 117 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU E 130 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU E 119 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU E 128 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER E 58 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU E 31 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS E 65 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 29 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS E 106 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'E' and resid 41 through 43 removed outlier: 3.581A pdb=" N ASP E 41 " --> pdb=" O THR E 52 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'G' and resid 70 through 73 removed outlier: 6.729A pdb=" N SER G 77 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU H 71 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA G 79 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'I' and resid 27 through 30 removed outlier: 5.419A pdb=" N ILE I 82 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS I 63 " --> pdb=" O PRO I 35 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'I' and resid 44 through 48 Processing sheet with id=12, first strand: chain 'J' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL J 61 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN J 59 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER J 44 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP J 57 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'J' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL J 61 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN J 59 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER J 44 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP J 57 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU J 115 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL J 107 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS J 117 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN J 105 " --> pdb=" O HIS J 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER J 119 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE J 103 " --> pdb=" O SER J 119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR J 121 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR J 101 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER J 123 " --> pdb=" O ASP J 99 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'K' and resid 24 through 25 removed outlier: 4.300A pdb=" N LYS K 106 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU K 132 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE K 117 " --> pdb=" O GLU K 130 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU K 130 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU K 119 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU K 128 " --> pdb=" O LEU K 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER K 58 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU K 31 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS K 65 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU K 29 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'K' and resid 24 through 25 removed outlier: 4.300A pdb=" N LYS K 106 " --> pdb=" O GLU K 92 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'K' and resid 41 through 43 removed outlier: 3.582A pdb=" N ASP K 41 " --> pdb=" O THR K 52 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'M' and resid 70 through 73 removed outlier: 6.729A pdb=" N SER M 77 " --> pdb=" O GLU N 71 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU N 71 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA M 79 " --> pdb=" O THR N 69 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'O' and resid 27 through 30 removed outlier: 5.419A pdb=" N ILE O 82 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU O 97 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS O 63 " --> pdb=" O PRO O 35 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'O' and resid 44 through 48 Processing sheet with id=20, first strand: chain 'P' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL P 61 " --> pdb=" O LYS P 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN P 59 " --> pdb=" O PRO P 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER P 44 " --> pdb=" O ASP P 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP P 57 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER P 53 " --> pdb=" O TYR P 49 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'P' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL P 61 " --> pdb=" O LYS P 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN P 59 " --> pdb=" O PRO P 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER P 44 " --> pdb=" O ASP P 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP P 57 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU P 115 " --> pdb=" O VAL P 107 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL P 107 " --> pdb=" O LEU P 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS P 117 " --> pdb=" O GLN P 105 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN P 105 " --> pdb=" O HIS P 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER P 119 " --> pdb=" O ILE P 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE P 103 " --> pdb=" O SER P 119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR P 121 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR P 101 " --> pdb=" O THR P 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER P 123 " --> pdb=" O ASP P 99 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'Q' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS Q 106 " --> pdb=" O GLU Q 92 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU Q 132 " --> pdb=" O ASN Q 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE Q 117 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU Q 130 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU Q 119 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU Q 128 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER Q 58 " --> pdb=" O VAL Q 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Q 31 " --> pdb=" O THR Q 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS Q 65 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU Q 29 " --> pdb=" O LYS Q 65 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'Q' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS Q 106 " --> pdb=" O GLU Q 92 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'Q' and resid 41 through 43 removed outlier: 3.582A pdb=" N ASP Q 41 " --> pdb=" O THR Q 52 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'S' and resid 70 through 73 removed outlier: 6.729A pdb=" N SER S 77 " --> pdb=" O GLU T 71 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU T 71 " --> pdb=" O SER S 77 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA S 79 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'U' and resid 27 through 30 removed outlier: 5.419A pdb=" N ILE U 82 " --> pdb=" O GLU U 97 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU U 97 " --> pdb=" O ILE U 82 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS U 63 " --> pdb=" O PRO U 35 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'U' and resid 44 through 48 Processing sheet with id=28, first strand: chain 'V' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL V 61 " --> pdb=" O LYS V 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN V 59 " --> pdb=" O PRO V 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER V 44 " --> pdb=" O ASP V 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP V 57 " --> pdb=" O SER V 44 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER V 53 " --> pdb=" O TYR V 49 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'V' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL V 61 " --> pdb=" O LYS V 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN V 59 " --> pdb=" O PRO V 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER V 44 " --> pdb=" O ASP V 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP V 57 " --> pdb=" O SER V 44 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU V 115 " --> pdb=" O VAL V 107 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL V 107 " --> pdb=" O LEU V 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS V 117 " --> pdb=" O GLN V 105 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN V 105 " --> pdb=" O HIS V 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER V 119 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE V 103 " --> pdb=" O SER V 119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR V 121 " --> pdb=" O THR V 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR V 101 " --> pdb=" O THR V 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER V 123 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'W' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS W 106 " --> pdb=" O GLU W 92 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU W 132 " --> pdb=" O ASN W 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE W 117 " --> pdb=" O GLU W 130 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU W 130 " --> pdb=" O PHE W 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU W 119 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU W 128 " --> pdb=" O LEU W 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER W 58 " --> pdb=" O VAL W 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU W 31 " --> pdb=" O THR W 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS W 65 " --> pdb=" O LEU W 29 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU W 29 " --> pdb=" O LYS W 65 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'W' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS W 106 " --> pdb=" O GLU W 92 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'W' and resid 41 through 43 removed outlier: 3.581A pdb=" N ASP W 41 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'Y' and resid 70 through 73 removed outlier: 6.729A pdb=" N SER Y 77 " --> pdb=" O GLU Z 71 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU Z 71 " --> pdb=" O SER Y 77 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA Y 79 " --> pdb=" O THR Z 69 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain '0' and resid 27 through 30 removed outlier: 5.419A pdb=" N ILE 0 82 " --> pdb=" O GLU 0 97 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU 0 97 " --> pdb=" O ILE 0 82 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS 0 63 " --> pdb=" O PRO 0 35 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain '0' and resid 44 through 48 Processing sheet with id=36, first strand: chain '1' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL 1 61 " --> pdb=" O LYS 1 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN 1 59 " --> pdb=" O PRO 1 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER 1 44 " --> pdb=" O ASP 1 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP 1 57 " --> pdb=" O SER 1 44 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER 1 53 " --> pdb=" O TYR 1 49 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain '1' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL 1 61 " --> pdb=" O LYS 1 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN 1 59 " --> pdb=" O PRO 1 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER 1 44 " --> pdb=" O ASP 1 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP 1 57 " --> pdb=" O SER 1 44 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU 1 115 " --> pdb=" O VAL 1 107 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL 1 107 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS 1 117 " --> pdb=" O GLN 1 105 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN 1 105 " --> pdb=" O HIS 1 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER 1 119 " --> pdb=" O ILE 1 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE 1 103 " --> pdb=" O SER 1 119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR 1 121 " --> pdb=" O THR 1 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR 1 101 " --> pdb=" O THR 1 121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER 1 123 " --> pdb=" O ASP 1 99 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain '2' and resid 24 through 25 removed outlier: 4.300A pdb=" N LYS 2 106 " --> pdb=" O GLU 2 92 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU 2 132 " --> pdb=" O ASN 2 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE 2 117 " --> pdb=" O GLU 2 130 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU 2 130 " --> pdb=" O PHE 2 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU 2 119 " --> pdb=" O GLU 2 128 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU 2 128 " --> pdb=" O LEU 2 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER 2 58 " --> pdb=" O VAL 2 135 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 31 " --> pdb=" O THR 2 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS 2 65 " --> pdb=" O LEU 2 29 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU 2 29 " --> pdb=" O LYS 2 65 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain '2' and resid 24 through 25 removed outlier: 4.300A pdb=" N LYS 2 106 " --> pdb=" O GLU 2 92 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain '2' and resid 41 through 43 removed outlier: 3.582A pdb=" N ASP 2 41 " --> pdb=" O THR 2 52 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain '4' and resid 70 through 73 removed outlier: 6.729A pdb=" N SER 4 77 " --> pdb=" O GLU 5 71 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU 5 71 " --> pdb=" O SER 4 77 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA 4 79 " --> pdb=" O THR 5 69 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain '6' and resid 27 through 30 removed outlier: 5.419A pdb=" N ILE 6 82 " --> pdb=" O GLU 6 97 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU 6 97 " --> pdb=" O ILE 6 82 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS 6 63 " --> pdb=" O PRO 6 35 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain '6' and resid 44 through 48 Processing sheet with id=44, first strand: chain '7' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL 7 61 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN 7 59 " --> pdb=" O PRO 7 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER 7 44 " --> pdb=" O ASP 7 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP 7 57 " --> pdb=" O SER 7 44 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER 7 53 " --> pdb=" O TYR 7 49 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain '7' and resid 22 through 23 removed outlier: 4.296A pdb=" N VAL 7 61 " --> pdb=" O LYS 7 40 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN 7 59 " --> pdb=" O PRO 7 42 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER 7 44 " --> pdb=" O ASP 7 57 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP 7 57 " --> pdb=" O SER 7 44 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU 7 115 " --> pdb=" O VAL 7 107 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL 7 107 " --> pdb=" O LEU 7 115 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS 7 117 " --> pdb=" O GLN 7 105 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN 7 105 " --> pdb=" O HIS 7 117 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER 7 119 " --> pdb=" O ILE 7 103 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE 7 103 " --> pdb=" O SER 7 119 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR 7 121 " --> pdb=" O THR 7 101 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR 7 101 " --> pdb=" O THR 7 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER 7 123 " --> pdb=" O ASP 7 99 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain '8' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS 8 106 " --> pdb=" O GLU 8 92 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU 8 132 " --> pdb=" O ASN 8 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE 8 117 " --> pdb=" O GLU 8 130 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU 8 130 " --> pdb=" O PHE 8 117 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU 8 119 " --> pdb=" O GLU 8 128 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU 8 128 " --> pdb=" O LEU 8 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N SER 8 58 " --> pdb=" O VAL 8 135 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 8 31 " --> pdb=" O THR 8 63 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS 8 65 " --> pdb=" O LEU 8 29 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU 8 29 " --> pdb=" O LYS 8 65 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain '8' and resid 24 through 25 removed outlier: 4.299A pdb=" N LYS 8 106 " --> pdb=" O GLU 8 92 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain '8' and resid 41 through 43 removed outlier: 3.582A pdb=" N ASP 8 41 " --> pdb=" O THR 8 52 " (cutoff:3.500A) 1434 hydrogen bonds defined for protein. 3942 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: 4.19 Time building geometry restraints manager: 2.73 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: 9405 1.34 - 1.46: 4188 1.46 - 1.57: 15645 1.57 - 1.69: 0 1.69 - 1.81: 204 Bond restraints: 29442 Sorted by residual: bond pdb=" N THR B 2 " pdb=" CA THR B 2 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.69e+00 bond pdb=" N THR Z 2 " pdb=" CA THR Z 2 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.69e+00 bond pdb=" N THR H 2 " pdb=" CA THR H 2 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.69e+00 bond pdb=" N THR T 2 " pdb=" CA THR T 2 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.69e+00 bond pdb=" N THR M 2 " pdb=" CA THR M 2 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.66e+00 ... (remaining 29437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 35125 1.48 - 2.97: 3877 2.97 - 4.45: 566 4.45 - 5.93: 86 5.93 - 7.41: 30 Bond angle restraints: 39684 Sorted by residual: angle pdb=" CB ARG H 10 " pdb=" CG ARG H 10 " pdb=" CD ARG H 10 " ideal model delta sigma weight residual 111.30 118.71 -7.41 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CB ARG Z 10 " pdb=" CG ARG Z 10 " pdb=" CD ARG Z 10 " ideal model delta sigma weight residual 111.30 118.71 -7.41 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CB ARG N 10 " pdb=" CG ARG N 10 " pdb=" CD ARG N 10 " ideal model delta sigma weight residual 111.30 118.70 -7.40 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CB ARG 5 10 " pdb=" CG ARG 5 10 " pdb=" CD ARG 5 10 " ideal model delta sigma weight residual 111.30 118.70 -7.40 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CB ARG B 10 " pdb=" CG ARG B 10 " pdb=" CD ARG B 10 " ideal model delta sigma weight residual 111.30 118.69 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 39679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 16406 17.33 - 34.66: 1228 34.66 - 51.99: 180 51.99 - 69.32: 48 69.32 - 86.65: 54 Dihedral angle restraints: 17916 sinusoidal: 7422 harmonic: 10494 Sorted by residual: dihedral pdb=" CA ILE V 62 " pdb=" C ILE V 62 " pdb=" N ASP V 63 " pdb=" CA ASP V 63 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ILE D 62 " pdb=" C ILE D 62 " pdb=" N ASP D 63 " pdb=" CA ASP D 63 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA ILE J 62 " pdb=" C ILE J 62 " pdb=" N ASP J 63 " pdb=" CA ASP J 63 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 17913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2379 0.042 - 0.084: 1262 0.084 - 0.127: 517 0.127 - 0.169: 120 0.169 - 0.211: 24 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA ILE P 120 " pdb=" N ILE P 120 " pdb=" C ILE P 120 " pdb=" CB ILE P 120 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE 7 120 " pdb=" N ILE 7 120 " pdb=" C ILE 7 120 " pdb=" CB ILE 7 120 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE 1 120 " pdb=" N ILE 1 120 " pdb=" C ILE 1 120 " pdb=" CB ILE 1 120 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4299 not shown) Planarity restraints: 5190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA S 56 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ALA S 56 " 0.066 2.00e-02 2.50e+03 pdb=" O ALA S 56 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL S 57 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 56 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ALA A 56 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA A 56 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A 57 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 56 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C ALA Y 56 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA Y 56 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL Y 57 " 0.022 2.00e-02 2.50e+03 ... (remaining 5187 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 11718 2.91 - 3.41: 25800 3.41 - 3.90: 46610 3.90 - 4.40: 54600 4.40 - 4.90: 95305 Nonbonded interactions: 234033 Sorted by model distance: nonbonded pdb=" OD1 ASP 1 75 " pdb=" OG1 THR 7 2 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASP J 75 " pdb=" OG1 THR P 2 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASP V 75 " pdb=" OG1 THR 1 2 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASP D 75 " pdb=" OG1 THR J 2 " model vdw 2.412 3.040 nonbonded pdb=" OG1 THR D 2 " pdb=" OD1 ASP 7 75 " model vdw 2.412 3.040 ... (remaining 234028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '6' selection = chain 'C' selection = chain 'I' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain '1' selection = chain '7' selection = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'V' } ncs_group { reference = chain '2' selection = chain '8' selection = chain 'E' selection = chain 'K' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain '3' selection = chain '9' selection = chain 'F' selection = chain 'L' selection = chain 'R' selection = chain 'X' } ncs_group { reference = chain '4' selection = chain '5' selection = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.006 0.057 29442 Z= 0.299 Angle : 0.988 7.412 39684 Z= 0.592 Chirality : 0.059 0.211 4302 Planarity : 0.013 0.133 5190 Dihedral : 13.617 86.646 11160 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.14), residues: 3486 helix: -1.46 (0.14), residues: 918 sheet: 0.41 (0.15), residues: 1110 loop : 0.16 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG 4 10 TYR 0.028 0.006 TYR B 50 PHE 0.028 0.004 PHE Q 67 TRP 0.054 0.012 TRP J 65 HIS 0.011 0.003 HIS J 74 Details of bonding type rmsd covalent geometry : bond 0.00618 (29442) covalent geometry : angle 0.98766 (39684) hydrogen bonds : bond 0.13135 ( 1302) hydrogen bonds : angle 7.45952 ( 3942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1138 time to evaluate : 1.252 Fit side-chains REVERT: A 17 LYS cc_start: 0.8796 (mttt) cc_final: 0.8580 (mtpt) REVERT: A 30 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 32 GLN cc_start: 0.8718 (tt0) cc_final: 0.8485 (tt0) REVERT: A 36 MET cc_start: 0.9064 (mtp) cc_final: 0.8486 (mtp) REVERT: B 34 LEU cc_start: 0.9079 (tp) cc_final: 0.8836 (tt) REVERT: B 92 ILE cc_start: 0.9010 (mt) cc_final: 0.8809 (mt) REVERT: C 89 ARG cc_start: 0.8995 (ttm-80) cc_final: 0.8727 (ttm-80) REVERT: D 71 LEU cc_start: 0.9110 (tp) cc_final: 0.8749 (mp) REVERT: D 125 LYS cc_start: 0.8506 (mttt) cc_final: 0.8225 (mtpp) REVERT: E 40 THR cc_start: 0.8672 (p) cc_final: 0.8390 (t) REVERT: E 46 MET cc_start: 0.3551 (ttt) cc_final: 0.3088 (tpt) REVERT: F 168 ASP cc_start: 0.8387 (t0) cc_final: 0.7757 (t0) REVERT: H 21 GLN cc_start: 0.8123 (mt0) cc_final: 0.7904 (mt0) REVERT: H 27 LYS cc_start: 0.8816 (tttt) cc_final: 0.8575 (mtpp) REVERT: I 16 THR cc_start: 0.9037 (m) cc_final: 0.8640 (t) REVERT: I 47 GLN cc_start: 0.8410 (tt0) cc_final: 0.8206 (mm-40) REVERT: J 45 ASN cc_start: 0.8994 (m-40) cc_final: 0.8673 (m-40) REVERT: J 69 ASP cc_start: 0.8182 (t0) cc_final: 0.7980 (p0) REVERT: J 71 LEU cc_start: 0.8877 (tp) cc_final: 0.8538 (mp) REVERT: J 79 LYS cc_start: 0.8521 (tptp) cc_final: 0.7958 (ttpt) REVERT: K 46 MET cc_start: 0.3217 (ttt) cc_final: 0.2319 (tpp) REVERT: K 111 GLN cc_start: 0.9106 (pt0) cc_final: 0.8553 (pt0) REVERT: L 168 ASP cc_start: 0.8558 (t0) cc_final: 0.8345 (t0) REVERT: M 30 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8293 (mt-10) REVERT: M 32 GLN cc_start: 0.8705 (tt0) cc_final: 0.8328 (tt0) REVERT: N 68 MET cc_start: 0.9423 (mtp) cc_final: 0.9178 (mtp) REVERT: N 92 ILE cc_start: 0.9023 (mt) cc_final: 0.8816 (mp) REVERT: P 13 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8320 (mt-10) REVERT: P 41 MET cc_start: 0.8751 (tpt) cc_final: 0.8535 (tpp) REVERT: P 66 SER cc_start: 0.8682 (t) cc_final: 0.8465 (m) REVERT: P 69 ASP cc_start: 0.7992 (t0) cc_final: 0.7739 (p0) REVERT: P 79 LYS cc_start: 0.8646 (tptp) cc_final: 0.8015 (ttpt) REVERT: P 106 LEU cc_start: 0.9028 (mt) cc_final: 0.8818 (mp) REVERT: P 125 LYS cc_start: 0.8612 (mttt) cc_final: 0.8330 (mtpp) REVERT: Q 40 THR cc_start: 0.8716 (p) cc_final: 0.8254 (t) REVERT: Q 41 ASP cc_start: 0.6725 (m-30) cc_final: 0.6467 (m-30) REVERT: Q 46 MET cc_start: 0.3121 (ttt) cc_final: 0.2477 (tpp) REVERT: S 17 LYS cc_start: 0.8796 (mttt) cc_final: 0.8579 (mtpt) REVERT: S 30 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8307 (mt-10) REVERT: S 32 GLN cc_start: 0.8718 (tt0) cc_final: 0.8488 (tt0) REVERT: S 36 MET cc_start: 0.9063 (mtp) cc_final: 0.8486 (mtp) REVERT: T 34 LEU cc_start: 0.9078 (tp) cc_final: 0.8836 (tt) REVERT: T 92 ILE cc_start: 0.9010 (mt) cc_final: 0.8808 (mt) REVERT: U 89 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8730 (ttm-80) REVERT: V 71 LEU cc_start: 0.9110 (tp) cc_final: 0.8751 (mp) REVERT: V 125 LYS cc_start: 0.8503 (mttt) cc_final: 0.8222 (mtpp) REVERT: W 40 THR cc_start: 0.8670 (p) cc_final: 0.8389 (t) REVERT: W 46 MET cc_start: 0.3548 (ttt) cc_final: 0.3080 (tpt) REVERT: X 168 ASP cc_start: 0.8385 (t0) cc_final: 0.7756 (t0) REVERT: Z 21 GLN cc_start: 0.8127 (mt0) cc_final: 0.7906 (mt0) REVERT: Z 27 LYS cc_start: 0.8816 (tttt) cc_final: 0.8577 (mtpp) REVERT: 0 16 THR cc_start: 0.9036 (m) cc_final: 0.8640 (t) REVERT: 0 47 GLN cc_start: 0.8408 (tt0) cc_final: 0.8206 (mm-40) REVERT: 1 45 ASN cc_start: 0.8995 (m-40) cc_final: 0.8674 (m-40) REVERT: 1 69 ASP cc_start: 0.8181 (t0) cc_final: 0.7979 (p0) REVERT: 1 71 LEU cc_start: 0.8881 (tp) cc_final: 0.8544 (mp) REVERT: 1 79 LYS cc_start: 0.8519 (tptp) cc_final: 0.7957 (ttpt) REVERT: 2 46 MET cc_start: 0.3217 (ttt) cc_final: 0.2318 (tpp) REVERT: 2 111 GLN cc_start: 0.9105 (pt0) cc_final: 0.8552 (pt0) REVERT: 3 168 ASP cc_start: 0.8557 (t0) cc_final: 0.8345 (t0) REVERT: 4 30 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8294 (mt-10) REVERT: 4 32 GLN cc_start: 0.8703 (tt0) cc_final: 0.8329 (tt0) REVERT: 5 68 MET cc_start: 0.9421 (mtp) cc_final: 0.9179 (mtp) REVERT: 5 92 ILE cc_start: 0.9021 (mt) cc_final: 0.8813 (mp) REVERT: 7 13 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8322 (mt-10) REVERT: 7 41 MET cc_start: 0.8753 (tpt) cc_final: 0.8534 (tpp) REVERT: 7 66 SER cc_start: 0.8680 (t) cc_final: 0.8463 (m) REVERT: 7 69 ASP cc_start: 0.7995 (t0) cc_final: 0.7741 (p0) REVERT: 7 79 LYS cc_start: 0.8647 (tptp) cc_final: 0.8020 (ttpt) REVERT: 7 106 LEU cc_start: 0.9029 (mt) cc_final: 0.8816 (mp) REVERT: 7 125 LYS cc_start: 0.8611 (mttt) cc_final: 0.8327 (mtpp) REVERT: 8 40 THR cc_start: 0.8717 (p) cc_final: 0.8253 (t) REVERT: 8 41 ASP cc_start: 0.6727 (m-30) cc_final: 0.6471 (m-30) REVERT: 8 46 MET cc_start: 0.3121 (ttt) cc_final: 0.2477 (tpp) outliers start: 0 outliers final: 0 residues processed: 1138 average time/residue: 0.2033 time to fit residues: 346.1151 Evaluate side-chains 812 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 812 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN D 74 HIS D 113 GLN D 117 HIS E 111 GLN E 136 ASN H 21 GLN I 76 ASN J 74 HIS J 113 GLN K 136 ASN O 76 ASN P 6 GLN P 74 HIS P 113 GLN P 117 HIS Q 136 ASN V 74 HIS V 113 GLN V 117 HIS W 136 ASN Z 21 GLN 0 76 ASN 1 74 HIS 1 113 GLN 2 136 ASN 6 76 ASN 7 6 GLN 7 74 HIS 7 113 GLN 7 117 HIS 8 136 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096490 restraints weight = 39310.969| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.14 r_work: 0.2977 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29442 Z= 0.154 Angle : 0.606 6.752 39684 Z= 0.337 Chirality : 0.044 0.151 4302 Planarity : 0.004 0.030 5190 Dihedral : 6.355 78.243 3924 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 9.67 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.14), residues: 3486 helix: 0.67 (0.17), residues: 918 sheet: 0.22 (0.14), residues: 1230 loop : 0.39 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 94 TYR 0.016 0.002 TYR 1 8 PHE 0.013 0.002 PHE S 96 TRP 0.009 0.001 TRP Q 89 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00359 (29442) covalent geometry : angle 0.60638 (39684) hydrogen bonds : bond 0.04567 ( 1302) hydrogen bonds : angle 4.74629 ( 3942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 898 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8998 (mttt) cc_final: 0.8650 (mtpt) REVERT: A 30 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8121 (mt-10) REVERT: A 32 GLN cc_start: 0.8683 (tt0) cc_final: 0.8392 (tt0) REVERT: B 92 ILE cc_start: 0.8895 (mt) cc_final: 0.8668 (mt) REVERT: C 16 THR cc_start: 0.9086 (m) cc_final: 0.8678 (t) REVERT: C 29 ILE cc_start: 0.9133 (mp) cc_final: 0.8917 (mt) REVERT: C 89 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8803 (ttm-80) REVERT: D 71 LEU cc_start: 0.9005 (tp) cc_final: 0.8665 (mp) REVERT: D 125 LYS cc_start: 0.8549 (mttt) cc_final: 0.8328 (mtpp) REVERT: E 37 GLU cc_start: 0.8562 (tt0) cc_final: 0.8358 (mt-10) REVERT: E 45 THR cc_start: 0.7505 (p) cc_final: 0.7129 (t) REVERT: F 168 ASP cc_start: 0.8497 (t0) cc_final: 0.7633 (t0) REVERT: H 27 LYS cc_start: 0.8824 (tttt) cc_final: 0.8601 (mtpp) REVERT: I 16 THR cc_start: 0.9021 (m) cc_final: 0.8745 (t) REVERT: I 24 LYS cc_start: 0.8020 (ptmt) cc_final: 0.7668 (ptmt) REVERT: I 47 GLN cc_start: 0.8968 (tt0) cc_final: 0.8541 (mm-40) REVERT: I 63 LYS cc_start: 0.8627 (tptm) cc_final: 0.8260 (tptt) REVERT: J 30 GLN cc_start: 0.8882 (tt0) cc_final: 0.8617 (tt0) REVERT: J 45 ASN cc_start: 0.8879 (m-40) cc_final: 0.8590 (m-40) REVERT: J 68 SER cc_start: 0.9103 (p) cc_final: 0.8317 (p) REVERT: J 69 ASP cc_start: 0.8325 (t0) cc_final: 0.7872 (p0) REVERT: J 71 LEU cc_start: 0.8650 (tp) cc_final: 0.8381 (mp) REVERT: J 79 LYS cc_start: 0.8532 (tptp) cc_final: 0.7829 (ttpt) REVERT: J 105 GLN cc_start: 0.8079 (tt0) cc_final: 0.7727 (mt0) REVERT: J 114 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: K 37 GLU cc_start: 0.8466 (tt0) cc_final: 0.8114 (tt0) REVERT: K 40 THR cc_start: 0.8710 (p) cc_final: 0.8359 (t) REVERT: K 46 MET cc_start: 0.4456 (ttt) cc_final: 0.2819 (tpt) REVERT: K 111 GLN cc_start: 0.9292 (pt0) cc_final: 0.8386 (pt0) REVERT: K 157 THR cc_start: 0.8591 (p) cc_final: 0.8291 (t) REVERT: L 168 ASP cc_start: 0.8576 (t0) cc_final: 0.7981 (t0) REVERT: M 16 GLU cc_start: 0.8042 (mp0) cc_final: 0.7689 (mp0) REVERT: M 32 GLN cc_start: 0.8766 (tt0) cc_final: 0.8024 (tt0) REVERT: M 87 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8024 (mt-10) REVERT: N 16 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8384 (mm-30) REVERT: N 20 GLU cc_start: 0.8437 (mp0) cc_final: 0.8076 (mp0) REVERT: N 44 ILE cc_start: 0.8934 (mp) cc_final: 0.8666 (mt) REVERT: O 24 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7665 (ptmt) REVERT: P 12 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8226 (t80) REVERT: P 13 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8348 (mt-10) REVERT: P 30 GLN cc_start: 0.8768 (tt0) cc_final: 0.8343 (tt0) REVERT: P 66 SER cc_start: 0.8892 (t) cc_final: 0.8687 (p) REVERT: P 69 ASP cc_start: 0.8014 (t0) cc_final: 0.7689 (p0) REVERT: P 79 LYS cc_start: 0.8557 (tptp) cc_final: 0.7818 (ttpt) REVERT: P 125 LYS cc_start: 0.8778 (mttt) cc_final: 0.8540 (mtpp) REVERT: Q 40 THR cc_start: 0.8801 (p) cc_final: 0.8429 (t) REVERT: Q 41 ASP cc_start: 0.6710 (m-30) cc_final: 0.6416 (m-30) REVERT: Q 46 MET cc_start: 0.3308 (ttt) cc_final: 0.2683 (tpt) REVERT: S 17 LYS cc_start: 0.9017 (mttt) cc_final: 0.8676 (mtpt) REVERT: S 30 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8095 (mt-10) REVERT: S 32 GLN cc_start: 0.8687 (tt0) cc_final: 0.8374 (tt0) REVERT: T 92 ILE cc_start: 0.8895 (mt) cc_final: 0.8665 (mt) REVERT: U 16 THR cc_start: 0.9093 (m) cc_final: 0.8690 (t) REVERT: U 29 ILE cc_start: 0.9126 (mp) cc_final: 0.8912 (mt) REVERT: U 89 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8804 (ttm-80) REVERT: V 71 LEU cc_start: 0.9016 (tp) cc_final: 0.8679 (mp) REVERT: V 125 LYS cc_start: 0.8531 (mttt) cc_final: 0.8316 (mtpp) REVERT: W 37 GLU cc_start: 0.8586 (tt0) cc_final: 0.8375 (mt-10) REVERT: W 45 THR cc_start: 0.7470 (p) cc_final: 0.7083 (t) REVERT: X 168 ASP cc_start: 0.8490 (t0) cc_final: 0.7623 (t0) REVERT: Z 27 LYS cc_start: 0.8823 (tttt) cc_final: 0.8600 (mtpp) REVERT: 0 16 THR cc_start: 0.9027 (m) cc_final: 0.8751 (t) REVERT: 0 24 LYS cc_start: 0.8019 (ptmt) cc_final: 0.7674 (ptmt) REVERT: 0 47 GLN cc_start: 0.8966 (tt0) cc_final: 0.8541 (mm-40) REVERT: 0 63 LYS cc_start: 0.8633 (tptm) cc_final: 0.8270 (tptt) REVERT: 1 30 GLN cc_start: 0.8892 (tt0) cc_final: 0.8630 (tt0) REVERT: 1 45 ASN cc_start: 0.8872 (m-40) cc_final: 0.8584 (m-40) REVERT: 1 68 SER cc_start: 0.9098 (p) cc_final: 0.8342 (p) REVERT: 1 69 ASP cc_start: 0.8321 (t0) cc_final: 0.7880 (p0) REVERT: 1 71 LEU cc_start: 0.8654 (tp) cc_final: 0.8392 (mp) REVERT: 1 79 LYS cc_start: 0.8521 (tptp) cc_final: 0.7818 (ttpt) REVERT: 1 105 GLN cc_start: 0.8088 (tt0) cc_final: 0.7739 (mt0) REVERT: 1 114 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: 2 37 GLU cc_start: 0.8477 (tt0) cc_final: 0.8126 (tt0) REVERT: 2 40 THR cc_start: 0.8710 (p) cc_final: 0.8364 (t) REVERT: 2 46 MET cc_start: 0.4477 (ttt) cc_final: 0.2836 (tpt) REVERT: 2 111 GLN cc_start: 0.9300 (pt0) cc_final: 0.8379 (pt0) REVERT: 2 157 THR cc_start: 0.8589 (p) cc_final: 0.8287 (t) REVERT: 3 168 ASP cc_start: 0.8580 (t0) cc_final: 0.7990 (t0) REVERT: 4 16 GLU cc_start: 0.8044 (mp0) cc_final: 0.7689 (mp0) REVERT: 4 32 GLN cc_start: 0.8765 (tt0) cc_final: 0.8027 (tt0) REVERT: 4 87 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8037 (mt-10) REVERT: 5 16 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8386 (mm-30) REVERT: 5 20 GLU cc_start: 0.8439 (mp0) cc_final: 0.8080 (mp0) REVERT: 5 44 ILE cc_start: 0.8935 (mp) cc_final: 0.8668 (mt) REVERT: 6 24 LYS cc_start: 0.8142 (ptmt) cc_final: 0.7671 (ptmt) REVERT: 7 12 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8233 (t80) REVERT: 7 13 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8345 (mt-10) REVERT: 7 30 GLN cc_start: 0.8776 (tt0) cc_final: 0.8344 (tt0) REVERT: 7 66 SER cc_start: 0.8892 (t) cc_final: 0.8688 (p) REVERT: 7 69 ASP cc_start: 0.8014 (t0) cc_final: 0.7697 (p0) REVERT: 7 79 LYS cc_start: 0.8541 (tptp) cc_final: 0.7801 (ttpt) REVERT: 7 125 LYS cc_start: 0.8770 (mttt) cc_final: 0.8542 (mtpp) REVERT: 8 40 THR cc_start: 0.8802 (p) cc_final: 0.8434 (t) REVERT: 8 41 ASP cc_start: 0.6721 (m-30) cc_final: 0.6431 (m-30) REVERT: 8 46 MET cc_start: 0.3294 (ttt) cc_final: 0.2666 (tpt) outliers start: 64 outliers final: 40 residues processed: 918 average time/residue: 0.1780 time to fit residues: 255.5507 Evaluate side-chains 864 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 820 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain Q residue 157 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 87 GLU Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Chi-restraints excluded: chain 8 residue 157 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 204 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN V 117 HIS 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087929 restraints weight = 41400.251| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.24 r_work: 0.2855 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29442 Z= 0.222 Angle : 0.605 7.797 39684 Z= 0.331 Chirality : 0.044 0.149 4302 Planarity : 0.004 0.041 5190 Dihedral : 6.056 85.798 3924 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.04 % Allowed : 13.15 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.14), residues: 3486 helix: 1.12 (0.17), residues: 918 sheet: -0.02 (0.14), residues: 1224 loop : 0.31 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 76 TYR 0.020 0.002 TYR J 8 PHE 0.014 0.002 PHE K 110 TRP 0.010 0.001 TRP W 89 HIS 0.005 0.001 HIS 1 74 Details of bonding type rmsd covalent geometry : bond 0.00538 (29442) covalent geometry : angle 0.60510 (39684) hydrogen bonds : bond 0.04506 ( 1302) hydrogen bonds : angle 4.62585 ( 3942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 797 time to evaluate : 0.843 Fit side-chains REVERT: A 17 LYS cc_start: 0.9088 (mttt) cc_final: 0.8707 (mtpt) REVERT: A 27 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8649 (ttpt) REVERT: A 30 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 16 THR cc_start: 0.9174 (m) cc_final: 0.8796 (p) REVERT: C 29 ILE cc_start: 0.9083 (mp) cc_final: 0.8860 (mt) REVERT: C 89 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8833 (ttm-80) REVERT: D 114 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: D 125 LYS cc_start: 0.8666 (mttt) cc_final: 0.8365 (mtpp) REVERT: E 37 GLU cc_start: 0.8616 (tt0) cc_final: 0.8342 (mt-10) REVERT: E 46 MET cc_start: 0.3403 (tpt) cc_final: 0.2913 (tpt) REVERT: F 168 ASP cc_start: 0.8505 (t0) cc_final: 0.7493 (t0) REVERT: H 19 ASP cc_start: 0.8922 (m-30) cc_final: 0.8707 (m-30) REVERT: I 16 THR cc_start: 0.9060 (m) cc_final: 0.8671 (t) REVERT: I 47 GLN cc_start: 0.9060 (tt0) cc_final: 0.8658 (mm-40) REVERT: I 63 LYS cc_start: 0.8655 (tptm) cc_final: 0.8295 (tptt) REVERT: I 98 GLU cc_start: 0.8882 (tt0) cc_final: 0.8590 (tt0) REVERT: J 30 GLN cc_start: 0.8943 (tt0) cc_final: 0.8665 (tt0) REVERT: J 68 SER cc_start: 0.9052 (p) cc_final: 0.8451 (p) REVERT: J 71 LEU cc_start: 0.8790 (tp) cc_final: 0.8438 (mp) REVERT: J 79 LYS cc_start: 0.8517 (tptp) cc_final: 0.7798 (ttpt) REVERT: J 105 GLN cc_start: 0.8155 (tt0) cc_final: 0.7665 (mt0) REVERT: J 114 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: K 37 GLU cc_start: 0.8559 (tt0) cc_final: 0.8189 (tt0) REVERT: K 40 THR cc_start: 0.8659 (p) cc_final: 0.8382 (t) REVERT: K 46 MET cc_start: 0.4322 (ttt) cc_final: 0.2878 (tpt) REVERT: K 157 THR cc_start: 0.8670 (p) cc_final: 0.8312 (t) REVERT: L 168 ASP cc_start: 0.8619 (t0) cc_final: 0.8023 (t0) REVERT: M 16 GLU cc_start: 0.8054 (mp0) cc_final: 0.7843 (mp0) REVERT: M 30 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8065 (mt-10) REVERT: M 32 GLN cc_start: 0.8762 (tt0) cc_final: 0.8086 (tt0) REVERT: N 44 ILE cc_start: 0.8929 (mp) cc_final: 0.8642 (mt) REVERT: N 93 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8250 (m-30) REVERT: P 12 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8076 (t80) REVERT: P 13 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8395 (mt-10) REVERT: P 66 SER cc_start: 0.8959 (t) cc_final: 0.8697 (p) REVERT: P 69 ASP cc_start: 0.7733 (t0) cc_final: 0.7439 (p0) REVERT: P 79 LYS cc_start: 0.8619 (tptp) cc_final: 0.7887 (ttpt) REVERT: P 80 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8062 (ttp-170) REVERT: P 125 LYS cc_start: 0.8632 (mttt) cc_final: 0.8390 (mtpp) REVERT: Q 40 THR cc_start: 0.8839 (p) cc_final: 0.8508 (t) REVERT: Q 45 THR cc_start: 0.6268 (m) cc_final: 0.5824 (p) REVERT: Q 46 MET cc_start: 0.3483 (ttt) cc_final: 0.2766 (tpt) REVERT: S 17 LYS cc_start: 0.9095 (mttt) cc_final: 0.8718 (mtpt) REVERT: S 27 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8654 (ttpt) REVERT: S 30 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8069 (mt-10) REVERT: U 16 THR cc_start: 0.9166 (m) cc_final: 0.8782 (p) REVERT: U 29 ILE cc_start: 0.9081 (mp) cc_final: 0.8862 (mt) REVERT: U 81 LYS cc_start: 0.8857 (tttt) cc_final: 0.8462 (tttm) REVERT: U 89 ARG cc_start: 0.9117 (ttm-80) cc_final: 0.8821 (ttm-80) REVERT: V 114 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: V 125 LYS cc_start: 0.8668 (mttt) cc_final: 0.8361 (mtpp) REVERT: W 37 GLU cc_start: 0.8628 (tt0) cc_final: 0.8350 (mt-10) REVERT: W 46 MET cc_start: 0.3393 (tpt) cc_final: 0.2901 (tpt) REVERT: X 168 ASP cc_start: 0.8496 (t0) cc_final: 0.7480 (t0) REVERT: Z 19 ASP cc_start: 0.8928 (m-30) cc_final: 0.8711 (m-30) REVERT: 0 16 THR cc_start: 0.9057 (m) cc_final: 0.8662 (t) REVERT: 0 47 GLN cc_start: 0.9057 (tt0) cc_final: 0.8662 (mm-40) REVERT: 0 63 LYS cc_start: 0.8653 (tptm) cc_final: 0.8297 (tptt) REVERT: 0 98 GLU cc_start: 0.8877 (tt0) cc_final: 0.8586 (tt0) REVERT: 1 30 GLN cc_start: 0.8941 (tt0) cc_final: 0.8655 (tt0) REVERT: 1 68 SER cc_start: 0.9047 (p) cc_final: 0.8443 (p) REVERT: 1 71 LEU cc_start: 0.8793 (tp) cc_final: 0.8442 (mp) REVERT: 1 79 LYS cc_start: 0.8510 (tptp) cc_final: 0.7790 (ttpt) REVERT: 1 105 GLN cc_start: 0.8149 (tt0) cc_final: 0.7668 (mt0) REVERT: 1 114 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: 2 37 GLU cc_start: 0.8557 (tt0) cc_final: 0.8186 (tt0) REVERT: 2 40 THR cc_start: 0.8666 (p) cc_final: 0.8387 (t) REVERT: 2 46 MET cc_start: 0.4345 (ttt) cc_final: 0.2893 (tpt) REVERT: 2 157 THR cc_start: 0.8667 (p) cc_final: 0.8308 (t) REVERT: 3 168 ASP cc_start: 0.8621 (t0) cc_final: 0.8035 (t0) REVERT: 4 16 GLU cc_start: 0.8063 (mp0) cc_final: 0.7854 (mp0) REVERT: 4 30 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8074 (mt-10) REVERT: 4 32 GLN cc_start: 0.8773 (tt0) cc_final: 0.8104 (tt0) REVERT: 4 87 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8114 (mt-10) REVERT: 5 44 ILE cc_start: 0.8934 (mp) cc_final: 0.8649 (mt) REVERT: 5 93 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: 7 12 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8085 (t80) REVERT: 7 13 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8384 (mt-10) REVERT: 7 66 SER cc_start: 0.8959 (t) cc_final: 0.8698 (p) REVERT: 7 69 ASP cc_start: 0.7725 (t0) cc_final: 0.7432 (p0) REVERT: 7 79 LYS cc_start: 0.8629 (tptp) cc_final: 0.7897 (ttpt) REVERT: 7 80 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.8076 (ttp-170) REVERT: 7 125 LYS cc_start: 0.8607 (mttt) cc_final: 0.8375 (mtpp) REVERT: 8 40 THR cc_start: 0.8834 (p) cc_final: 0.8513 (t) REVERT: 8 45 THR cc_start: 0.6225 (m) cc_final: 0.5786 (p) REVERT: 8 46 MET cc_start: 0.3459 (ttt) cc_final: 0.2746 (tpt) outliers start: 97 outliers final: 77 residues processed: 825 average time/residue: 0.1766 time to fit residues: 224.7629 Evaluate side-chains 826 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 741 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 114 GLU Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 70 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 61 SER Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 93 ASP Chi-restraints excluded: chain 6 residue 30 THR Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 98 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 334 optimal weight: 8.9990 chunk 339 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS 0 76 ASN ** 6 76 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 = 0.3274 r_free = 0.3274 target = 0.109307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.092066 restraints weight = 40313.895| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.17 r_work: 0.2904 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29442 Z= 0.172 Angle : 0.549 7.550 39684 Z= 0.299 Chirality : 0.042 0.142 4302 Planarity : 0.004 0.040 5190 Dihedral : 5.765 87.446 3924 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.83 % Allowed : 13.81 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3486 helix: 1.36 (0.17), residues: 918 sheet: -0.09 (0.15), residues: 1224 loop : 0.25 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 10 TYR 0.014 0.001 TYR 1 8 PHE 0.012 0.002 PHE K 110 TRP 0.008 0.001 TRP 2 89 HIS 0.004 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00413 (29442) covalent geometry : angle 0.54890 (39684) hydrogen bonds : bond 0.03990 ( 1302) hydrogen bonds : angle 4.47711 ( 3942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 798 time to evaluate : 1.037 Fit side-chains REVERT: A 17 LYS cc_start: 0.9105 (mttt) cc_final: 0.8698 (mtpt) REVERT: A 27 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8702 (ttpt) REVERT: A 30 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8150 (mt-10) REVERT: A 97 ASN cc_start: 0.6489 (m-40) cc_final: 0.6174 (m-40) REVERT: C 16 THR cc_start: 0.9211 (m) cc_final: 0.8862 (p) REVERT: C 29 ILE cc_start: 0.9069 (mp) cc_final: 0.8861 (mt) REVERT: C 89 ARG cc_start: 0.9160 (ttm-80) cc_final: 0.8891 (ttm-80) REVERT: C 98 GLU cc_start: 0.8954 (tt0) cc_final: 0.8649 (tt0) REVERT: D 39 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8870 (mt) REVERT: D 125 LYS cc_start: 0.8694 (mttt) cc_final: 0.8439 (mtpp) REVERT: E 37 GLU cc_start: 0.8638 (tt0) cc_final: 0.8366 (mt-10) REVERT: E 46 MET cc_start: 0.3666 (tpt) cc_final: 0.3241 (tpt) REVERT: E 52 THR cc_start: 0.6815 (OUTLIER) cc_final: 0.6477 (p) REVERT: F 168 ASP cc_start: 0.8522 (t0) cc_final: 0.7580 (t0) REVERT: H 19 ASP cc_start: 0.8882 (m-30) cc_final: 0.8676 (m-30) REVERT: H 40 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: H 94 ASN cc_start: 0.8701 (m-40) cc_final: 0.8308 (m110) REVERT: I 10 GLN cc_start: 0.9089 (mt0) cc_final: 0.8769 (mt0) REVERT: I 16 THR cc_start: 0.9025 (m) cc_final: 0.8662 (t) REVERT: I 47 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8699 (mm-40) REVERT: I 63 LYS cc_start: 0.8673 (tptm) cc_final: 0.8337 (tptt) REVERT: J 30 GLN cc_start: 0.8925 (tt0) cc_final: 0.8618 (tt0) REVERT: J 68 SER cc_start: 0.9091 (p) cc_final: 0.8377 (p) REVERT: J 69 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7806 (p0) REVERT: J 71 LEU cc_start: 0.8922 (tp) cc_final: 0.8487 (mp) REVERT: J 79 LYS cc_start: 0.8587 (tptp) cc_final: 0.7874 (ttpt) REVERT: J 105 GLN cc_start: 0.8126 (tt0) cc_final: 0.7671 (mt0) REVERT: J 114 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: K 37 GLU cc_start: 0.8567 (tt0) cc_final: 0.8195 (tt0) REVERT: K 40 THR cc_start: 0.8726 (p) cc_final: 0.8425 (t) REVERT: K 46 MET cc_start: 0.4231 (ttt) cc_final: 0.2992 (tpt) REVERT: K 111 GLN cc_start: 0.9315 (pt0) cc_final: 0.8427 (pt0) REVERT: K 157 THR cc_start: 0.8719 (p) cc_final: 0.8359 (t) REVERT: L 168 ASP cc_start: 0.8618 (t0) cc_final: 0.8199 (t0) REVERT: M 16 GLU cc_start: 0.8153 (mp0) cc_final: 0.7872 (mp0) REVERT: M 32 GLN cc_start: 0.8790 (tt0) cc_final: 0.8135 (tt0) REVERT: N 44 ILE cc_start: 0.8929 (mp) cc_final: 0.8627 (mt) REVERT: O 24 LYS cc_start: 0.8312 (ptmt) cc_final: 0.8015 (ptmt) REVERT: O 63 LYS cc_start: 0.8529 (tttm) cc_final: 0.8297 (tttt) REVERT: P 1 MET cc_start: 0.8830 (mtp) cc_final: 0.8490 (mtm) REVERT: P 12 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8068 (t80) REVERT: P 13 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8314 (mt-10) REVERT: P 30 GLN cc_start: 0.8834 (tt0) cc_final: 0.8345 (tt0) REVERT: P 79 LYS cc_start: 0.8685 (tptp) cc_final: 0.7963 (ttpt) REVERT: P 80 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8125 (ttp-170) REVERT: Q 40 THR cc_start: 0.8786 (p) cc_final: 0.8524 (t) REVERT: Q 45 THR cc_start: 0.6382 (m) cc_final: 0.5894 (p) REVERT: Q 46 MET cc_start: 0.3687 (ttt) cc_final: 0.2885 (tpt) REVERT: Q 132 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8689 (tt0) REVERT: S 17 LYS cc_start: 0.9125 (mttt) cc_final: 0.8729 (mtpt) REVERT: S 27 LYS cc_start: 0.9052 (ttmt) cc_final: 0.8697 (ttpt) REVERT: S 30 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8141 (mt-10) REVERT: S 97 ASN cc_start: 0.6506 (m-40) cc_final: 0.6190 (m-40) REVERT: U 16 THR cc_start: 0.9209 (m) cc_final: 0.8858 (p) REVERT: U 29 ILE cc_start: 0.9059 (mp) cc_final: 0.8850 (mt) REVERT: U 89 ARG cc_start: 0.9146 (ttm-80) cc_final: 0.8881 (ttm-80) REVERT: U 98 GLU cc_start: 0.8948 (tt0) cc_final: 0.8647 (tt0) REVERT: V 39 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8877 (mt) REVERT: V 125 LYS cc_start: 0.8692 (mttt) cc_final: 0.8434 (mtpp) REVERT: W 37 GLU cc_start: 0.8634 (tt0) cc_final: 0.8360 (mt-10) REVERT: W 46 MET cc_start: 0.3710 (tpt) cc_final: 0.3297 (tpt) REVERT: W 52 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6476 (p) REVERT: X 168 ASP cc_start: 0.8518 (t0) cc_final: 0.7573 (t0) REVERT: Z 19 ASP cc_start: 0.8886 (m-30) cc_final: 0.8678 (m-30) REVERT: Z 40 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: Z 94 ASN cc_start: 0.8708 (m-40) cc_final: 0.8325 (m110) REVERT: 0 10 GLN cc_start: 0.9087 (mt0) cc_final: 0.8764 (mt0) REVERT: 0 16 THR cc_start: 0.9018 (m) cc_final: 0.8649 (t) REVERT: 0 47 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8697 (mm-40) REVERT: 0 63 LYS cc_start: 0.8674 (tptm) cc_final: 0.8339 (tptt) REVERT: 1 30 GLN cc_start: 0.8926 (tt0) cc_final: 0.8619 (tt0) REVERT: 1 68 SER cc_start: 0.9086 (p) cc_final: 0.8385 (p) REVERT: 1 69 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7816 (p0) REVERT: 1 71 LEU cc_start: 0.8933 (tp) cc_final: 0.8497 (mp) REVERT: 1 79 LYS cc_start: 0.8598 (tptp) cc_final: 0.7886 (ttpt) REVERT: 1 105 GLN cc_start: 0.8127 (tt0) cc_final: 0.7677 (mt0) REVERT: 1 114 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: 2 37 GLU cc_start: 0.8577 (tt0) cc_final: 0.8205 (tt0) REVERT: 2 40 THR cc_start: 0.8733 (p) cc_final: 0.8427 (t) REVERT: 2 46 MET cc_start: 0.4251 (ttt) cc_final: 0.3000 (tpt) REVERT: 2 111 GLN cc_start: 0.9315 (pt0) cc_final: 0.8419 (pt0) REVERT: 2 157 THR cc_start: 0.8708 (p) cc_final: 0.8347 (t) REVERT: 3 168 ASP cc_start: 0.8612 (t0) cc_final: 0.8196 (t0) REVERT: 4 16 GLU cc_start: 0.8144 (mp0) cc_final: 0.7864 (mp0) REVERT: 4 32 GLN cc_start: 0.8801 (tt0) cc_final: 0.8146 (tt0) REVERT: 4 51 MET cc_start: 0.9360 (mtt) cc_final: 0.9157 (mtt) REVERT: 4 87 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8002 (mt-10) REVERT: 5 44 ILE cc_start: 0.8927 (mp) cc_final: 0.8621 (mt) REVERT: 6 24 LYS cc_start: 0.8317 (ptmt) cc_final: 0.8019 (ptmt) REVERT: 6 63 LYS cc_start: 0.8535 (tttm) cc_final: 0.8305 (tttt) REVERT: 7 1 MET cc_start: 0.8833 (mtp) cc_final: 0.8489 (mtm) REVERT: 7 12 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8086 (t80) REVERT: 7 13 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8320 (mt-10) REVERT: 7 30 GLN cc_start: 0.8842 (tt0) cc_final: 0.8352 (tt0) REVERT: 7 69 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7601 (p0) REVERT: 7 79 LYS cc_start: 0.8695 (tptp) cc_final: 0.7972 (ttpt) REVERT: 7 80 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8121 (ttp-170) REVERT: 8 40 THR cc_start: 0.8781 (p) cc_final: 0.8522 (t) REVERT: 8 45 THR cc_start: 0.6366 (m) cc_final: 0.5883 (p) REVERT: 8 46 MET cc_start: 0.3691 (ttt) cc_final: 0.2891 (tpt) REVERT: 8 132 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8684 (tt0) outliers start: 122 outliers final: 80 residues processed: 844 average time/residue: 0.1691 time to fit residues: 223.2284 Evaluate side-chains 829 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 734 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 110 PHE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 110 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 19 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 287 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 292 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.089923 restraints weight = 41022.036| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.20 r_work: 0.2872 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29442 Z= 0.199 Angle : 0.557 6.239 39684 Z= 0.303 Chirality : 0.043 0.136 4302 Planarity : 0.004 0.032 5190 Dihedral : 5.705 86.397 3924 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.05 % Allowed : 14.38 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.14), residues: 3486 helix: 1.42 (0.17), residues: 918 sheet: -0.24 (0.15), residues: 1224 loop : 0.18 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 8 94 TYR 0.017 0.002 TYR J 8 PHE 0.014 0.002 PHE K 110 TRP 0.007 0.001 TRP 8 89 HIS 0.004 0.001 HIS 1 117 Details of bonding type rmsd covalent geometry : bond 0.00481 (29442) covalent geometry : angle 0.55717 (39684) hydrogen bonds : bond 0.04022 ( 1302) hydrogen bonds : angle 4.50325 ( 3942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 750 time to evaluate : 1.035 Fit side-chains REVERT: A 17 LYS cc_start: 0.9121 (mttt) cc_final: 0.8699 (mtpt) REVERT: A 27 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8736 (ttpt) REVERT: A 30 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 41 VAL cc_start: 0.8773 (t) cc_final: 0.8451 (m) REVERT: C 16 THR cc_start: 0.9212 (m) cc_final: 0.8880 (p) REVERT: C 89 ARG cc_start: 0.9180 (ttm-80) cc_final: 0.8917 (ttm-80) REVERT: C 98 GLU cc_start: 0.8850 (tt0) cc_final: 0.8548 (tt0) REVERT: D 39 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8842 (mt) REVERT: D 90 LYS cc_start: 0.8811 (tptm) cc_final: 0.8499 (tptp) REVERT: D 125 LYS cc_start: 0.8796 (mttt) cc_final: 0.8536 (mtpp) REVERT: E 46 MET cc_start: 0.3470 (tpt) cc_final: 0.2680 (tpt) REVERT: E 52 THR cc_start: 0.6858 (OUTLIER) cc_final: 0.6546 (p) REVERT: E 94 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8764 (mmm160) REVERT: F 168 ASP cc_start: 0.8458 (t0) cc_final: 0.7495 (t0) REVERT: H 94 ASN cc_start: 0.8764 (m-40) cc_final: 0.8014 (m110) REVERT: I 10 GLN cc_start: 0.9103 (mt0) cc_final: 0.8776 (mt0) REVERT: I 13 GLN cc_start: 0.8380 (mt0) cc_final: 0.8159 (mt0) REVERT: I 16 THR cc_start: 0.9023 (m) cc_final: 0.8636 (t) REVERT: I 47 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8693 (mm-40) REVERT: I 63 LYS cc_start: 0.8707 (tptm) cc_final: 0.8380 (tptt) REVERT: J 13 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8604 (mt-10) REVERT: J 30 GLN cc_start: 0.8961 (tt0) cc_final: 0.8687 (tt0) REVERT: J 68 SER cc_start: 0.9115 (p) cc_final: 0.8412 (p) REVERT: J 69 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8000 (p0) REVERT: J 79 LYS cc_start: 0.8620 (tptp) cc_final: 0.7853 (ttpt) REVERT: J 105 GLN cc_start: 0.8403 (tt0) cc_final: 0.7759 (mt0) REVERT: J 114 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: K 40 THR cc_start: 0.8725 (p) cc_final: 0.8418 (t) REVERT: K 46 MET cc_start: 0.4356 (ttt) cc_final: 0.3219 (tpt) REVERT: K 157 THR cc_start: 0.8723 (p) cc_final: 0.8361 (t) REVERT: L 168 ASP cc_start: 0.8621 (t0) cc_final: 0.8176 (t0) REVERT: M 16 GLU cc_start: 0.8135 (mp0) cc_final: 0.7855 (mp0) REVERT: M 32 GLN cc_start: 0.8764 (tt0) cc_final: 0.8128 (tt0) REVERT: M 50 TYR cc_start: 0.9235 (p90) cc_final: 0.8969 (p90) REVERT: M 51 MET cc_start: 0.9313 (mtt) cc_final: 0.9080 (mtt) REVERT: N 44 ILE cc_start: 0.8943 (mp) cc_final: 0.8630 (mt) REVERT: O 24 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8161 (ptmt) REVERT: O 63 LYS cc_start: 0.8542 (tttm) cc_final: 0.8332 (tttt) REVERT: P 1 MET cc_start: 0.8867 (mtp) cc_final: 0.8552 (mtm) REVERT: P 12 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8237 (t80) REVERT: P 13 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8322 (mt-10) REVERT: P 15 LEU cc_start: 0.9079 (mt) cc_final: 0.8728 (mm) REVERT: P 30 GLN cc_start: 0.8843 (tt0) cc_final: 0.8384 (tt0) REVERT: P 79 LYS cc_start: 0.8680 (tptp) cc_final: 0.7964 (ttpt) REVERT: P 80 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.8155 (ttp-170) REVERT: Q 40 THR cc_start: 0.8817 (p) cc_final: 0.8543 (t) REVERT: Q 45 THR cc_start: 0.6578 (m) cc_final: 0.6073 (p) REVERT: Q 46 MET cc_start: 0.3709 (ttt) cc_final: 0.2981 (tpt) REVERT: S 17 LYS cc_start: 0.9138 (mttt) cc_final: 0.8719 (mtpt) REVERT: S 27 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8725 (ttpt) REVERT: S 30 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8152 (mt-10) REVERT: T 41 VAL cc_start: 0.8793 (t) cc_final: 0.8471 (m) REVERT: U 16 THR cc_start: 0.9212 (m) cc_final: 0.8870 (p) REVERT: U 89 ARG cc_start: 0.9161 (ttm-80) cc_final: 0.8907 (ttm-80) REVERT: U 98 GLU cc_start: 0.8830 (tt0) cc_final: 0.8529 (tt0) REVERT: V 39 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8849 (mt) REVERT: V 90 LYS cc_start: 0.8820 (tptm) cc_final: 0.8503 (tptp) REVERT: V 125 LYS cc_start: 0.8765 (mttt) cc_final: 0.8509 (mtpp) REVERT: W 46 MET cc_start: 0.3415 (tpt) cc_final: 0.2647 (tpt) REVERT: W 52 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6529 (p) REVERT: W 94 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8785 (mmm160) REVERT: X 168 ASP cc_start: 0.8457 (t0) cc_final: 0.7492 (t0) REVERT: Z 94 ASN cc_start: 0.8774 (m-40) cc_final: 0.8038 (m110) REVERT: 0 10 GLN cc_start: 0.9102 (mt0) cc_final: 0.8771 (mt0) REVERT: 0 13 GLN cc_start: 0.8389 (mt0) cc_final: 0.8161 (mt0) REVERT: 0 16 THR cc_start: 0.9014 (m) cc_final: 0.8619 (t) REVERT: 0 47 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8683 (mm-40) REVERT: 0 63 LYS cc_start: 0.8709 (tptm) cc_final: 0.8381 (tptt) REVERT: 1 13 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8603 (mt-10) REVERT: 1 30 GLN cc_start: 0.8972 (tt0) cc_final: 0.8695 (tt0) REVERT: 1 68 SER cc_start: 0.9108 (p) cc_final: 0.8414 (p) REVERT: 1 69 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8005 (p0) REVERT: 1 79 LYS cc_start: 0.8621 (tptp) cc_final: 0.7850 (ttpt) REVERT: 1 105 GLN cc_start: 0.8394 (tt0) cc_final: 0.7762 (mt0) REVERT: 1 114 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: 2 40 THR cc_start: 0.8728 (p) cc_final: 0.8423 (t) REVERT: 2 46 MET cc_start: 0.4359 (ttt) cc_final: 0.3221 (tpt) REVERT: 2 157 THR cc_start: 0.8720 (p) cc_final: 0.8354 (t) REVERT: 3 168 ASP cc_start: 0.8610 (t0) cc_final: 0.8164 (t0) REVERT: 4 16 GLU cc_start: 0.8134 (mp0) cc_final: 0.7850 (mp0) REVERT: 4 32 GLN cc_start: 0.8765 (tt0) cc_final: 0.8102 (tt0) REVERT: 4 50 TYR cc_start: 0.9258 (p90) cc_final: 0.8973 (p90) REVERT: 4 87 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8137 (mt-10) REVERT: 5 44 ILE cc_start: 0.8946 (mp) cc_final: 0.8630 (mt) REVERT: 6 24 LYS cc_start: 0.8338 (ptmt) cc_final: 0.8133 (ptmt) REVERT: 6 63 LYS cc_start: 0.8552 (tttm) cc_final: 0.8345 (tttt) REVERT: 7 1 MET cc_start: 0.8889 (mtp) cc_final: 0.8576 (mtm) REVERT: 7 12 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8249 (t80) REVERT: 7 13 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8336 (mt-10) REVERT: 7 15 LEU cc_start: 0.9070 (mt) cc_final: 0.8724 (mm) REVERT: 7 30 GLN cc_start: 0.8844 (tt0) cc_final: 0.8389 (tt0) REVERT: 7 69 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7591 (p0) REVERT: 7 79 LYS cc_start: 0.8692 (tptp) cc_final: 0.7972 (ttpt) REVERT: 7 80 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8146 (ttp-170) REVERT: 8 40 THR cc_start: 0.8812 (p) cc_final: 0.8543 (t) REVERT: 8 45 THR cc_start: 0.6555 (m) cc_final: 0.6053 (p) REVERT: 8 46 MET cc_start: 0.3705 (ttt) cc_final: 0.2970 (tpt) outliers start: 129 outliers final: 106 residues processed: 797 average time/residue: 0.1733 time to fit residues: 216.7224 Evaluate side-chains 839 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 718 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 31 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain Q residue 110 PHE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 15 ASP Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 61 SER Chi-restraints excluded: chain 2 residue 74 ASP Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 39 ILE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 7 residue 126 THR Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 29 LEU Chi-restraints excluded: chain 8 residue 61 SER Chi-restraints excluded: chain 8 residue 110 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 305 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 201 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 256 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 ASN J 117 HIS ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 76 ASN 1 117 HIS 6 26 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087311 restraints weight = 41502.438| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.27 r_work: 0.2909 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29442 Z= 0.168 Angle : 0.528 6.054 39684 Z= 0.287 Chirality : 0.042 0.130 4302 Planarity : 0.004 0.033 5190 Dihedral : 5.543 84.539 3924 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.24 % Allowed : 15.19 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3486 helix: 1.59 (0.17), residues: 918 sheet: -0.46 (0.15), residues: 1140 loop : 0.17 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 160 TYR 0.014 0.001 TYR D 124 PHE 0.012 0.001 PHE K 110 TRP 0.007 0.001 TRP 8 89 HIS 0.004 0.001 HIS J 117 Details of bonding type rmsd covalent geometry : bond 0.00405 (29442) covalent geometry : angle 0.52813 (39684) hydrogen bonds : bond 0.03767 ( 1302) hydrogen bonds : angle 4.44058 ( 3942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 748 time to evaluate : 0.880 Fit side-chains REVERT: A 17 LYS cc_start: 0.9127 (mttt) cc_final: 0.8704 (mtpt) REVERT: A 27 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8710 (ttpt) REVERT: A 30 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 16 THR cc_start: 0.9234 (m) cc_final: 0.8916 (p) REVERT: C 89 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8887 (ttm-80) REVERT: C 98 GLU cc_start: 0.8926 (tt0) cc_final: 0.8630 (tt0) REVERT: D 39 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 125 LYS cc_start: 0.8753 (mttt) cc_final: 0.8489 (mtpp) REVERT: E 37 GLU cc_start: 0.8626 (tt0) cc_final: 0.8304 (mt-10) REVERT: E 46 MET cc_start: 0.3087 (tpt) cc_final: 0.2340 (tpt) REVERT: E 94 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8719 (mmm160) REVERT: F 168 ASP cc_start: 0.8521 (t0) cc_final: 0.7511 (t0) REVERT: G 50 TYR cc_start: 0.9300 (p90) cc_final: 0.9079 (p90) REVERT: H 6 ASP cc_start: 0.8711 (m-30) cc_final: 0.8508 (m-30) REVERT: H 40 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: I 10 GLN cc_start: 0.9076 (mt0) cc_final: 0.8752 (mt0) REVERT: I 13 GLN cc_start: 0.8361 (mt0) cc_final: 0.8061 (mt0) REVERT: I 16 THR cc_start: 0.9007 (m) cc_final: 0.8591 (t) REVERT: I 47 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8656 (mm-40) REVERT: I 56 ASP cc_start: 0.9066 (t0) cc_final: 0.8845 (t0) REVERT: I 63 LYS cc_start: 0.8635 (tptm) cc_final: 0.8399 (tptt) REVERT: I 76 ASN cc_start: 0.8489 (m-40) cc_final: 0.8241 (m110) REVERT: J 13 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8590 (mt-10) REVERT: J 30 GLN cc_start: 0.8882 (tt0) cc_final: 0.8587 (tt0) REVERT: J 68 SER cc_start: 0.9147 (p) cc_final: 0.8488 (p) REVERT: J 69 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8107 (p0) REVERT: J 79 LYS cc_start: 0.8521 (tptp) cc_final: 0.7712 (ttpt) REVERT: J 105 GLN cc_start: 0.8385 (tt0) cc_final: 0.7788 (mt0) REVERT: J 114 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: K 37 GLU cc_start: 0.8521 (tt0) cc_final: 0.8256 (tt0) REVERT: K 40 THR cc_start: 0.8678 (p) cc_final: 0.8421 (t) REVERT: K 46 MET cc_start: 0.4284 (ttt) cc_final: 0.3200 (tpt) REVERT: K 111 GLN cc_start: 0.9317 (pt0) cc_final: 0.8485 (pt0) REVERT: K 157 THR cc_start: 0.8663 (p) cc_final: 0.8280 (t) REVERT: L 168 ASP cc_start: 0.8614 (t0) cc_final: 0.8141 (t0) REVERT: M 16 GLU cc_start: 0.8156 (mp0) cc_final: 0.7848 (mp0) REVERT: M 32 GLN cc_start: 0.8702 (tt0) cc_final: 0.8115 (tt0) REVERT: M 50 TYR cc_start: 0.9172 (p90) cc_final: 0.8924 (p90) REVERT: N 20 GLU cc_start: 0.8607 (mp0) cc_final: 0.8210 (mp0) REVERT: N 44 ILE cc_start: 0.8896 (mp) cc_final: 0.8575 (mt) REVERT: O 24 LYS cc_start: 0.8363 (ptmt) cc_final: 0.8148 (ptmt) REVERT: O 91 GLU cc_start: 0.8045 (tt0) cc_final: 0.7735 (tt0) REVERT: P 1 MET cc_start: 0.8886 (mtp) cc_final: 0.8612 (mtm) REVERT: P 12 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8192 (t80) REVERT: P 13 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8240 (mt-10) REVERT: P 15 LEU cc_start: 0.8978 (mt) cc_final: 0.8644 (mm) REVERT: P 30 GLN cc_start: 0.8796 (tt0) cc_final: 0.8299 (tt0) REVERT: P 79 LYS cc_start: 0.8595 (tptp) cc_final: 0.7884 (ttpt) REVERT: P 80 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8060 (ttp-170) REVERT: Q 40 THR cc_start: 0.8776 (p) cc_final: 0.8521 (t) REVERT: Q 45 THR cc_start: 0.6483 (m) cc_final: 0.5992 (p) REVERT: Q 46 MET cc_start: 0.3734 (ttt) cc_final: 0.3038 (tpt) REVERT: S 17 LYS cc_start: 0.9142 (mttt) cc_final: 0.8727 (mtpt) REVERT: S 27 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8712 (ttpt) REVERT: S 30 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8073 (mt-10) REVERT: U 16 THR cc_start: 0.9233 (m) cc_final: 0.8907 (p) REVERT: U 89 ARG cc_start: 0.9142 (ttm-80) cc_final: 0.8878 (ttm-80) REVERT: U 98 GLU cc_start: 0.8911 (tt0) cc_final: 0.8618 (tt0) REVERT: V 39 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8815 (mt) REVERT: V 125 LYS cc_start: 0.8732 (mttt) cc_final: 0.8475 (mtpp) REVERT: W 37 GLU cc_start: 0.8643 (tt0) cc_final: 0.8320 (mt-10) REVERT: W 46 MET cc_start: 0.3076 (tpt) cc_final: 0.2374 (tpt) REVERT: W 52 THR cc_start: 0.6753 (OUTLIER) cc_final: 0.6548 (p) REVERT: W 94 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8733 (mmm160) REVERT: X 168 ASP cc_start: 0.8521 (t0) cc_final: 0.7514 (t0) REVERT: Y 50 TYR cc_start: 0.9307 (p90) cc_final: 0.9088 (p90) REVERT: Z 4 LEU cc_start: 0.8568 (tp) cc_final: 0.8364 (tp) REVERT: Z 6 ASP cc_start: 0.8702 (m-30) cc_final: 0.8499 (m-30) REVERT: Z 40 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: 0 10 GLN cc_start: 0.9073 (mt0) cc_final: 0.8747 (mt0) REVERT: 0 13 GLN cc_start: 0.8356 (mt0) cc_final: 0.8050 (mt0) REVERT: 0 16 THR cc_start: 0.9003 (m) cc_final: 0.8580 (t) REVERT: 0 47 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8653 (mm-40) REVERT: 0 56 ASP cc_start: 0.9074 (t0) cc_final: 0.8855 (t0) REVERT: 0 63 LYS cc_start: 0.8637 (tptm) cc_final: 0.8403 (tptt) REVERT: 0 76 ASN cc_start: 0.8485 (m-40) cc_final: 0.8238 (m110) REVERT: 1 13 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8598 (mt-10) REVERT: 1 30 GLN cc_start: 0.8891 (tt0) cc_final: 0.8593 (tt0) REVERT: 1 68 SER cc_start: 0.9143 (p) cc_final: 0.8494 (p) REVERT: 1 69 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8111 (p0) REVERT: 1 79 LYS cc_start: 0.8514 (tptp) cc_final: 0.7702 (ttpt) REVERT: 1 105 GLN cc_start: 0.8379 (tt0) cc_final: 0.7787 (mt0) REVERT: 1 114 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: 2 37 GLU cc_start: 0.8539 (tt0) cc_final: 0.8279 (tt0) REVERT: 2 40 THR cc_start: 0.8675 (p) cc_final: 0.8425 (t) REVERT: 2 46 MET cc_start: 0.4288 (ttt) cc_final: 0.3203 (tpt) REVERT: 2 111 GLN cc_start: 0.9319 (pt0) cc_final: 0.8463 (pt0) REVERT: 2 157 THR cc_start: 0.8654 (p) cc_final: 0.8271 (t) REVERT: 3 168 ASP cc_start: 0.8604 (t0) cc_final: 0.8134 (t0) REVERT: 4 16 GLU cc_start: 0.8173 (mp0) cc_final: 0.7856 (mp0) REVERT: 4 32 GLN cc_start: 0.8695 (tt0) cc_final: 0.8107 (tt0) REVERT: 4 50 TYR cc_start: 0.9219 (p90) cc_final: 0.8929 (p90) REVERT: 5 20 GLU cc_start: 0.8590 (mp0) cc_final: 0.8194 (mp0) REVERT: 5 44 ILE cc_start: 0.8895 (mp) cc_final: 0.8572 (mt) REVERT: 6 91 GLU cc_start: 0.8047 (tt0) cc_final: 0.7743 (tt0) REVERT: 7 1 MET cc_start: 0.8902 (mtp) cc_final: 0.8638 (mtm) REVERT: 7 12 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8211 (t80) REVERT: 7 13 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8261 (mt-10) REVERT: 7 15 LEU cc_start: 0.8987 (mt) cc_final: 0.8657 (mm) REVERT: 7 30 GLN cc_start: 0.8799 (tt0) cc_final: 0.8306 (tt0) REVERT: 7 69 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7621 (p0) REVERT: 7 79 LYS cc_start: 0.8608 (tptp) cc_final: 0.7893 (ttpt) REVERT: 7 80 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8054 (ttp-170) REVERT: 8 40 THR cc_start: 0.8771 (p) cc_final: 0.8515 (t) REVERT: 8 45 THR cc_start: 0.6460 (m) cc_final: 0.5971 (p) REVERT: 8 46 MET cc_start: 0.3730 (ttt) cc_final: 0.3030 (tpt) outliers start: 135 outliers final: 101 residues processed: 805 average time/residue: 0.1728 time to fit residues: 216.6349 Evaluate side-chains 845 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 728 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain Q residue 110 PHE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 39 ILE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 7 residue 125 LYS Chi-restraints excluded: chain 7 residue 126 THR Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Chi-restraints excluded: chain 8 residue 110 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 247 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 18 GLN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.089774 restraints weight = 41161.384| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.24 r_work: 0.2888 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29442 Z= 0.150 Angle : 0.515 5.825 39684 Z= 0.280 Chirality : 0.041 0.127 4302 Planarity : 0.003 0.032 5190 Dihedral : 5.408 82.521 3924 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.17 % Allowed : 16.13 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.15), residues: 3486 helix: 1.79 (0.17), residues: 918 sheet: -0.45 (0.15), residues: 1140 loop : 0.16 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 160 TYR 0.013 0.001 TYR 1 8 PHE 0.012 0.001 PHE E 14 TRP 0.007 0.001 TRP 8 89 HIS 0.003 0.001 HIS P 74 Details of bonding type rmsd covalent geometry : bond 0.00359 (29442) covalent geometry : angle 0.51500 (39684) hydrogen bonds : bond 0.03613 ( 1302) hydrogen bonds : angle 4.39063 ( 3942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 753 time to evaluate : 1.225 Fit side-chains REVERT: A 17 LYS cc_start: 0.9102 (mttt) cc_final: 0.8682 (mtpt) REVERT: A 27 LYS cc_start: 0.9074 (ttmt) cc_final: 0.8715 (ttpt) REVERT: A 30 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 13 GLN cc_start: 0.8166 (mt0) cc_final: 0.7855 (mt0) REVERT: C 16 THR cc_start: 0.9216 (m) cc_final: 0.8917 (p) REVERT: C 89 ARG cc_start: 0.9154 (ttm-80) cc_final: 0.8902 (ttm-80) REVERT: C 98 GLU cc_start: 0.8871 (tt0) cc_final: 0.8581 (tt0) REVERT: D 39 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8831 (mt) REVERT: D 90 LYS cc_start: 0.8830 (tptm) cc_final: 0.8501 (tptp) REVERT: D 99 ASP cc_start: 0.8700 (t70) cc_final: 0.8351 (t0) REVERT: D 125 LYS cc_start: 0.8842 (mttt) cc_final: 0.8506 (mtpp) REVERT: E 37 GLU cc_start: 0.8624 (tt0) cc_final: 0.8315 (mt-10) REVERT: E 46 MET cc_start: 0.3013 (tpt) cc_final: 0.2336 (tpt) REVERT: E 94 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8724 (mmm160) REVERT: F 168 ASP cc_start: 0.8538 (t0) cc_final: 0.7510 (t0) REVERT: H 6 ASP cc_start: 0.8720 (m-30) cc_final: 0.8495 (m-30) REVERT: H 40 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: H 66 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: I 10 GLN cc_start: 0.9077 (mt0) cc_final: 0.8765 (mt0) REVERT: I 13 GLN cc_start: 0.8356 (mt0) cc_final: 0.8068 (mt0) REVERT: I 16 THR cc_start: 0.9004 (m) cc_final: 0.8596 (t) REVERT: I 47 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8643 (mm-40) REVERT: I 56 ASP cc_start: 0.9033 (t0) cc_final: 0.8781 (t0) REVERT: J 13 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8596 (mt-10) REVERT: J 30 GLN cc_start: 0.8906 (tt0) cc_final: 0.8621 (tt0) REVERT: J 68 SER cc_start: 0.9116 (p) cc_final: 0.8438 (p) REVERT: J 69 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8107 (p0) REVERT: J 79 LYS cc_start: 0.8557 (tptp) cc_final: 0.7759 (ttpt) REVERT: J 105 GLN cc_start: 0.8385 (tt0) cc_final: 0.7791 (mt0) REVERT: J 114 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: K 37 GLU cc_start: 0.8482 (tt0) cc_final: 0.8228 (tt0) REVERT: K 40 THR cc_start: 0.8665 (p) cc_final: 0.8436 (t) REVERT: K 46 MET cc_start: 0.3866 (ttt) cc_final: 0.2770 (tpt) REVERT: K 59 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8831 (m) REVERT: K 111 GLN cc_start: 0.9311 (pt0) cc_final: 0.8405 (pt0) REVERT: K 157 THR cc_start: 0.8679 (p) cc_final: 0.8293 (t) REVERT: L 168 ASP cc_start: 0.8634 (t0) cc_final: 0.8188 (t0) REVERT: M 16 GLU cc_start: 0.8146 (mp0) cc_final: 0.7935 (mp0) REVERT: M 32 GLN cc_start: 0.8735 (tt0) cc_final: 0.8099 (tt0) REVERT: M 50 TYR cc_start: 0.9216 (p90) cc_final: 0.8945 (p90) REVERT: N 20 GLU cc_start: 0.8545 (mp0) cc_final: 0.8111 (mp0) REVERT: N 44 ILE cc_start: 0.8913 (mp) cc_final: 0.8595 (mt) REVERT: O 91 GLU cc_start: 0.8042 (tt0) cc_final: 0.7746 (tt0) REVERT: P 1 MET cc_start: 0.8829 (mtp) cc_final: 0.8076 (mtp) REVERT: P 12 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8229 (t80) REVERT: P 13 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8238 (mt-10) REVERT: P 15 LEU cc_start: 0.8969 (mt) cc_final: 0.8643 (mm) REVERT: P 30 GLN cc_start: 0.8802 (tt0) cc_final: 0.8326 (tt0) REVERT: P 52 ASP cc_start: 0.8706 (m-30) cc_final: 0.8460 (m-30) REVERT: P 79 LYS cc_start: 0.8624 (tptp) cc_final: 0.7908 (ttpt) REVERT: P 80 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8094 (ttp-170) REVERT: Q 40 THR cc_start: 0.8823 (p) cc_final: 0.8540 (t) REVERT: Q 45 THR cc_start: 0.6563 (m) cc_final: 0.6036 (p) REVERT: Q 46 MET cc_start: 0.3622 (ttt) cc_final: 0.2957 (tpt) REVERT: Q 132 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8689 (tt0) REVERT: S 17 LYS cc_start: 0.9117 (mttt) cc_final: 0.8698 (mtpt) REVERT: S 27 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8713 (ttpt) REVERT: S 30 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8094 (mt-10) REVERT: U 13 GLN cc_start: 0.8180 (mt0) cc_final: 0.7868 (mt0) REVERT: U 16 THR cc_start: 0.9219 (m) cc_final: 0.8915 (p) REVERT: U 89 ARG cc_start: 0.9145 (ttm-80) cc_final: 0.8896 (ttm-80) REVERT: U 98 GLU cc_start: 0.8855 (tt0) cc_final: 0.8573 (tt0) REVERT: V 39 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8837 (mt) REVERT: V 90 LYS cc_start: 0.8835 (tptm) cc_final: 0.8507 (tptp) REVERT: V 99 ASP cc_start: 0.8669 (t70) cc_final: 0.8307 (t0) REVERT: V 125 LYS cc_start: 0.8818 (mttt) cc_final: 0.8485 (mtpp) REVERT: W 37 GLU cc_start: 0.8635 (tt0) cc_final: 0.8322 (mt-10) REVERT: W 46 MET cc_start: 0.2982 (tpt) cc_final: 0.2329 (tpt) REVERT: W 94 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8737 (mmm160) REVERT: W 111 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.9059 (pt0) REVERT: X 168 ASP cc_start: 0.8535 (t0) cc_final: 0.7502 (t0) REVERT: Z 40 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: Z 66 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: 0 10 GLN cc_start: 0.9077 (mt0) cc_final: 0.8764 (mt0) REVERT: 0 13 GLN cc_start: 0.8361 (mt0) cc_final: 0.8071 (mt0) REVERT: 0 16 THR cc_start: 0.9005 (m) cc_final: 0.8591 (t) REVERT: 0 47 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8654 (mm-40) REVERT: 0 56 ASP cc_start: 0.9047 (t0) cc_final: 0.8804 (t0) REVERT: 1 13 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8606 (mt-10) REVERT: 1 30 GLN cc_start: 0.8913 (tt0) cc_final: 0.8625 (tt0) REVERT: 1 68 SER cc_start: 0.9112 (p) cc_final: 0.8447 (p) REVERT: 1 69 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8112 (p0) REVERT: 1 79 LYS cc_start: 0.8546 (tptp) cc_final: 0.7747 (ttpt) REVERT: 1 105 GLN cc_start: 0.8370 (tt0) cc_final: 0.7785 (mt0) REVERT: 1 114 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: 2 37 GLU cc_start: 0.8501 (tt0) cc_final: 0.8096 (tt0) REVERT: 2 40 THR cc_start: 0.8671 (p) cc_final: 0.8441 (t) REVERT: 2 46 MET cc_start: 0.3859 (ttt) cc_final: 0.2771 (tpt) REVERT: 2 59 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8824 (m) REVERT: 2 111 GLN cc_start: 0.9311 (pt0) cc_final: 0.8397 (pt0) REVERT: 2 157 THR cc_start: 0.8672 (p) cc_final: 0.8287 (t) REVERT: 3 168 ASP cc_start: 0.8624 (t0) cc_final: 0.8181 (t0) REVERT: 4 16 GLU cc_start: 0.8138 (mp0) cc_final: 0.7921 (mp0) REVERT: 4 32 GLN cc_start: 0.8738 (tt0) cc_final: 0.8102 (tt0) REVERT: 4 50 TYR cc_start: 0.9210 (p90) cc_final: 0.8960 (p90) REVERT: 4 51 MET cc_start: 0.9309 (mtt) cc_final: 0.9099 (mtt) REVERT: 5 20 GLU cc_start: 0.8537 (mp0) cc_final: 0.8102 (mp0) REVERT: 5 44 ILE cc_start: 0.8918 (mp) cc_final: 0.8592 (mt) REVERT: 6 63 LYS cc_start: 0.8412 (tttm) cc_final: 0.8212 (tttt) REVERT: 6 91 GLU cc_start: 0.8042 (tt0) cc_final: 0.7752 (tt0) REVERT: 7 1 MET cc_start: 0.8840 (mtp) cc_final: 0.8076 (mtp) REVERT: 7 12 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8251 (t80) REVERT: 7 13 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8255 (mt-10) REVERT: 7 15 LEU cc_start: 0.8981 (mt) cc_final: 0.8658 (mm) REVERT: 7 30 GLN cc_start: 0.8807 (tt0) cc_final: 0.8332 (tt0) REVERT: 7 69 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7652 (p0) REVERT: 7 79 LYS cc_start: 0.8634 (tptp) cc_final: 0.7914 (ttpt) REVERT: 7 80 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.8072 (ttp-170) REVERT: 8 40 THR cc_start: 0.8811 (p) cc_final: 0.8533 (t) REVERT: 8 45 THR cc_start: 0.6543 (m) cc_final: 0.6022 (p) REVERT: 8 46 MET cc_start: 0.3611 (ttt) cc_final: 0.2950 (tpt) REVERT: 8 132 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8707 (tt0) outliers start: 133 outliers final: 101 residues processed: 810 average time/residue: 0.1758 time to fit residues: 221.7307 Evaluate side-chains 853 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 732 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 111 GLN Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 39 ILE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 7 residue 125 LYS Chi-restraints excluded: chain 7 residue 126 THR Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 241 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS G 18 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS Y 18 GLN 0 76 ASN 6 26 ASN ** 6 76 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 = 0.3281 r_free = 0.3281 target = 0.109781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092410 restraints weight = 40428.602| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.19 r_work: 0.2906 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29442 Z= 0.160 Angle : 0.521 5.984 39684 Z= 0.282 Chirality : 0.042 0.129 4302 Planarity : 0.003 0.033 5190 Dihedral : 5.398 82.277 3924 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.92 % Allowed : 16.48 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3486 helix: 1.75 (0.17), residues: 924 sheet: -0.49 (0.15), residues: 1140 loop : 0.15 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 160 TYR 0.014 0.001 TYR J 8 PHE 0.013 0.001 PHE Q 110 TRP 0.007 0.001 TRP Q 89 HIS 0.003 0.001 HIS P 74 Details of bonding type rmsd covalent geometry : bond 0.00385 (29442) covalent geometry : angle 0.52138 (39684) hydrogen bonds : bond 0.03645 ( 1302) hydrogen bonds : angle 4.40753 ( 3942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 742 time to evaluate : 1.078 Fit side-chains REVERT: A 17 LYS cc_start: 0.9112 (mttt) cc_final: 0.8689 (mtpt) REVERT: A 27 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8557 (ttpp) REVERT: A 30 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 42 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7727 (tp30) REVERT: A 77 SER cc_start: 0.9130 (m) cc_final: 0.8908 (t) REVERT: B 40 GLU cc_start: 0.7475 (mp0) cc_final: 0.7238 (pt0) REVERT: C 13 GLN cc_start: 0.8207 (mt0) cc_final: 0.7899 (mt0) REVERT: C 16 THR cc_start: 0.9212 (m) cc_final: 0.8924 (p) REVERT: C 89 ARG cc_start: 0.9160 (ttm-80) cc_final: 0.8931 (ttm-80) REVERT: C 98 GLU cc_start: 0.8853 (tt0) cc_final: 0.8613 (tt0) REVERT: D 39 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8827 (mt) REVERT: D 90 LYS cc_start: 0.8834 (tptm) cc_final: 0.8496 (tptp) REVERT: D 99 ASP cc_start: 0.8666 (t70) cc_final: 0.8316 (t0) REVERT: D 125 LYS cc_start: 0.8840 (mttt) cc_final: 0.8528 (mtpp) REVERT: E 37 GLU cc_start: 0.8640 (tt0) cc_final: 0.8346 (mt-10) REVERT: E 46 MET cc_start: 0.3061 (tpt) cc_final: 0.2403 (tpt) REVERT: E 94 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8737 (mmm160) REVERT: F 168 ASP cc_start: 0.8544 (t0) cc_final: 0.7563 (t0) REVERT: H 66 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: H 95 TYR cc_start: 0.8397 (t80) cc_final: 0.7799 (t80) REVERT: I 10 GLN cc_start: 0.9085 (mt0) cc_final: 0.8781 (mt0) REVERT: I 13 GLN cc_start: 0.8392 (mt0) cc_final: 0.8126 (mt0) REVERT: I 16 THR cc_start: 0.9011 (m) cc_final: 0.8682 (p) REVERT: I 47 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8649 (mm-40) REVERT: I 56 ASP cc_start: 0.9033 (t0) cc_final: 0.8776 (t0) REVERT: J 13 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8591 (mt-10) REVERT: J 30 GLN cc_start: 0.8940 (tt0) cc_final: 0.8684 (tt0) REVERT: J 68 SER cc_start: 0.9124 (p) cc_final: 0.8430 (p) REVERT: J 69 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8151 (p0) REVERT: J 79 LYS cc_start: 0.8627 (tptp) cc_final: 0.7904 (ttpt) REVERT: J 105 GLN cc_start: 0.8342 (tt0) cc_final: 0.7801 (mt0) REVERT: J 114 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: K 40 THR cc_start: 0.8687 (p) cc_final: 0.8449 (t) REVERT: K 46 MET cc_start: 0.3881 (ttt) cc_final: 0.2809 (tpt) REVERT: K 59 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8828 (m) REVERT: K 111 GLN cc_start: 0.9310 (pt0) cc_final: 0.8421 (pt0) REVERT: K 157 THR cc_start: 0.8652 (p) cc_final: 0.8242 (t) REVERT: L 168 ASP cc_start: 0.8622 (t0) cc_final: 0.8195 (t0) REVERT: M 32 GLN cc_start: 0.8792 (tt0) cc_final: 0.8208 (tt0) REVERT: M 50 TYR cc_start: 0.9224 (p90) cc_final: 0.8982 (p90) REVERT: M 51 MET cc_start: 0.9306 (mtt) cc_final: 0.9081 (mtt) REVERT: N 20 GLU cc_start: 0.8479 (mp0) cc_final: 0.8052 (mp0) REVERT: N 44 ILE cc_start: 0.8938 (mp) cc_final: 0.8624 (mt) REVERT: O 20 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8623 (mmmt) REVERT: O 91 GLU cc_start: 0.7996 (tt0) cc_final: 0.7659 (tt0) REVERT: P 1 MET cc_start: 0.8838 (mtp) cc_final: 0.8148 (mtp) REVERT: P 12 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8229 (t80) REVERT: P 13 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8252 (mt-10) REVERT: P 15 LEU cc_start: 0.9020 (mt) cc_final: 0.8697 (mm) REVERT: P 30 GLN cc_start: 0.8841 (tt0) cc_final: 0.8365 (tt0) REVERT: P 79 LYS cc_start: 0.8685 (tptp) cc_final: 0.7987 (ttpt) REVERT: P 80 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8125 (ttp-170) REVERT: Q 40 THR cc_start: 0.8836 (p) cc_final: 0.8552 (t) REVERT: Q 45 THR cc_start: 0.6641 (m) cc_final: 0.6119 (p) REVERT: Q 46 MET cc_start: 0.3697 (ttt) cc_final: 0.3066 (tpt) REVERT: S 17 LYS cc_start: 0.9122 (mttt) cc_final: 0.8700 (mtpt) REVERT: S 27 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8734 (ttpt) REVERT: S 30 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8112 (mt-10) REVERT: S 42 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7727 (tp30) REVERT: S 77 SER cc_start: 0.9140 (m) cc_final: 0.8912 (t) REVERT: T 40 GLU cc_start: 0.7469 (mp0) cc_final: 0.7238 (pt0) REVERT: U 13 GLN cc_start: 0.8237 (mt0) cc_final: 0.7928 (mt0) REVERT: U 16 THR cc_start: 0.9215 (m) cc_final: 0.8920 (p) REVERT: U 89 ARG cc_start: 0.9144 (ttm-80) cc_final: 0.8926 (ttm-80) REVERT: U 98 GLU cc_start: 0.8864 (tt0) cc_final: 0.8584 (tt0) REVERT: V 39 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8824 (mt) REVERT: V 90 LYS cc_start: 0.8844 (tptm) cc_final: 0.8507 (tptp) REVERT: V 99 ASP cc_start: 0.8646 (t70) cc_final: 0.8288 (t0) REVERT: V 125 LYS cc_start: 0.8785 (mttt) cc_final: 0.8512 (mtpp) REVERT: W 37 GLU cc_start: 0.8636 (tt0) cc_final: 0.8339 (mt-10) REVERT: W 46 MET cc_start: 0.3027 (tpt) cc_final: 0.2379 (tpt) REVERT: W 94 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8748 (mmm160) REVERT: W 111 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9077 (pt0) REVERT: X 168 ASP cc_start: 0.8548 (t0) cc_final: 0.7568 (t0) REVERT: Z 66 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: Z 95 TYR cc_start: 0.8399 (t80) cc_final: 0.7808 (t80) REVERT: 0 10 GLN cc_start: 0.9084 (mt0) cc_final: 0.8781 (mt0) REVERT: 0 13 GLN cc_start: 0.8390 (mt0) cc_final: 0.8117 (mt0) REVERT: 0 16 THR cc_start: 0.9008 (m) cc_final: 0.8674 (p) REVERT: 0 47 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8659 (mm-40) REVERT: 0 56 ASP cc_start: 0.9048 (t0) cc_final: 0.8801 (t0) REVERT: 1 13 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8591 (mt-10) REVERT: 1 30 GLN cc_start: 0.8946 (tt0) cc_final: 0.8691 (tt0) REVERT: 1 68 SER cc_start: 0.9120 (p) cc_final: 0.8446 (p) REVERT: 1 69 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8156 (p0) REVERT: 1 79 LYS cc_start: 0.8616 (tptp) cc_final: 0.7888 (ttpt) REVERT: 1 105 GLN cc_start: 0.8352 (tt0) cc_final: 0.7812 (mt0) REVERT: 1 114 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: 2 40 THR cc_start: 0.8687 (p) cc_final: 0.8450 (t) REVERT: 2 46 MET cc_start: 0.3893 (ttt) cc_final: 0.2822 (tpt) REVERT: 2 59 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8819 (m) REVERT: 2 111 GLN cc_start: 0.9317 (pt0) cc_final: 0.8423 (pt0) REVERT: 2 157 THR cc_start: 0.8643 (p) cc_final: 0.8232 (t) REVERT: 3 168 ASP cc_start: 0.8612 (t0) cc_final: 0.8185 (t0) REVERT: 4 32 GLN cc_start: 0.8791 (tt0) cc_final: 0.8210 (tt0) REVERT: 4 50 TYR cc_start: 0.9231 (p90) cc_final: 0.8984 (p90) REVERT: 4 51 MET cc_start: 0.9322 (mtt) cc_final: 0.9090 (mtt) REVERT: 5 20 GLU cc_start: 0.8467 (mp0) cc_final: 0.8039 (mp0) REVERT: 5 44 ILE cc_start: 0.8936 (mp) cc_final: 0.8616 (mt) REVERT: 6 13 GLN cc_start: 0.8479 (mt0) cc_final: 0.8225 (mt0) REVERT: 6 91 GLU cc_start: 0.7993 (tt0) cc_final: 0.7667 (tt0) REVERT: 7 1 MET cc_start: 0.8864 (mtp) cc_final: 0.8156 (mtp) REVERT: 7 12 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8252 (t80) REVERT: 7 13 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8267 (mt-10) REVERT: 7 15 LEU cc_start: 0.9029 (mt) cc_final: 0.8712 (mm) REVERT: 7 30 GLN cc_start: 0.8851 (tt0) cc_final: 0.8373 (tt0) REVERT: 7 69 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7753 (p0) REVERT: 7 79 LYS cc_start: 0.8697 (tptp) cc_final: 0.7998 (ttpt) REVERT: 7 80 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8133 (ttp-170) REVERT: 8 40 THR cc_start: 0.8834 (p) cc_final: 0.8552 (t) REVERT: 8 45 THR cc_start: 0.6606 (m) cc_final: 0.6088 (p) REVERT: 8 46 MET cc_start: 0.3680 (ttt) cc_final: 0.3055 (tpt) outliers start: 125 outliers final: 103 residues processed: 796 average time/residue: 0.1793 time to fit residues: 223.7552 Evaluate side-chains 849 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 728 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 110 PHE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 111 GLN Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 39 ILE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 7 residue 125 LYS Chi-restraints excluded: chain 7 residue 126 THR Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 110 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 242 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 154 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN D 117 HIS G 18 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS Y 18 GLN 0 76 ASN 4 97 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.091474 restraints weight = 40591.712| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.19 r_work: 0.2908 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29442 Z= 0.185 Angle : 0.548 6.489 39684 Z= 0.296 Chirality : 0.042 0.133 4302 Planarity : 0.004 0.035 5190 Dihedral : 5.461 83.677 3924 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.08 % Allowed : 16.85 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.14), residues: 3486 helix: 1.74 (0.17), residues: 924 sheet: -0.53 (0.15), residues: 1140 loop : 0.10 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 160 TYR 0.015 0.002 TYR J 8 PHE 0.013 0.001 PHE 2 110 TRP 0.006 0.001 TRP 8 89 HIS 0.004 0.001 HIS P 74 Details of bonding type rmsd covalent geometry : bond 0.00447 (29442) covalent geometry : angle 0.54764 (39684) hydrogen bonds : bond 0.03769 ( 1302) hydrogen bonds : angle 4.45903 ( 3942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 731 time to evaluate : 1.061 Fit side-chains REVERT: A 17 LYS cc_start: 0.9141 (mttt) cc_final: 0.8702 (mtpt) REVERT: A 27 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8496 (ttpp) REVERT: A 30 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8209 (mt-10) REVERT: A 42 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7727 (tp30) REVERT: C 13 GLN cc_start: 0.8149 (mt0) cc_final: 0.7861 (mt0) REVERT: C 16 THR cc_start: 0.9240 (m) cc_final: 0.8949 (p) REVERT: C 89 ARG cc_start: 0.9150 (ttm-80) cc_final: 0.8924 (ttm-80) REVERT: C 98 GLU cc_start: 0.8795 (tt0) cc_final: 0.8526 (tt0) REVERT: D 39 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8788 (mt) REVERT: D 90 LYS cc_start: 0.8836 (tptm) cc_final: 0.8500 (tptp) REVERT: D 99 ASP cc_start: 0.8689 (t70) cc_final: 0.8340 (t0) REVERT: D 125 LYS cc_start: 0.8824 (mttt) cc_final: 0.8497 (mtpp) REVERT: E 37 GLU cc_start: 0.8606 (tt0) cc_final: 0.8286 (mt-10) REVERT: E 46 MET cc_start: 0.2859 (tpt) cc_final: 0.2205 (tpt) REVERT: E 94 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8713 (mmm160) REVERT: F 168 ASP cc_start: 0.8554 (t0) cc_final: 0.7555 (t0) REVERT: H 40 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: H 66 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: I 10 GLN cc_start: 0.9079 (mt0) cc_final: 0.8762 (mt0) REVERT: I 13 GLN cc_start: 0.8391 (mt0) cc_final: 0.8101 (mt0) REVERT: I 16 THR cc_start: 0.9021 (m) cc_final: 0.8690 (p) REVERT: I 20 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8271 (mmmt) REVERT: I 47 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8653 (mm-40) REVERT: I 56 ASP cc_start: 0.9051 (t0) cc_final: 0.8800 (t0) REVERT: J 13 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8593 (mt-10) REVERT: J 30 GLN cc_start: 0.8975 (tt0) cc_final: 0.8708 (tt0) REVERT: J 68 SER cc_start: 0.9122 (p) cc_final: 0.8532 (p) REVERT: J 69 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8108 (p0) REVERT: J 79 LYS cc_start: 0.8583 (tptp) cc_final: 0.7777 (ttpt) REVERT: J 105 GLN cc_start: 0.8358 (tt0) cc_final: 0.7794 (mt0) REVERT: J 114 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: K 40 THR cc_start: 0.8684 (p) cc_final: 0.8434 (t) REVERT: K 46 MET cc_start: 0.3828 (ttt) cc_final: 0.2764 (tpt) REVERT: K 111 GLN cc_start: 0.9327 (pt0) cc_final: 0.8508 (pt0) REVERT: K 157 THR cc_start: 0.8627 (p) cc_final: 0.8210 (t) REVERT: L 168 ASP cc_start: 0.8636 (t0) cc_final: 0.8187 (t0) REVERT: M 32 GLN cc_start: 0.8777 (tt0) cc_final: 0.8177 (tt0) REVERT: M 50 TYR cc_start: 0.9213 (p90) cc_final: 0.8951 (p90) REVERT: M 51 MET cc_start: 0.9293 (mtt) cc_final: 0.9067 (mtt) REVERT: N 44 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8567 (mt) REVERT: P 12 TYR cc_start: 0.9161 (OUTLIER) cc_final: 0.8228 (t80) REVERT: P 13 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8068 (mt-10) REVERT: P 15 LEU cc_start: 0.9014 (mt) cc_final: 0.8691 (mm) REVERT: P 30 GLN cc_start: 0.8883 (tt0) cc_final: 0.8442 (tt0) REVERT: P 79 LYS cc_start: 0.8653 (tptp) cc_final: 0.7946 (ttpt) REVERT: P 80 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8112 (ttp-170) REVERT: Q 40 THR cc_start: 0.8795 (p) cc_final: 0.8541 (t) REVERT: Q 45 THR cc_start: 0.6615 (m) cc_final: 0.6090 (p) REVERT: Q 46 MET cc_start: 0.3676 (ttt) cc_final: 0.3059 (tpt) REVERT: S 17 LYS cc_start: 0.9152 (mttt) cc_final: 0.8718 (mtpt) REVERT: S 27 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8740 (ttpt) REVERT: S 30 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8102 (mt-10) REVERT: S 42 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7721 (tp30) REVERT: S 77 SER cc_start: 0.9224 (m) cc_final: 0.8998 (t) REVERT: U 13 GLN cc_start: 0.8172 (mt0) cc_final: 0.7886 (mt0) REVERT: U 16 THR cc_start: 0.9254 (m) cc_final: 0.8954 (p) REVERT: U 89 ARG cc_start: 0.9140 (ttm-80) cc_final: 0.8917 (ttm-80) REVERT: U 98 GLU cc_start: 0.8808 (tt0) cc_final: 0.8515 (tt0) REVERT: V 39 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8788 (mt) REVERT: V 90 LYS cc_start: 0.8846 (tptm) cc_final: 0.8516 (tptp) REVERT: V 125 LYS cc_start: 0.8815 (mttt) cc_final: 0.8497 (mtpp) REVERT: W 37 GLU cc_start: 0.8601 (tt0) cc_final: 0.8281 (mt-10) REVERT: W 46 MET cc_start: 0.3003 (tpt) cc_final: 0.2365 (tpt) REVERT: W 94 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8753 (mmm160) REVERT: W 111 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9070 (pt0) REVERT: X 168 ASP cc_start: 0.8549 (t0) cc_final: 0.7545 (t0) REVERT: Z 40 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: Z 66 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: 0 10 GLN cc_start: 0.9078 (mt0) cc_final: 0.8758 (mt0) REVERT: 0 13 GLN cc_start: 0.8381 (mt0) cc_final: 0.8085 (mt0) REVERT: 0 16 THR cc_start: 0.9015 (m) cc_final: 0.8678 (p) REVERT: 0 20 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8263 (mmmt) REVERT: 0 47 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8657 (mm-40) REVERT: 0 56 ASP cc_start: 0.9066 (t0) cc_final: 0.8821 (t0) REVERT: 1 13 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8585 (mt-10) REVERT: 1 30 GLN cc_start: 0.8988 (tt0) cc_final: 0.8720 (tt0) REVERT: 1 68 SER cc_start: 0.9121 (p) cc_final: 0.8503 (p) REVERT: 1 69 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8117 (p0) REVERT: 1 79 LYS cc_start: 0.8579 (tptp) cc_final: 0.7768 (ttpt) REVERT: 1 105 GLN cc_start: 0.8363 (tt0) cc_final: 0.7798 (mt0) REVERT: 1 114 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: 2 40 THR cc_start: 0.8688 (p) cc_final: 0.8441 (t) REVERT: 2 46 MET cc_start: 0.3835 (ttt) cc_final: 0.2768 (tpt) REVERT: 2 111 GLN cc_start: 0.9329 (pt0) cc_final: 0.8496 (pt0) REVERT: 2 157 THR cc_start: 0.8616 (p) cc_final: 0.8200 (t) REVERT: 3 168 ASP cc_start: 0.8631 (t0) cc_final: 0.8186 (t0) REVERT: 4 32 GLN cc_start: 0.8782 (tt0) cc_final: 0.8182 (tt0) REVERT: 4 50 TYR cc_start: 0.9194 (p90) cc_final: 0.8930 (p90) REVERT: 4 51 MET cc_start: 0.9296 (mtt) cc_final: 0.9058 (mtt) REVERT: 5 44 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8557 (mt) REVERT: 7 12 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8253 (t80) REVERT: 7 13 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8086 (mt-10) REVERT: 7 15 LEU cc_start: 0.9026 (mt) cc_final: 0.8708 (mm) REVERT: 7 30 GLN cc_start: 0.8893 (tt0) cc_final: 0.8451 (tt0) REVERT: 7 69 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7760 (p0) REVERT: 7 79 LYS cc_start: 0.8667 (tptp) cc_final: 0.7932 (ttpt) REVERT: 7 80 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8117 (ttp-170) REVERT: 8 40 THR cc_start: 0.8792 (p) cc_final: 0.8533 (t) REVERT: 8 45 THR cc_start: 0.6583 (m) cc_final: 0.6060 (p) REVERT: 8 46 MET cc_start: 0.3678 (ttt) cc_final: 0.3057 (tpt) outliers start: 130 outliers final: 110 residues processed: 787 average time/residue: 0.1799 time to fit residues: 222.2195 Evaluate side-chains 848 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 718 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 84 ASP Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 110 PHE Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 111 GLN Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 39 ILE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 44 ILE Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 7 residue 125 LYS Chi-restraints excluded: chain 7 residue 126 THR Chi-restraints excluded: chain 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 271 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 111 optimal weight: 0.0170 chunk 286 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS E 111 GLN G 18 GLN G 97 ASN I 76 ASN M 18 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS V 117 HIS Y 97 ASN 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095745 restraints weight = 39664.091| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.16 r_work: 0.2962 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29442 Z= 0.120 Angle : 0.504 7.583 39684 Z= 0.273 Chirality : 0.041 0.124 4302 Planarity : 0.003 0.037 5190 Dihedral : 5.204 81.193 3924 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.42 % Allowed : 17.70 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 3486 helix: 1.98 (0.17), residues: 918 sheet: -0.47 (0.15), residues: 1140 loop : 0.09 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 9 160 TYR 0.014 0.001 TYR 7 8 PHE 0.011 0.001 PHE E 14 TRP 0.009 0.001 TRP 8 89 HIS 0.003 0.001 HIS V 74 Details of bonding type rmsd covalent geometry : bond 0.00283 (29442) covalent geometry : angle 0.50443 (39684) hydrogen bonds : bond 0.03330 ( 1302) hydrogen bonds : angle 4.32849 ( 3942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6972 Ramachandran restraints generated. 3486 Oldfield, 0 Emsley, 3486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 752 time to evaluate : 0.944 Fit side-chains REVERT: A 17 LYS cc_start: 0.9128 (mttt) cc_final: 0.8715 (mtpt) REVERT: A 27 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8552 (ttpp) REVERT: A 30 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 42 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7725 (tp30) REVERT: C 13 GLN cc_start: 0.8237 (mt0) cc_final: 0.7896 (mt0) REVERT: C 16 THR cc_start: 0.9246 (m) cc_final: 0.8992 (p) REVERT: C 89 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8903 (ttm-80) REVERT: D 90 LYS cc_start: 0.8829 (tptm) cc_final: 0.8501 (tptp) REVERT: D 99 ASP cc_start: 0.8619 (t70) cc_final: 0.8282 (t0) REVERT: D 125 LYS cc_start: 0.8745 (mttt) cc_final: 0.8492 (mmtm) REVERT: E 46 MET cc_start: 0.3125 (tpt) cc_final: 0.2580 (tpt) REVERT: E 94 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8718 (mmm160) REVERT: F 168 ASP cc_start: 0.8695 (t0) cc_final: 0.7884 (t0) REVERT: H 40 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: H 95 TYR cc_start: 0.8438 (t80) cc_final: 0.7868 (t80) REVERT: I 10 GLN cc_start: 0.9061 (mt0) cc_final: 0.8765 (mt0) REVERT: I 16 THR cc_start: 0.8997 (m) cc_final: 0.8691 (p) REVERT: I 20 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8264 (mmmt) REVERT: I 47 GLN cc_start: 0.8961 (tt0) cc_final: 0.8629 (mm-40) REVERT: I 56 ASP cc_start: 0.8979 (t0) cc_final: 0.8696 (t0) REVERT: J 1 MET cc_start: 0.8346 (mtm) cc_final: 0.8146 (mtm) REVERT: J 13 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8550 (mt-10) REVERT: J 30 GLN cc_start: 0.8931 (tt0) cc_final: 0.8707 (tt0) REVERT: J 68 SER cc_start: 0.9108 (p) cc_final: 0.8559 (p) REVERT: J 69 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8041 (p0) REVERT: J 79 LYS cc_start: 0.8581 (tptp) cc_final: 0.7875 (ttpt) REVERT: J 105 GLN cc_start: 0.8326 (tt0) cc_final: 0.7763 (mt0) REVERT: J 114 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: K 46 MET cc_start: 0.3746 (ttt) cc_final: 0.2819 (tpt) REVERT: K 111 GLN cc_start: 0.9246 (pt0) cc_final: 0.8226 (pt0) REVERT: K 157 THR cc_start: 0.8618 (p) cc_final: 0.8197 (t) REVERT: L 168 ASP cc_start: 0.8631 (t0) cc_final: 0.8221 (t0) REVERT: M 32 GLN cc_start: 0.8717 (tt0) cc_final: 0.8111 (tt0) REVERT: M 50 TYR cc_start: 0.9191 (p90) cc_final: 0.8974 (p90) REVERT: M 51 MET cc_start: 0.9262 (mtt) cc_final: 0.9060 (mtt) REVERT: P 12 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8027 (t80) REVERT: P 13 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8064 (mt-10) REVERT: P 15 LEU cc_start: 0.8969 (mt) cc_final: 0.8642 (mm) REVERT: P 30 GLN cc_start: 0.8835 (tt0) cc_final: 0.8380 (tt0) REVERT: P 52 ASP cc_start: 0.8639 (m-30) cc_final: 0.8382 (m-30) REVERT: P 79 LYS cc_start: 0.8644 (tptp) cc_final: 0.7938 (ttpt) REVERT: P 80 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8120 (ttp-170) REVERT: Q 45 THR cc_start: 0.6661 (m) cc_final: 0.6106 (p) REVERT: Q 46 MET cc_start: 0.3614 (ttt) cc_final: 0.3070 (tpt) REVERT: Q 132 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8743 (tt0) REVERT: R 168 ASP cc_start: 0.8559 (t0) cc_final: 0.8284 (t0) REVERT: S 17 LYS cc_start: 0.9138 (mttt) cc_final: 0.8713 (mtpt) REVERT: S 27 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8734 (ttpt) REVERT: S 30 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8099 (mt-10) REVERT: S 42 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7730 (tp30) REVERT: S 59 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8531 (mmt90) REVERT: U 13 GLN cc_start: 0.8260 (mt0) cc_final: 0.7917 (mt0) REVERT: U 16 THR cc_start: 0.9251 (m) cc_final: 0.8994 (p) REVERT: U 89 ARG cc_start: 0.9174 (ttm-80) cc_final: 0.8928 (ttm-80) REVERT: V 90 LYS cc_start: 0.8827 (tptm) cc_final: 0.8501 (tptp) REVERT: V 99 ASP cc_start: 0.8692 (t70) cc_final: 0.8308 (t0) REVERT: V 125 LYS cc_start: 0.8726 (mttt) cc_final: 0.8492 (mmtm) REVERT: W 37 GLU cc_start: 0.8555 (tt0) cc_final: 0.8252 (tt0) REVERT: W 46 MET cc_start: 0.2962 (tpt) cc_final: 0.2379 (tpt) REVERT: W 94 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8739 (mmm160) REVERT: W 111 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.9011 (pt0) REVERT: X 168 ASP cc_start: 0.8698 (t0) cc_final: 0.7886 (t0) REVERT: Z 40 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: Z 95 TYR cc_start: 0.8442 (t80) cc_final: 0.7874 (t80) REVERT: 0 10 GLN cc_start: 0.9059 (mt0) cc_final: 0.8762 (mt0) REVERT: 0 16 THR cc_start: 0.8996 (m) cc_final: 0.8685 (p) REVERT: 0 20 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8250 (mmmt) REVERT: 0 47 GLN cc_start: 0.8968 (tt0) cc_final: 0.8642 (mm-40) REVERT: 0 56 ASP cc_start: 0.8990 (t0) cc_final: 0.8713 (t0) REVERT: 1 1 MET cc_start: 0.8352 (mtm) cc_final: 0.8143 (mtm) REVERT: 1 13 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8565 (mt-10) REVERT: 1 30 GLN cc_start: 0.8930 (tt0) cc_final: 0.8694 (tt0) REVERT: 1 68 SER cc_start: 0.9151 (p) cc_final: 0.8575 (p) REVERT: 1 69 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8048 (p0) REVERT: 1 79 LYS cc_start: 0.8568 (tptp) cc_final: 0.7858 (ttpt) REVERT: 1 105 GLN cc_start: 0.8352 (tt0) cc_final: 0.7781 (mt0) REVERT: 1 114 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: 2 46 MET cc_start: 0.3748 (ttt) cc_final: 0.2828 (tpt) REVERT: 2 111 GLN cc_start: 0.9247 (pt0) cc_final: 0.8217 (pt0) REVERT: 2 157 THR cc_start: 0.8613 (p) cc_final: 0.8193 (t) REVERT: 3 168 ASP cc_start: 0.8627 (t0) cc_final: 0.8216 (t0) REVERT: 4 32 GLN cc_start: 0.8715 (tt0) cc_final: 0.8113 (tt0) REVERT: 4 50 TYR cc_start: 0.9190 (p90) cc_final: 0.8813 (p90) REVERT: 4 51 MET cc_start: 0.9267 (mtt) cc_final: 0.8987 (mtt) REVERT: 7 12 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8051 (t80) REVERT: 7 13 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8078 (mt-10) REVERT: 7 15 LEU cc_start: 0.8980 (mt) cc_final: 0.8661 (mm) REVERT: 7 30 GLN cc_start: 0.8841 (tt0) cc_final: 0.8377 (tt0) REVERT: 7 52 ASP cc_start: 0.8637 (m-30) cc_final: 0.8377 (m-30) REVERT: 7 69 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7792 (p0) REVERT: 7 79 LYS cc_start: 0.8655 (tptp) cc_final: 0.7950 (ttpt) REVERT: 7 80 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8137 (ttp-170) REVERT: 8 45 THR cc_start: 0.6613 (m) cc_final: 0.6063 (p) REVERT: 8 46 MET cc_start: 0.3513 (ttt) cc_final: 0.2996 (tpt) REVERT: 8 132 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8711 (tt0) outliers start: 109 outliers final: 78 residues processed: 796 average time/residue: 0.1780 time to fit residues: 222.4313 Evaluate side-chains 807 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 717 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain N residue 15 ASP Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain T residue 70 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 111 GLN Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 101 THR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 39 ILE Chi-restraints excluded: chain 4 residue 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 7 residue 126 THR Chi-restraints excluded: chain 8 residue 26 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 283 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 333 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 196 optimal weight: 2.9990 chunk 303 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS I 76 ASN N 97 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS V 117 HIS 0 76 ASN 5 97 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.086086 restraints weight = 41808.304| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.27 r_work: 0.2826 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29442 Z= 0.241 Angle : 0.591 7.819 39684 Z= 0.317 Chirality : 0.044 0.142 4302 Planarity : 0.004 0.040 5190 Dihedral : 5.559 84.536 3924 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.42 % Allowed : 17.39 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.14), residues: 3486 helix: 1.67 (0.17), residues: 924 sheet: -0.61 (0.15), residues: 1140 loop : 0.06 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 94 TYR 0.019 0.002 TYR J 8 PHE 0.016 0.002 PHE K 110 TRP 0.006 0.001 TRP W 89 HIS 0.005 0.001 HIS P 117 Details of bonding type rmsd covalent geometry : bond 0.00589 (29442) covalent geometry : angle 0.59141 (39684) hydrogen bonds : bond 0.04058 ( 1302) hydrogen bonds : angle 4.52518 ( 3942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6714.95 seconds wall clock time: 115 minutes 44.35 seconds (6944.35 seconds total)