Starting phenix.real_space_refine on Tue Jun 24 11:30:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu3_48618/06_2025/9mu3_48618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu3_48618/06_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_48618/06_2025/9mu3_48618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu3_48618/06_2025/9mu3_48618.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu3_48618/06_2025/9mu3_48618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu3_48618/06_2025/9mu3_48618.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.018 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.48, per 1000 atoms: 0.57 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: 6.88 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 4.39 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: 10.21 Time building geometry restraints manager: 8.15 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: 0.05 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: 0.890 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: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 63.470 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (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 TRP 0.054 0.012 TRP J 65 HIS 0.011 0.003 HIS J 74 PHE 0.028 0.004 PHE Q 67 TYR 0.028 0.006 TYR B 50 ARG 0.017 0.002 ARG 4 10 Details of bonding type rmsd hydrogen bonds : bond 0.13135 ( 1302) hydrogen bonds : angle 7.45952 ( 3942) covalent geometry : bond 0.00618 (29442) covalent geometry : angle 0.98766 (39684) *********************** 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 : 3.197 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: 0.4810 time to fit residues: 812.7347 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 : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 0.0000 chunk 138 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 HIS D 113 GLN D 117 HIS E 111 GLN E 136 ASN I 76 ASN J 74 HIS J 113 GLN J 117 HIS 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 111 GLN W 136 ASN 0 76 ASN 1 74 HIS 1 113 GLN 1 117 HIS 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 = 0.3345 r_free = 0.3345 target = 0.114536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097083 restraints weight = 39601.578| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.16 r_work: 0.2986 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29442 Z= 0.131 Angle : 0.576 6.963 39684 Z= 0.319 Chirality : 0.043 0.146 4302 Planarity : 0.004 0.030 5190 Dihedral : 6.116 77.260 3924 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.95 % Allowed : 8.95 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3486 helix: 0.74 (0.17), residues: 918 sheet: 0.28 (0.14), residues: 1230 loop : 0.41 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 89 HIS 0.003 0.001 HIS U 72 PHE 0.013 0.001 PHE S 96 TYR 0.015 0.001 TYR 2 133 ARG 0.005 0.001 ARG K 94 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1302) hydrogen bonds : angle 4.55207 ( 3942) covalent geometry : bond 0.00288 (29442) covalent geometry : angle 0.57629 (39684) *********************** 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 1015 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 953 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9001 (mttt) cc_final: 0.8668 (mtpt) REVERT: A 30 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 32 GLN cc_start: 0.8735 (tt0) cc_final: 0.8449 (tt0) REVERT: B 92 ILE cc_start: 0.8904 (mt) cc_final: 0.8693 (mt) REVERT: C 16 THR cc_start: 0.9072 (m) cc_final: 0.8709 (t) REVERT: C 29 ILE cc_start: 0.9136 (mp) cc_final: 0.8918 (mt) REVERT: C 89 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8789 (ttm-80) REVERT: D 13 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8234 (mt-10) REVERT: D 57 ASP cc_start: 0.7773 (t70) cc_final: 0.7473 (t70) REVERT: D 71 LEU cc_start: 0.8969 (tp) cc_final: 0.8651 (mp) REVERT: D 99 ASP cc_start: 0.8424 (t70) cc_final: 0.8077 (t0) REVERT: D 105 GLN cc_start: 0.8257 (tt0) cc_final: 0.7805 (mt0) REVERT: D 125 LYS cc_start: 0.8596 (mttt) cc_final: 0.8260 (mmtm) REVERT: E 45 THR cc_start: 0.7463 (p) cc_final: 0.7070 (t) REVERT: E 46 MET cc_start: 0.3150 (ttt) cc_final: 0.2631 (tpt) REVERT: E 71 ASP cc_start: 0.7562 (p0) cc_final: 0.7345 (p0) REVERT: F 168 ASP cc_start: 0.8597 (t0) cc_final: 0.7864 (t0) REVERT: I 10 GLN cc_start: 0.9054 (mt0) cc_final: 0.8773 (mt0) REVERT: I 16 THR cc_start: 0.8999 (m) cc_final: 0.8760 (t) REVERT: I 24 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7565 (ptmt) REVERT: I 47 GLN cc_start: 0.8961 (tt0) cc_final: 0.8666 (mm-40) REVERT: I 63 LYS cc_start: 0.8593 (tptm) cc_final: 0.8235 (tptt) REVERT: J 30 GLN cc_start: 0.8828 (tt0) cc_final: 0.8567 (tt0) REVERT: J 45 ASN cc_start: 0.8854 (m-40) cc_final: 0.8556 (m-40) REVERT: J 68 SER cc_start: 0.9090 (p) cc_final: 0.8263 (p) REVERT: J 69 ASP cc_start: 0.8283 (t0) cc_final: 0.7884 (p0) REVERT: J 71 LEU cc_start: 0.8655 (tp) cc_final: 0.8434 (mp) REVERT: J 79 LYS cc_start: 0.8568 (tptp) cc_final: 0.7843 (ttpt) REVERT: J 114 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: K 37 GLU cc_start: 0.8453 (tt0) cc_final: 0.8111 (tt0) REVERT: K 40 THR cc_start: 0.8637 (p) cc_final: 0.8397 (t) REVERT: K 46 MET cc_start: 0.4700 (ttt) cc_final: 0.2847 (tpt) REVERT: K 111 GLN cc_start: 0.9217 (pt0) cc_final: 0.8187 (pt0) REVERT: K 157 THR cc_start: 0.8595 (p) cc_final: 0.8301 (t) REVERT: L 168 ASP cc_start: 0.8599 (t0) cc_final: 0.8185 (t0) REVERT: M 16 GLU cc_start: 0.8011 (mp0) cc_final: 0.7725 (mp0) REVERT: M 17 LYS cc_start: 0.9019 (mttt) cc_final: 0.8632 (mtpt) REVERT: M 32 GLN cc_start: 0.8799 (tt0) cc_final: 0.8080 (tt0) REVERT: M 87 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8017 (mt-10) REVERT: N 16 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8357 (mm-30) REVERT: N 20 GLU cc_start: 0.8382 (mp0) cc_final: 0.8012 (mp0) REVERT: N 44 ILE cc_start: 0.8935 (mp) cc_final: 0.8674 (mt) REVERT: O 24 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7631 (ptmt) REVERT: P 12 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8198 (t80) REVERT: P 13 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8307 (mt-10) REVERT: P 30 GLN cc_start: 0.8725 (tt0) cc_final: 0.8258 (tt0) REVERT: P 41 MET cc_start: 0.8639 (tpt) cc_final: 0.8385 (tpp) REVERT: P 69 ASP cc_start: 0.7988 (t0) cc_final: 0.7706 (p0) REVERT: P 79 LYS cc_start: 0.8553 (tptp) cc_final: 0.8334 (tptm) REVERT: P 80 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8174 (ttp-170) REVERT: P 125 LYS cc_start: 0.8780 (mttt) cc_final: 0.8573 (mtpp) REVERT: Q 40 THR cc_start: 0.8765 (p) cc_final: 0.8462 (t) REVERT: Q 46 MET cc_start: 0.3223 (ttt) cc_final: 0.2676 (tpt) REVERT: R 168 ASP cc_start: 0.8632 (t0) cc_final: 0.8432 (t0) REVERT: S 17 LYS cc_start: 0.9019 (mttt) cc_final: 0.8691 (mtpt) REVERT: S 30 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8062 (mt-10) REVERT: S 32 GLN cc_start: 0.8719 (tt0) cc_final: 0.8425 (tt0) REVERT: T 92 ILE cc_start: 0.8911 (mt) cc_final: 0.8697 (mt) REVERT: U 16 THR cc_start: 0.9082 (m) cc_final: 0.8718 (t) REVERT: U 29 ILE cc_start: 0.9134 (mp) cc_final: 0.8915 (mt) REVERT: U 89 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8790 (ttm-80) REVERT: V 13 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8238 (mt-10) REVERT: V 57 ASP cc_start: 0.7765 (t70) cc_final: 0.7468 (t70) REVERT: V 71 LEU cc_start: 0.8973 (tp) cc_final: 0.8656 (mp) REVERT: V 99 ASP cc_start: 0.8450 (t70) cc_final: 0.8103 (t0) REVERT: V 105 GLN cc_start: 0.8264 (tt0) cc_final: 0.7805 (mt0) REVERT: V 125 LYS cc_start: 0.8591 (mttt) cc_final: 0.8253 (mmtm) REVERT: W 45 THR cc_start: 0.7464 (p) cc_final: 0.7067 (t) REVERT: W 46 MET cc_start: 0.3137 (ttt) cc_final: 0.2624 (tpt) REVERT: W 71 ASP cc_start: 0.7545 (p0) cc_final: 0.7329 (p0) REVERT: X 168 ASP cc_start: 0.8584 (t0) cc_final: 0.7845 (t0) REVERT: 0 10 GLN cc_start: 0.9044 (mt0) cc_final: 0.8761 (mt0) REVERT: 0 16 THR cc_start: 0.9004 (m) cc_final: 0.8764 (t) REVERT: 0 24 LYS cc_start: 0.7940 (ptmt) cc_final: 0.7572 (ptmt) REVERT: 0 47 GLN cc_start: 0.8940 (tt0) cc_final: 0.8644 (mm-40) REVERT: 0 63 LYS cc_start: 0.8595 (tptm) cc_final: 0.8238 (tptt) REVERT: 1 30 GLN cc_start: 0.8836 (tt0) cc_final: 0.8579 (tt0) REVERT: 1 45 ASN cc_start: 0.8841 (m-40) cc_final: 0.8544 (m-40) REVERT: 1 68 SER cc_start: 0.9081 (p) cc_final: 0.8256 (p) REVERT: 1 69 ASP cc_start: 0.8271 (t0) cc_final: 0.7883 (p0) REVERT: 1 71 LEU cc_start: 0.8662 (tp) cc_final: 0.8443 (mp) REVERT: 1 79 LYS cc_start: 0.8552 (tptp) cc_final: 0.7825 (ttpt) REVERT: 1 114 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: 2 37 GLU cc_start: 0.8463 (tt0) cc_final: 0.8127 (tt0) REVERT: 2 40 THR cc_start: 0.8635 (p) cc_final: 0.8401 (t) REVERT: 2 46 MET cc_start: 0.4714 (ttt) cc_final: 0.2869 (tpt) REVERT: 2 111 GLN cc_start: 0.9223 (pt0) cc_final: 0.8185 (pt0) REVERT: 2 157 THR cc_start: 0.8599 (p) cc_final: 0.8304 (t) REVERT: 3 168 ASP cc_start: 0.8591 (t0) cc_final: 0.8180 (t0) REVERT: 4 16 GLU cc_start: 0.8024 (mp0) cc_final: 0.7730 (mp0) REVERT: 4 17 LYS cc_start: 0.9028 (mttt) cc_final: 0.8642 (mtpt) REVERT: 4 32 GLN cc_start: 0.8799 (tt0) cc_final: 0.8080 (tt0) REVERT: 4 87 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7988 (mt-10) REVERT: 5 16 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8257 (mm-30) REVERT: 5 20 GLU cc_start: 0.8384 (mp0) cc_final: 0.8017 (mp0) REVERT: 5 44 ILE cc_start: 0.8937 (mp) cc_final: 0.8673 (mt) REVERT: 6 24 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7621 (ptmt) REVERT: 7 12 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8212 (t80) REVERT: 7 13 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8314 (mt-10) REVERT: 7 30 GLN cc_start: 0.8735 (tt0) cc_final: 0.8262 (tt0) REVERT: 7 41 MET cc_start: 0.8629 (tpt) cc_final: 0.8374 (tpp) REVERT: 7 69 ASP cc_start: 0.8004 (t0) cc_final: 0.7712 (p0) REVERT: 7 79 LYS cc_start: 0.8536 (tptp) cc_final: 0.8321 (tptm) REVERT: 7 80 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8172 (ttp-170) REVERT: 7 125 LYS cc_start: 0.8777 (mttt) cc_final: 0.8568 (mtpp) REVERT: 8 40 THR cc_start: 0.8765 (p) cc_final: 0.8470 (t) REVERT: 8 46 MET cc_start: 0.3221 (ttt) cc_final: 0.2670 (tpt) REVERT: 9 168 ASP cc_start: 0.8630 (t0) cc_final: 0.8424 (t0) outliers start: 62 outliers final: 30 residues processed: 969 average time/residue: 0.4905 time to fit residues: 730.6171 Evaluate side-chains 851 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 817 time to evaluate : 3.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 42 SER 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 93 ASP Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 88 SER Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 157 THR 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 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 93 ASP Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 88 SER Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 8 residue 26 MET 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 49 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 337 optimal weight: 8.9990 chunk 258 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN I 76 ASN J 105 GLN J 117 HIS O 26 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN 0 76 ASN 1 105 GLN 1 117 HIS 6 26 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.086481 restraints weight = 41545.516| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.25 r_work: 0.2874 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29442 Z= 0.223 Angle : 0.602 7.913 39684 Z= 0.328 Chirality : 0.044 0.146 4302 Planarity : 0.004 0.045 5190 Dihedral : 5.991 84.815 3924 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.26 % Allowed : 13.97 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3486 helix: 1.20 (0.17), residues: 918 sheet: 0.08 (0.14), residues: 1230 loop : 0.35 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 89 HIS 0.005 0.001 HIS O 90 PHE 0.014 0.002 PHE 2 110 TYR 0.020 0.002 TYR J 8 ARG 0.008 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 1302) hydrogen bonds : angle 4.53537 ( 3942) covalent geometry : bond 0.00539 (29442) covalent geometry : angle 0.60171 (39684) *********************** 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 895 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 791 time to evaluate : 4.439 Fit side-chains REVERT: A 17 LYS cc_start: 0.9035 (mttt) cc_final: 0.8644 (mtpt) REVERT: A 27 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8703 (ttpt) REVERT: A 30 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 16 THR cc_start: 0.9180 (m) cc_final: 0.8786 (p) REVERT: C 89 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8853 (ttm-80) REVERT: D 13 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8299 (mt-10) REVERT: D 90 LYS cc_start: 0.8733 (tptm) cc_final: 0.8401 (tptp) REVERT: D 114 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: D 125 LYS cc_start: 0.8600 (mttt) cc_final: 0.8360 (mtpp) REVERT: E 46 MET cc_start: 0.2907 (ttt) cc_final: 0.2378 (tpt) REVERT: E 132 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8605 (tt0) REVERT: E 146 LEU cc_start: 0.8464 (mt) cc_final: 0.8223 (mt) REVERT: F 168 ASP cc_start: 0.8473 (t0) cc_final: 0.7505 (t0) REVERT: H 19 ASP cc_start: 0.8925 (m-30) cc_final: 0.8692 (m-30) REVERT: I 10 GLN cc_start: 0.9058 (mt0) cc_final: 0.8726 (mt0) REVERT: I 16 THR cc_start: 0.9066 (m) cc_final: 0.8682 (t) REVERT: I 47 GLN cc_start: 0.9050 (tt0) cc_final: 0.8672 (mm-40) REVERT: I 63 LYS cc_start: 0.8617 (tptm) cc_final: 0.8270 (tptt) REVERT: J 30 GLN cc_start: 0.8971 (tt0) cc_final: 0.8735 (tt0) REVERT: J 68 SER cc_start: 0.9031 (p) cc_final: 0.8478 (p) REVERT: J 71 LEU cc_start: 0.8742 (tp) cc_final: 0.8428 (mp) REVERT: J 79 LYS cc_start: 0.8503 (tptp) cc_final: 0.7786 (ttpt) REVERT: J 105 GLN cc_start: 0.8393 (mt0) cc_final: 0.7988 (mt0) REVERT: J 114 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: K 37 GLU cc_start: 0.8526 (tt0) cc_final: 0.8140 (tt0) REVERT: K 40 THR cc_start: 0.8670 (p) cc_final: 0.8417 (t) REVERT: K 46 MET cc_start: 0.4300 (ttt) cc_final: 0.2873 (tpt) REVERT: K 111 GLN cc_start: 0.9325 (pt0) cc_final: 0.8470 (pt0) REVERT: K 157 THR cc_start: 0.8684 (p) cc_final: 0.8342 (t) REVERT: L 168 ASP cc_start: 0.8615 (t0) cc_final: 0.8170 (t0) REVERT: M 16 GLU cc_start: 0.7970 (mp0) cc_final: 0.7762 (mp0) REVERT: M 30 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8208 (mt-10) REVERT: M 32 GLN cc_start: 0.8725 (tt0) cc_final: 0.8064 (tt0) REVERT: M 87 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8108 (mt-10) REVERT: N 44 ILE cc_start: 0.8893 (mp) cc_final: 0.8640 (mt) REVERT: N 93 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: O 52 ASP cc_start: 0.9074 (m-30) cc_final: 0.8839 (m-30) REVERT: P 12 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8061 (t80) REVERT: P 13 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8385 (mt-10) REVERT: P 41 MET cc_start: 0.8762 (tpt) cc_final: 0.8544 (tpp) REVERT: P 69 ASP cc_start: 0.7702 (t0) cc_final: 0.7391 (p0) REVERT: P 79 LYS cc_start: 0.8591 (tptp) cc_final: 0.7843 (ttpt) REVERT: P 80 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8104 (ttp-170) REVERT: P 125 LYS cc_start: 0.8624 (mttt) cc_final: 0.8415 (mtpp) REVERT: Q 40 THR cc_start: 0.8831 (p) cc_final: 0.8538 (t) REVERT: Q 45 THR cc_start: 0.6212 (m) cc_final: 0.5777 (p) REVERT: Q 46 MET cc_start: 0.3460 (ttt) cc_final: 0.2727 (tpt) REVERT: S 17 LYS cc_start: 0.9056 (mttt) cc_final: 0.8671 (mtpt) REVERT: S 27 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8704 (ttpt) REVERT: S 30 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8069 (mt-10) REVERT: S 93 ASP cc_start: 0.8735 (t0) cc_final: 0.8535 (t0) REVERT: U 16 THR cc_start: 0.9176 (m) cc_final: 0.8784 (p) REVERT: U 89 ARG cc_start: 0.9150 (ttm-80) cc_final: 0.8846 (ttm-80) REVERT: V 13 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8320 (mt-10) REVERT: V 90 LYS cc_start: 0.8718 (tptm) cc_final: 0.8378 (tptp) REVERT: V 114 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: V 125 LYS cc_start: 0.8589 (mttt) cc_final: 0.8348 (mtpp) REVERT: W 46 MET cc_start: 0.2899 (ttt) cc_final: 0.2363 (tpt) REVERT: W 132 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8603 (tt0) REVERT: W 146 LEU cc_start: 0.8457 (mt) cc_final: 0.8221 (mt) REVERT: X 168 ASP cc_start: 0.8468 (t0) cc_final: 0.7495 (t0) REVERT: Z 19 ASP cc_start: 0.8925 (m-30) cc_final: 0.8692 (m-30) REVERT: 0 10 GLN cc_start: 0.9059 (mt0) cc_final: 0.8729 (mt0) REVERT: 0 16 THR cc_start: 0.9060 (m) cc_final: 0.8671 (t) REVERT: 0 47 GLN cc_start: 0.9054 (tt0) cc_final: 0.8671 (mm-40) REVERT: 0 63 LYS cc_start: 0.8624 (tptm) cc_final: 0.8280 (tptt) REVERT: 1 30 GLN cc_start: 0.8965 (tt0) cc_final: 0.8720 (tt0) REVERT: 1 68 SER cc_start: 0.9031 (p) cc_final: 0.8472 (p) REVERT: 1 71 LEU cc_start: 0.8741 (tp) cc_final: 0.8428 (mp) REVERT: 1 79 LYS cc_start: 0.8498 (tptp) cc_final: 0.7782 (ttpt) REVERT: 1 105 GLN cc_start: 0.8383 (mt0) cc_final: 0.7975 (mt0) REVERT: 1 114 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: 2 37 GLU cc_start: 0.8533 (tt0) cc_final: 0.8143 (tt0) REVERT: 2 40 THR cc_start: 0.8674 (p) cc_final: 0.8417 (t) REVERT: 2 46 MET cc_start: 0.4285 (ttt) cc_final: 0.2873 (tpt) REVERT: 2 111 GLN cc_start: 0.9325 (pt0) cc_final: 0.8462 (pt0) REVERT: 2 157 THR cc_start: 0.8677 (p) cc_final: 0.8337 (t) REVERT: 3 168 ASP cc_start: 0.8621 (t0) cc_final: 0.8184 (t0) REVERT: 4 16 GLU cc_start: 0.7966 (mp0) cc_final: 0.7766 (mp0) REVERT: 4 30 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8221 (mt-10) REVERT: 4 32 GLN cc_start: 0.8741 (tt0) cc_final: 0.8082 (tt0) REVERT: 4 87 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8110 (mt-10) REVERT: 5 44 ILE cc_start: 0.8892 (mp) cc_final: 0.8636 (mt) REVERT: 5 93 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: 6 52 ASP cc_start: 0.9089 (m-30) cc_final: 0.8853 (m-30) REVERT: 7 12 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.8070 (t80) REVERT: 7 13 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8381 (mt-10) REVERT: 7 41 MET cc_start: 0.8745 (tpt) cc_final: 0.8526 (tpp) REVERT: 7 69 ASP cc_start: 0.7716 (t0) cc_final: 0.7393 (p0) REVERT: 7 79 LYS cc_start: 0.8597 (tptp) cc_final: 0.7852 (ttpt) REVERT: 7 80 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.8097 (ttp-170) REVERT: 7 125 LYS cc_start: 0.8607 (mttt) cc_final: 0.8404 (mtpp) REVERT: 8 40 THR cc_start: 0.8830 (p) cc_final: 0.8543 (t) REVERT: 8 45 THR cc_start: 0.6187 (m) cc_final: 0.5751 (p) REVERT: 8 46 MET cc_start: 0.3457 (ttt) cc_final: 0.2716 (tpt) outliers start: 104 outliers final: 76 residues processed: 825 average time/residue: 0.4441 time to fit residues: 568.7065 Evaluate side-chains 823 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 739 time to evaluate : 3.314 ------------------------------------------------------------------------------- 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 49 SER Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B 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 41 ILE 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 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 44 ILE 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 114 GLU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 74 ASP 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 27 THR Chi-restraints excluded: chain O residue 85 THR 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 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 49 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 44 ILE 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 41 ILE 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 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 44 ILE 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 114 GLU Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 74 ASP 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 27 THR Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR 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 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 0 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.087759 restraints weight = 41674.749| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.27 r_work: 0.2900 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29442 Z= 0.161 Angle : 0.538 7.010 39684 Z= 0.294 Chirality : 0.042 0.141 4302 Planarity : 0.004 0.043 5190 Dihedral : 5.688 86.430 3924 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 4.02 % Allowed : 14.28 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3486 helix: 1.47 (0.18), residues: 918 sheet: 0.03 (0.15), residues: 1224 loop : 0.31 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 89 HIS 0.004 0.001 HIS 1 74 PHE 0.012 0.001 PHE E 110 TYR 0.013 0.001 TYR D 8 ARG 0.008 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1302) hydrogen bonds : angle 4.37358 ( 3942) covalent geometry : bond 0.00385 (29442) covalent geometry : angle 0.53820 (39684) *********************** 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 916 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 788 time to evaluate : 3.783 Fit side-chains REVERT: A 17 LYS cc_start: 0.9093 (mttt) cc_final: 0.8691 (mtpt) REVERT: A 27 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8757 (ttpt) REVERT: A 30 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 19 ASP cc_start: 0.9065 (m-30) cc_final: 0.8724 (m-30) REVERT: C 16 THR cc_start: 0.9190 (m) cc_final: 0.8822 (p) REVERT: C 89 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8838 (ttm-80) REVERT: C 98 GLU cc_start: 0.8984 (tt0) cc_final: 0.8663 (tt0) REVERT: D 13 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8249 (mt-10) REVERT: D 39 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8863 (mt) REVERT: D 125 LYS cc_start: 0.8666 (mttt) cc_final: 0.8401 (mtpp) REVERT: E 46 MET cc_start: 0.3663 (ttt) cc_final: 0.2702 (tpt) REVERT: E 52 THR cc_start: 0.6712 (OUTLIER) cc_final: 0.6329 (p) REVERT: F 168 ASP cc_start: 0.8495 (t0) cc_final: 0.7499 (t0) REVERT: H 19 ASP cc_start: 0.8935 (m-30) cc_final: 0.8659 (m-30) REVERT: H 40 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: H 94 ASN cc_start: 0.8688 (m-40) cc_final: 0.8434 (m110) REVERT: I 10 GLN cc_start: 0.9065 (mt0) cc_final: 0.8739 (mt0) REVERT: I 16 THR cc_start: 0.9049 (m) cc_final: 0.8670 (t) REVERT: I 47 GLN cc_start: 0.9035 (tt0) cc_final: 0.8649 (mm-40) REVERT: I 63 LYS cc_start: 0.8615 (tptm) cc_final: 0.8249 (tptt) REVERT: I 76 ASN cc_start: 0.8451 (m-40) cc_final: 0.8199 (m110) REVERT: J 30 GLN cc_start: 0.8885 (tt0) cc_final: 0.8620 (tt0) REVERT: J 68 SER cc_start: 0.9049 (p) cc_final: 0.8396 (p) REVERT: J 69 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7750 (p0) REVERT: J 71 LEU cc_start: 0.8709 (tp) cc_final: 0.8432 (mp) REVERT: J 79 LYS cc_start: 0.8472 (tptp) cc_final: 0.7747 (ttpt) REVERT: J 105 GLN cc_start: 0.8389 (mt0) cc_final: 0.7997 (mt0) REVERT: J 114 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: K 37 GLU cc_start: 0.8522 (tt0) cc_final: 0.8110 (tt0) REVERT: K 40 THR cc_start: 0.8651 (p) cc_final: 0.8419 (t) REVERT: K 46 MET cc_start: 0.4393 (ttt) cc_final: 0.3190 (tpt) REVERT: K 157 THR cc_start: 0.8676 (p) cc_final: 0.8319 (t) REVERT: L 168 ASP cc_start: 0.8625 (t0) cc_final: 0.8161 (t0) REVERT: M 16 GLU cc_start: 0.8053 (mp0) cc_final: 0.7814 (mp0) REVERT: M 32 GLN cc_start: 0.8728 (tt0) cc_final: 0.8128 (tt0) REVERT: N 20 GLU cc_start: 0.8591 (mp0) cc_final: 0.8155 (mp0) REVERT: N 44 ILE cc_start: 0.8871 (mp) cc_final: 0.8604 (mt) REVERT: O 24 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7928 (ptmt) REVERT: P 12 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8077 (t80) REVERT: P 13 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8298 (mt-10) REVERT: P 30 GLN cc_start: 0.8784 (tt0) cc_final: 0.8292 (tt0) REVERT: P 39 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8629 (mt) REVERT: P 41 MET cc_start: 0.8783 (tpt) cc_final: 0.8550 (tpp) REVERT: P 67 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8649 (t) REVERT: P 69 ASP cc_start: 0.7733 (t0) cc_final: 0.7436 (p0) REVERT: P 79 LYS cc_start: 0.8570 (tptp) cc_final: 0.7843 (ttpt) REVERT: P 80 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.8028 (ttp-170) REVERT: Q 40 THR cc_start: 0.8804 (p) cc_final: 0.8521 (t) REVERT: Q 45 THR cc_start: 0.6261 (m) cc_final: 0.5808 (p) REVERT: Q 46 MET cc_start: 0.3633 (ttt) cc_final: 0.2812 (tpt) REVERT: Q 132 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8676 (tt0) REVERT: R 168 ASP cc_start: 0.8550 (t0) cc_final: 0.8300 (t0) REVERT: S 17 LYS cc_start: 0.9111 (mttt) cc_final: 0.8716 (mtpt) REVERT: S 27 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8753 (ttpt) REVERT: S 30 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8105 (mt-10) REVERT: T 19 ASP cc_start: 0.9061 (m-30) cc_final: 0.8711 (m-30) REVERT: U 16 THR cc_start: 0.9192 (m) cc_final: 0.8829 (p) REVERT: U 89 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8834 (ttm-80) REVERT: U 98 GLU cc_start: 0.8986 (tt0) cc_final: 0.8666 (tt0) REVERT: V 13 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8277 (mt-10) REVERT: V 39 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8872 (mt) REVERT: V 125 LYS cc_start: 0.8671 (mttt) cc_final: 0.8402 (mtpp) REVERT: W 46 MET cc_start: 0.3652 (ttt) cc_final: 0.2690 (tpt) REVERT: W 52 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6318 (p) REVERT: X 168 ASP cc_start: 0.8484 (t0) cc_final: 0.7479 (t0) REVERT: Z 19 ASP cc_start: 0.8928 (m-30) cc_final: 0.8649 (m-30) REVERT: Z 40 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: Z 94 ASN cc_start: 0.8698 (m-40) cc_final: 0.8441 (m110) REVERT: 0 10 GLN cc_start: 0.9064 (mt0) cc_final: 0.8740 (mt0) REVERT: 0 16 THR cc_start: 0.9039 (m) cc_final: 0.8656 (t) REVERT: 0 47 GLN cc_start: 0.9045 (tt0) cc_final: 0.8665 (mm-40) REVERT: 0 63 LYS cc_start: 0.8616 (tptm) cc_final: 0.8253 (tptt) REVERT: 0 76 ASN cc_start: 0.8453 (m-40) cc_final: 0.8204 (m110) REVERT: 1 30 GLN cc_start: 0.8883 (tt0) cc_final: 0.8612 (tt0) REVERT: 1 68 SER cc_start: 0.9047 (p) cc_final: 0.8406 (p) REVERT: 1 69 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7757 (p0) REVERT: 1 71 LEU cc_start: 0.8715 (tp) cc_final: 0.8438 (mp) REVERT: 1 79 LYS cc_start: 0.8481 (tptp) cc_final: 0.7758 (ttpt) REVERT: 1 105 GLN cc_start: 0.8380 (mt0) cc_final: 0.7988 (mt0) REVERT: 1 114 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: 2 37 GLU cc_start: 0.8536 (tt0) cc_final: 0.8124 (tt0) REVERT: 2 40 THR cc_start: 0.8658 (p) cc_final: 0.8422 (t) REVERT: 2 46 MET cc_start: 0.4406 (ttt) cc_final: 0.3199 (tpt) REVERT: 2 157 THR cc_start: 0.8669 (p) cc_final: 0.8312 (t) REVERT: 3 168 ASP cc_start: 0.8629 (t0) cc_final: 0.8168 (t0) REVERT: 4 16 GLU cc_start: 0.8060 (mp0) cc_final: 0.7824 (mp0) REVERT: 4 32 GLN cc_start: 0.8716 (tt0) cc_final: 0.8117 (tt0) REVERT: 5 44 ILE cc_start: 0.8875 (mp) cc_final: 0.8604 (mt) REVERT: 6 24 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7933 (ptmt) REVERT: 7 12 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8083 (t80) REVERT: 7 13 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8299 (mt-10) REVERT: 7 30 GLN cc_start: 0.8781 (tt0) cc_final: 0.8289 (tt0) REVERT: 7 39 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8627 (mt) REVERT: 7 41 MET cc_start: 0.8786 (tpt) cc_final: 0.8553 (tpp) REVERT: 7 67 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8649 (t) REVERT: 7 69 ASP cc_start: 0.7748 (t0) cc_final: 0.7440 (p0) REVERT: 7 79 LYS cc_start: 0.8588 (tptp) cc_final: 0.7859 (ttpt) REVERT: 7 80 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.8020 (ttp-170) REVERT: 8 40 THR cc_start: 0.8803 (p) cc_final: 0.8532 (t) REVERT: 8 45 THR cc_start: 0.6235 (m) cc_final: 0.5783 (p) REVERT: 8 46 MET cc_start: 0.3628 (ttt) cc_final: 0.2802 (tpt) REVERT: 8 132 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8658 (tt0) REVERT: 9 168 ASP cc_start: 0.8547 (t0) cc_final: 0.8296 (t0) outliers start: 128 outliers final: 97 residues processed: 847 average time/residue: 0.5163 time to fit residues: 691.6953 Evaluate side-chains 843 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 730 time to evaluate : 3.543 ------------------------------------------------------------------------------- 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 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 41 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 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 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS 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 H residue 70 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 9 LYS 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 30 THR Chi-restraints excluded: chain O residue 58 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 67 VAL Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 88 SER 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 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 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 41 ILE Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 58 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 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS 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 Z residue 70 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 9 LYS 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 30 THR Chi-restraints excluded: chain 6 residue 58 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 67 VAL Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 88 SER 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 61 SER 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 197 optimal weight: 0.9990 chunk 337 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 325 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 chunk 251 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS M 97 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 97 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 = 0.3187 r_free = 0.3187 target = 0.104309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.086631 restraints weight = 41606.882| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.26 r_work: 0.2889 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3531 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= 0.175 Angle : 0.536 5.598 39684 Z= 0.292 Chirality : 0.042 0.135 4302 Planarity : 0.004 0.041 5190 Dihedral : 5.586 84.941 3924 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.52 % Allowed : 14.53 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3486 helix: 1.53 (0.17), residues: 924 sheet: -0.25 (0.15), residues: 1128 loop : 0.32 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 89 HIS 0.004 0.001 HIS 1 117 PHE 0.013 0.001 PHE K 110 TYR 0.015 0.002 TYR J 8 ARG 0.010 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 1302) hydrogen bonds : angle 4.36368 ( 3942) covalent geometry : bond 0.00420 (29442) covalent geometry : angle 0.53588 (39684) *********************** 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 894 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 750 time to evaluate : 3.551 Fit side-chains REVERT: A 17 LYS cc_start: 0.9116 (mttt) cc_final: 0.8709 (mtpt) REVERT: A 27 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8736 (ttpt) REVERT: A 30 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 93 ASP cc_start: 0.8826 (t0) cc_final: 0.8586 (t0) REVERT: B 41 VAL cc_start: 0.8688 (t) cc_final: 0.8332 (m) REVERT: C 16 THR cc_start: 0.9214 (m) cc_final: 0.8861 (p) REVERT: C 89 ARG cc_start: 0.9146 (ttm-80) cc_final: 0.8867 (ttm-80) REVERT: D 13 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8256 (mt-10) REVERT: D 39 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8849 (mt) REVERT: D 90 LYS cc_start: 0.8818 (tptm) cc_final: 0.8501 (tptp) REVERT: D 99 ASP cc_start: 0.8679 (t70) cc_final: 0.8296 (t0) REVERT: D 125 LYS cc_start: 0.8747 (mttt) cc_final: 0.8485 (mtpp) REVERT: E 46 MET cc_start: 0.3706 (ttt) cc_final: 0.2819 (tpt) REVERT: E 52 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6472 (p) REVERT: E 94 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8710 (mmm160) REVERT: F 168 ASP cc_start: 0.8511 (t0) cc_final: 0.7511 (t0) REVERT: G 50 TYR cc_start: 0.9313 (p90) cc_final: 0.9107 (p90) REVERT: H 94 ASN cc_start: 0.8751 (m-40) cc_final: 0.8015 (m110) REVERT: I 10 GLN cc_start: 0.9076 (mt0) cc_final: 0.8741 (mt0) REVERT: I 13 GLN cc_start: 0.8349 (mt0) cc_final: 0.8052 (mt0) REVERT: I 16 THR cc_start: 0.9037 (m) cc_final: 0.8626 (t) REVERT: I 47 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8626 (mm-40) REVERT: I 63 LYS cc_start: 0.8655 (tptm) cc_final: 0.8309 (tptt) REVERT: J 13 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8577 (mt-10) REVERT: J 30 GLN cc_start: 0.8895 (tt0) cc_final: 0.8617 (tt0) REVERT: J 68 SER cc_start: 0.9056 (p) cc_final: 0.8397 (p) REVERT: J 69 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7978 (p0) REVERT: J 71 LEU cc_start: 0.8903 (tp) cc_final: 0.8496 (mp) REVERT: J 79 LYS cc_start: 0.8478 (tptp) cc_final: 0.7749 (ttpt) REVERT: J 105 GLN cc_start: 0.8386 (mt0) cc_final: 0.7981 (mt0) REVERT: J 114 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: K 37 GLU cc_start: 0.8530 (tt0) cc_final: 0.8123 (tt0) REVERT: K 40 THR cc_start: 0.8663 (p) cc_final: 0.8428 (t) REVERT: K 46 MET cc_start: 0.4248 (ttt) cc_final: 0.3140 (tpt) REVERT: K 157 THR cc_start: 0.8679 (p) cc_final: 0.8308 (t) REVERT: L 168 ASP cc_start: 0.8635 (t0) cc_final: 0.8153 (t0) REVERT: M 16 GLU cc_start: 0.8033 (mp0) cc_final: 0.7726 (mp0) REVERT: M 32 GLN cc_start: 0.8640 (tt0) cc_final: 0.8023 (tt0) REVERT: N 20 GLU cc_start: 0.8534 (mp0) cc_final: 0.8162 (mp0) REVERT: N 44 ILE cc_start: 0.8869 (mp) cc_final: 0.8573 (mt) REVERT: O 91 GLU cc_start: 0.8033 (tt0) cc_final: 0.7790 (tt0) REVERT: P 12 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.8049 (t80) REVERT: P 13 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8276 (mt-10) REVERT: P 30 GLN cc_start: 0.8788 (tt0) cc_final: 0.8331 (tt0) REVERT: P 41 MET cc_start: 0.8800 (tpt) cc_final: 0.8555 (tpp) REVERT: P 67 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8716 (t) REVERT: P 69 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7511 (p0) REVERT: P 79 LYS cc_start: 0.8562 (tptp) cc_final: 0.7846 (ttpt) REVERT: P 80 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.8049 (ttp-170) REVERT: Q 40 THR cc_start: 0.8816 (p) cc_final: 0.8543 (t) REVERT: Q 45 THR cc_start: 0.6444 (m) cc_final: 0.5955 (p) REVERT: Q 46 MET cc_start: 0.3664 (ttt) cc_final: 0.2945 (tpt) REVERT: S 17 LYS cc_start: 0.9129 (mttt) cc_final: 0.8726 (mtpt) REVERT: S 27 LYS cc_start: 0.9010 (ttpt) cc_final: 0.8737 (ttpt) REVERT: S 30 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8086 (mt-10) REVERT: T 41 VAL cc_start: 0.8693 (t) cc_final: 0.8334 (m) REVERT: U 16 THR cc_start: 0.9219 (m) cc_final: 0.8867 (p) REVERT: U 89 ARG cc_start: 0.9143 (ttm-80) cc_final: 0.8872 (ttm-80) REVERT: V 13 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8282 (mt-10) REVERT: V 39 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8852 (mt) REVERT: V 90 LYS cc_start: 0.8819 (tptm) cc_final: 0.8501 (tptp) REVERT: V 99 ASP cc_start: 0.8677 (t70) cc_final: 0.8292 (t0) REVERT: V 125 LYS cc_start: 0.8745 (mttt) cc_final: 0.8486 (mtpp) REVERT: W 46 MET cc_start: 0.3669 (ttt) cc_final: 0.2785 (tpt) REVERT: W 52 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6454 (p) REVERT: W 94 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8716 (mmm160) REVERT: X 168 ASP cc_start: 0.8501 (t0) cc_final: 0.7493 (t0) REVERT: Y 50 TYR cc_start: 0.9317 (p90) cc_final: 0.9106 (p90) REVERT: Z 94 ASN cc_start: 0.8763 (m-40) cc_final: 0.8029 (m110) REVERT: 0 10 GLN cc_start: 0.9075 (mt0) cc_final: 0.8742 (mt0) REVERT: 0 13 GLN cc_start: 0.8354 (mt0) cc_final: 0.8060 (mt0) REVERT: 0 16 THR cc_start: 0.9031 (m) cc_final: 0.8614 (t) REVERT: 0 47 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: 0 63 LYS cc_start: 0.8669 (tptm) cc_final: 0.8324 (tptt) REVERT: 1 13 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8567 (mt-10) REVERT: 1 30 GLN cc_start: 0.8892 (tt0) cc_final: 0.8606 (tt0) REVERT: 1 68 SER cc_start: 0.9058 (p) cc_final: 0.8408 (p) REVERT: 1 69 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7980 (p0) REVERT: 1 71 LEU cc_start: 0.8914 (tp) cc_final: 0.8506 (mp) REVERT: 1 79 LYS cc_start: 0.8490 (tptp) cc_final: 0.7762 (ttpt) REVERT: 1 105 GLN cc_start: 0.8366 (mt0) cc_final: 0.7957 (mt0) REVERT: 1 114 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: 2 37 GLU cc_start: 0.8504 (tt0) cc_final: 0.8089 (tt0) REVERT: 2 40 THR cc_start: 0.8665 (p) cc_final: 0.8428 (t) REVERT: 2 46 MET cc_start: 0.4270 (ttt) cc_final: 0.3151 (tpt) REVERT: 2 157 THR cc_start: 0.8669 (p) cc_final: 0.8299 (t) REVERT: 3 168 ASP cc_start: 0.8640 (t0) cc_final: 0.8159 (t0) REVERT: 4 16 GLU cc_start: 0.8019 (mp0) cc_final: 0.7723 (mp0) REVERT: 4 32 GLN cc_start: 0.8636 (tt0) cc_final: 0.8046 (tt0) REVERT: 4 50 TYR cc_start: 0.9211 (p90) cc_final: 0.8913 (p90) REVERT: 4 51 MET cc_start: 0.9274 (mtt) cc_final: 0.9035 (mtt) REVERT: 5 44 ILE cc_start: 0.8877 (mp) cc_final: 0.8579 (mt) REVERT: 6 91 GLU cc_start: 0.8019 (tt0) cc_final: 0.7778 (tt0) REVERT: 7 12 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8043 (t80) REVERT: 7 13 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8284 (mt-10) REVERT: 7 30 GLN cc_start: 0.8792 (tt0) cc_final: 0.8338 (tt0) REVERT: 7 41 MET cc_start: 0.8790 (tpt) cc_final: 0.8547 (tpp) REVERT: 7 67 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8720 (t) REVERT: 7 69 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7520 (p0) REVERT: 7 79 LYS cc_start: 0.8578 (tptp) cc_final: 0.7859 (ttpt) REVERT: 7 80 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8041 (ttp-170) REVERT: 8 40 THR cc_start: 0.8813 (p) cc_final: 0.8549 (t) REVERT: 8 45 THR cc_start: 0.6425 (m) cc_final: 0.5937 (p) REVERT: 8 46 MET cc_start: 0.3671 (ttt) cc_final: 0.2943 (tpt) REVERT: 8 132 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8674 (tt0) outliers start: 144 outliers final: 112 residues processed: 810 average time/residue: 0.5543 time to fit residues: 709.3914 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 : 3.442 ------------------------------------------------------------------------------- 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 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 42 SER Chi-restraints excluded: chain C residue 58 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 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS 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 70 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 28 LEU 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 1 MET 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 114 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 9 LYS 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 55 SER Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 88 SER 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 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 42 SER Chi-restraints excluded: chain U residue 58 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 94 ARG Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS 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 70 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 28 LEU 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 1 MET 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 114 GLU Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 9 LYS 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 55 SER Chi-restraints excluded: chain 7 residue 67 VAL Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 88 SER 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 170 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 202 optimal weight: 0.0030 chunk 261 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS W 111 GLN 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.093626 restraints weight = 40455.495| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.23 r_work: 0.2950 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29442 Z= 0.097 Angle : 0.477 5.728 39684 Z= 0.259 Chirality : 0.040 0.125 4302 Planarity : 0.004 0.049 5190 Dihedral : 5.132 81.381 3924 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.45 % Allowed : 16.07 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3486 helix: 1.92 (0.18), residues: 918 sheet: -0.07 (0.14), residues: 1242 loop : 0.18 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 89 HIS 0.003 0.001 HIS 1 74 PHE 0.009 0.001 PHE 8 14 TYR 0.011 0.001 TYR 8 133 ARG 0.013 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 1302) hydrogen bonds : angle 4.15731 ( 3942) covalent geometry : bond 0.00215 (29442) covalent geometry : angle 0.47662 (39684) *********************** 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 891 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 781 time to evaluate : 3.434 Fit side-chains REVERT: A 17 LYS cc_start: 0.9074 (mttt) cc_final: 0.8628 (mtpt) REVERT: A 27 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8666 (ttpt) REVERT: A 30 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8099 (mt-10) REVERT: B 16 GLU cc_start: 0.8227 (mm-30) cc_final: 0.8018 (mm-30) REVERT: C 16 THR cc_start: 0.9193 (m) cc_final: 0.8879 (p) REVERT: C 89 ARG cc_start: 0.9122 (ttm-80) cc_final: 0.8887 (ttm-80) REVERT: D 13 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8285 (mt-10) REVERT: D 99 ASP cc_start: 0.8669 (t70) cc_final: 0.8245 (t0) REVERT: D 125 LYS cc_start: 0.8747 (mttt) cc_final: 0.8489 (mmtm) REVERT: E 46 MET cc_start: 0.3465 (ttt) cc_final: 0.2772 (tpt) REVERT: E 94 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8624 (mmm160) REVERT: F 168 ASP cc_start: 0.8700 (t0) cc_final: 0.7835 (t0) REVERT: H 40 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: H 94 ASN cc_start: 0.8748 (m-40) cc_final: 0.7978 (m110) REVERT: H 95 TYR cc_start: 0.8348 (t80) cc_final: 0.7774 (t80) REVERT: I 10 GLN cc_start: 0.9045 (mt0) cc_final: 0.8740 (mt0) REVERT: I 16 THR cc_start: 0.9000 (m) cc_final: 0.8624 (t) REVERT: I 56 ASP cc_start: 0.8911 (t0) cc_final: 0.8628 (t0) REVERT: I 63 LYS cc_start: 0.8662 (tptm) cc_final: 0.8410 (tptt) REVERT: I 86 ARG cc_start: 0.8672 (mmm-85) cc_final: 0.8217 (mtt180) REVERT: J 13 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8563 (mt-10) REVERT: J 30 GLN cc_start: 0.8804 (tt0) cc_final: 0.8573 (tt0) REVERT: J 68 SER cc_start: 0.9077 (p) cc_final: 0.8684 (p) REVERT: J 69 ASP cc_start: 0.8242 (t0) cc_final: 0.7795 (p0) REVERT: J 71 LEU cc_start: 0.8811 (tp) cc_final: 0.8484 (mp) REVERT: J 79 LYS cc_start: 0.8546 (tptp) cc_final: 0.7825 (ttpt) REVERT: J 105 GLN cc_start: 0.8382 (mt0) cc_final: 0.8015 (mt0) REVERT: J 114 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: K 37 GLU cc_start: 0.8354 (tt0) cc_final: 0.7960 (tt0) REVERT: K 46 MET cc_start: 0.4144 (ttt) cc_final: 0.3231 (tpt) REVERT: K 111 GLN cc_start: 0.9311 (pt0) cc_final: 0.8671 (pt0) REVERT: K 157 THR cc_start: 0.8684 (p) cc_final: 0.8313 (t) REVERT: L 168 ASP cc_start: 0.8629 (t0) cc_final: 0.8161 (t0) REVERT: M 32 GLN cc_start: 0.8627 (tt0) cc_final: 0.7989 (tt0) REVERT: M 50 TYR cc_start: 0.9244 (p90) cc_final: 0.8959 (p90) REVERT: M 51 MET cc_start: 0.9305 (mtt) cc_final: 0.9080 (mtt) REVERT: N 44 ILE cc_start: 0.8827 (mp) cc_final: 0.8557 (mt) REVERT: O 91 GLU cc_start: 0.7921 (tt0) cc_final: 0.7680 (tt0) REVERT: P 12 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7993 (t80) REVERT: P 13 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8271 (mt-10) REVERT: P 30 GLN cc_start: 0.8724 (tt0) cc_final: 0.8230 (tt0) REVERT: P 39 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8648 (mt) REVERT: P 41 MET cc_start: 0.8827 (tpt) cc_final: 0.8607 (tpp) REVERT: P 52 ASP cc_start: 0.8485 (m-30) cc_final: 0.8244 (m-30) REVERT: P 67 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8682 (t) REVERT: P 69 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7523 (p0) REVERT: P 79 LYS cc_start: 0.8575 (tptp) cc_final: 0.7862 (ttpt) REVERT: P 80 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8102 (ttp80) REVERT: Q 40 THR cc_start: 0.8758 (p) cc_final: 0.8524 (t) REVERT: Q 45 THR cc_start: 0.6520 (m) cc_final: 0.5995 (p) REVERT: Q 46 MET cc_start: 0.3535 (ttt) cc_final: 0.2973 (tpt) REVERT: S 17 LYS cc_start: 0.9074 (mttt) cc_final: 0.8626 (mtpt) REVERT: S 27 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8655 (ttpt) REVERT: S 30 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8078 (mt-10) REVERT: T 16 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8029 (mm-30) REVERT: U 16 THR cc_start: 0.9192 (m) cc_final: 0.8878 (p) REVERT: U 89 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8892 (ttm-80) REVERT: V 13 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8299 (mt-10) REVERT: V 99 ASP cc_start: 0.8674 (t70) cc_final: 0.8253 (t0) REVERT: V 125 LYS cc_start: 0.8734 (mttt) cc_final: 0.8483 (mmtm) REVERT: W 46 MET cc_start: 0.3446 (ttt) cc_final: 0.2761 (tpt) REVERT: X 168 ASP cc_start: 0.8712 (t0) cc_final: 0.7842 (t0) REVERT: Z 40 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: Z 94 ASN cc_start: 0.8754 (m-40) cc_final: 0.7985 (m110) REVERT: Z 95 TYR cc_start: 0.8349 (t80) cc_final: 0.7779 (t80) REVERT: 0 10 GLN cc_start: 0.9055 (mt0) cc_final: 0.8748 (mt0) REVERT: 0 16 THR cc_start: 0.9000 (m) cc_final: 0.8614 (t) REVERT: 0 56 ASP cc_start: 0.8926 (t0) cc_final: 0.8649 (t0) REVERT: 0 63 LYS cc_start: 0.8678 (tptm) cc_final: 0.8428 (tptt) REVERT: 0 86 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8231 (mtt180) REVERT: 1 13 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8548 (mt-10) REVERT: 1 30 GLN cc_start: 0.8812 (tt0) cc_final: 0.8570 (tt0) REVERT: 1 68 SER cc_start: 0.9081 (p) cc_final: 0.8704 (p) REVERT: 1 69 ASP cc_start: 0.8257 (t0) cc_final: 0.7807 (p0) REVERT: 1 71 LEU cc_start: 0.8830 (tp) cc_final: 0.8499 (mp) REVERT: 1 79 LYS cc_start: 0.8534 (tptp) cc_final: 0.7815 (ttpt) REVERT: 1 105 GLN cc_start: 0.8360 (mt0) cc_final: 0.7992 (mt0) REVERT: 2 37 GLU cc_start: 0.8384 (tt0) cc_final: 0.7995 (tt0) REVERT: 2 46 MET cc_start: 0.4162 (ttt) cc_final: 0.3241 (tpt) REVERT: 2 111 GLN cc_start: 0.9308 (pt0) cc_final: 0.8678 (pt0) REVERT: 2 157 THR cc_start: 0.8685 (p) cc_final: 0.8314 (t) REVERT: 3 168 ASP cc_start: 0.8630 (t0) cc_final: 0.8163 (t0) REVERT: 4 32 GLN cc_start: 0.8660 (tt0) cc_final: 0.8133 (tt0) REVERT: 4 50 TYR cc_start: 0.9216 (p90) cc_final: 0.8992 (p90) REVERT: 4 51 MET cc_start: 0.9253 (mtt) cc_final: 0.9005 (mtt) REVERT: 5 20 GLU cc_start: 0.8426 (mp0) cc_final: 0.8087 (mp0) REVERT: 5 44 ILE cc_start: 0.8828 (mp) cc_final: 0.8553 (mt) REVERT: 6 91 GLU cc_start: 0.7960 (tt0) cc_final: 0.7713 (tt0) REVERT: 7 12 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7997 (t80) REVERT: 7 13 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8258 (mt-10) REVERT: 7 30 GLN cc_start: 0.8736 (tt0) cc_final: 0.8234 (tt0) REVERT: 7 39 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8648 (mt) REVERT: 7 41 MET cc_start: 0.8818 (tpt) cc_final: 0.8595 (tpp) REVERT: 7 52 ASP cc_start: 0.8476 (m-30) cc_final: 0.8226 (m-30) REVERT: 7 67 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8681 (t) REVERT: 7 69 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7458 (p0) REVERT: 7 79 LYS cc_start: 0.8583 (tptp) cc_final: 0.7898 (ttpt) REVERT: 7 80 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8096 (ttp80) REVERT: 8 40 THR cc_start: 0.8759 (p) cc_final: 0.8528 (t) REVERT: 8 45 THR cc_start: 0.6488 (m) cc_final: 0.5975 (p) REVERT: 8 46 MET cc_start: 0.3533 (ttt) cc_final: 0.2960 (tpt) outliers start: 110 outliers final: 72 residues processed: 827 average time/residue: 0.4594 time to fit residues: 589.0173 Evaluate side-chains 806 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 722 time to evaluate : 3.837 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain D residue 12 TYR 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 94 ARG Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 27 LYS 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 40 GLU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 9 LYS 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 58 SER 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 55 SER Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 114 GLU 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 34 LEU Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 49 SER Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 58 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 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 27 LYS 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 40 GLU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 2 residue 110 PHE Chi-restraints excluded: chain 4 residue 9 LYS 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 58 SER 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 55 SER Chi-restraints excluded: chain 7 residue 67 VAL 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 8 residue 26 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 292 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 J 16 GLN M 97 ASN N 61 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 GLN P 117 HIS Y 18 GLN 0 76 ASN 1 16 GLN 4 97 ASN 5 61 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 GLN 7 117 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.086750 restraints weight = 41215.268| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.23 r_work: 0.2818 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 29442 Z= 0.288 Angle : 0.611 8.743 39684 Z= 0.330 Chirality : 0.045 0.150 4302 Planarity : 0.004 0.052 5190 Dihedral : 5.696 85.763 3924 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.08 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3486 helix: 1.49 (0.17), residues: 924 sheet: -0.45 (0.15), residues: 1140 loop : 0.14 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 89 HIS 0.006 0.002 HIS 7 117 PHE 0.019 0.002 PHE K 110 TYR 0.023 0.002 TYR 1 8 ARG 0.011 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1302) hydrogen bonds : angle 4.52302 ( 3942) covalent geometry : bond 0.00702 (29442) covalent geometry : angle 0.61141 (39684) *********************** 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 831 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 701 time to evaluate : 3.183 Fit side-chains REVERT: A 17 LYS cc_start: 0.9107 (mttt) cc_final: 0.8666 (mtpt) REVERT: A 27 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8753 (ttpt) REVERT: A 30 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 16 THR cc_start: 0.9267 (m) cc_final: 0.8947 (p) REVERT: C 89 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8911 (ttm-80) REVERT: C 98 GLU cc_start: 0.8781 (tt0) cc_final: 0.8518 (tt0) REVERT: D 13 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8273 (mt-10) REVERT: D 90 LYS cc_start: 0.8838 (tptm) cc_final: 0.8625 (tptp) REVERT: D 125 LYS cc_start: 0.8792 (mttt) cc_final: 0.8517 (mtpp) REVERT: E 46 MET cc_start: 0.3460 (ttt) cc_final: 0.2681 (tpt) REVERT: E 94 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8702 (mmm160) REVERT: F 168 ASP cc_start: 0.8474 (t0) cc_final: 0.7464 (t0) REVERT: H 40 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: I 10 GLN cc_start: 0.9099 (mt0) cc_final: 0.8791 (mt0) REVERT: I 13 GLN cc_start: 0.8276 (mt0) cc_final: 0.8065 (mt0) REVERT: I 16 THR cc_start: 0.9032 (m) cc_final: 0.8579 (t) REVERT: I 56 ASP cc_start: 0.9113 (t0) cc_final: 0.8907 (t0) REVERT: I 65 SER cc_start: 0.9415 (p) cc_final: 0.9207 (t) REVERT: J 13 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8606 (mt-10) REVERT: J 30 GLN cc_start: 0.9005 (tt0) cc_final: 0.8765 (tt0) REVERT: J 69 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8133 (p0) REVERT: J 79 LYS cc_start: 0.8559 (tptp) cc_final: 0.7829 (ttpt) REVERT: J 114 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: K 37 GLU cc_start: 0.8564 (tt0) cc_final: 0.8283 (tt0) REVERT: K 46 MET cc_start: 0.4385 (ttt) cc_final: 0.3252 (tpt) REVERT: K 111 GLN cc_start: 0.9376 (pt0) cc_final: 0.8830 (pt0) REVERT: K 157 THR cc_start: 0.8646 (p) cc_final: 0.8242 (t) REVERT: L 168 ASP cc_start: 0.8656 (t0) cc_final: 0.7861 (t0) REVERT: M 32 GLN cc_start: 0.8786 (tt0) cc_final: 0.8093 (tt0) REVERT: N 20 GLU cc_start: 0.8454 (mp0) cc_final: 0.8115 (mp0) REVERT: N 44 ILE cc_start: 0.8941 (mp) cc_final: 0.8608 (mt) REVERT: P 12 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8217 (t80) REVERT: P 13 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8337 (mt-10) REVERT: P 15 LEU cc_start: 0.9150 (mt) cc_final: 0.8820 (mm) REVERT: P 41 MET cc_start: 0.8778 (tpt) cc_final: 0.8529 (tpp) REVERT: P 69 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7425 (p0) REVERT: P 79 LYS cc_start: 0.8613 (tptp) cc_final: 0.7904 (ttpt) REVERT: P 80 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8103 (ttp80) REVERT: Q 40 THR cc_start: 0.8774 (p) cc_final: 0.8524 (t) REVERT: Q 45 THR cc_start: 0.6551 (m) cc_final: 0.6045 (p) REVERT: Q 46 MET cc_start: 0.3804 (ttt) cc_final: 0.3113 (tpt) REVERT: S 17 LYS cc_start: 0.9118 (mttt) cc_final: 0.8684 (mtpt) REVERT: S 27 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8758 (ttpt) REVERT: S 30 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8138 (mt-10) REVERT: U 16 THR cc_start: 0.9276 (m) cc_final: 0.8958 (p) REVERT: U 89 ARG cc_start: 0.9152 (ttm-80) cc_final: 0.8919 (ttm-80) REVERT: U 98 GLU cc_start: 0.8788 (tt0) cc_final: 0.8528 (tt0) REVERT: V 13 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8266 (mt-10) REVERT: V 125 LYS cc_start: 0.8762 (mttt) cc_final: 0.8489 (mtpp) REVERT: W 46 MET cc_start: 0.3403 (ttt) cc_final: 0.2641 (tpt) REVERT: X 168 ASP cc_start: 0.8478 (t0) cc_final: 0.7473 (t0) REVERT: Z 40 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: 0 10 GLN cc_start: 0.9103 (mt0) cc_final: 0.8794 (mt0) REVERT: 0 13 GLN cc_start: 0.8269 (mt0) cc_final: 0.8060 (mt0) REVERT: 0 16 THR cc_start: 0.9028 (m) cc_final: 0.8569 (t) REVERT: 0 56 ASP cc_start: 0.9113 (t0) cc_final: 0.8910 (t0) REVERT: 0 65 SER cc_start: 0.9409 (p) cc_final: 0.9200 (t) REVERT: 1 13 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8597 (mt-10) REVERT: 1 30 GLN cc_start: 0.9007 (tt0) cc_final: 0.8761 (tt0) REVERT: 1 68 SER cc_start: 0.9025 (p) cc_final: 0.8411 (p) REVERT: 1 69 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7985 (p0) REVERT: 1 79 LYS cc_start: 0.8550 (tptp) cc_final: 0.7817 (ttpt) REVERT: 1 114 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: 2 37 GLU cc_start: 0.8576 (tt0) cc_final: 0.8300 (tt0) REVERT: 2 46 MET cc_start: 0.4385 (ttt) cc_final: 0.3259 (tpt) REVERT: 2 111 GLN cc_start: 0.9376 (pt0) cc_final: 0.8835 (pt0) REVERT: 2 157 THR cc_start: 0.8637 (p) cc_final: 0.8236 (t) REVERT: 3 168 ASP cc_start: 0.8665 (t0) cc_final: 0.7874 (t0) REVERT: 4 32 GLN cc_start: 0.8773 (tt0) cc_final: 0.8091 (tt0) REVERT: 4 51 MET cc_start: 0.9321 (mtt) cc_final: 0.9120 (mtt) REVERT: 4 61 ASN cc_start: 0.8620 (m-40) cc_final: 0.8273 (m110) REVERT: 5 20 GLU cc_start: 0.8508 (mp0) cc_final: 0.8070 (mp0) REVERT: 5 44 ILE cc_start: 0.8942 (mp) cc_final: 0.8603 (mt) REVERT: 7 12 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8217 (t80) REVERT: 7 13 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8326 (mt-10) REVERT: 7 15 LEU cc_start: 0.9150 (mt) cc_final: 0.8823 (mm) REVERT: 7 41 MET cc_start: 0.8767 (tpt) cc_final: 0.8519 (tpp) REVERT: 7 69 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7418 (p0) REVERT: 7 79 LYS cc_start: 0.8620 (tptp) cc_final: 0.7913 (ttpt) REVERT: 7 80 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8100 (ttp80) REVERT: 8 40 THR cc_start: 0.8777 (p) cc_final: 0.8525 (t) REVERT: 8 45 THR cc_start: 0.6560 (m) cc_final: 0.6054 (p) REVERT: 8 46 MET cc_start: 0.3802 (ttt) cc_final: 0.3115 (tpt) outliers start: 130 outliers final: 110 residues processed: 759 average time/residue: 0.4226 time to fit residues: 501.1916 Evaluate side-chains 805 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 684 time to evaluate : 3.513 ------------------------------------------------------------------------------- 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 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 42 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 THR 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 D residue 126 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 27 LYS 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 28 LEU Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 21 VAL 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 58 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 55 SER Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ASP 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 S residue 39 ILE Chi-restraints excluded: chain T 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 58 SER 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 71 LEU Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain W residue 31 GLU 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 27 LYS 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 28 LEU Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 21 VAL 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 58 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 55 SER Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 67 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 236 optimal weight: 6.9990 chunk 258 optimal weight: 0.0370 chunk 223 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 G 97 ASN I 76 ASN M 18 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS Y 18 GLN Y 97 ASN 0 76 ASN 4 18 GLN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.090307 restraints weight = 41122.206| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.25 r_work: 0.2885 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29442 Z= 0.127 Angle : 0.506 5.969 39684 Z= 0.275 Chirality : 0.041 0.127 4302 Planarity : 0.003 0.045 5190 Dihedral : 5.313 84.576 3924 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.05 % Allowed : 16.67 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3486 helix: 1.81 (0.17), residues: 924 sheet: -0.39 (0.15), residues: 1140 loop : 0.17 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 89 HIS 0.004 0.001 HIS J 74 PHE 0.010 0.001 PHE E 110 TYR 0.014 0.001 TYR V 124 ARG 0.010 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1302) hydrogen bonds : angle 4.29398 ( 3942) covalent geometry : bond 0.00299 (29442) covalent geometry : angle 0.50587 (39684) *********************** 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 864 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 735 time to evaluate : 3.440 Fit side-chains REVERT: A 17 LYS cc_start: 0.9090 (mttt) cc_final: 0.8672 (mtpt) REVERT: A 27 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8703 (ttpt) REVERT: A 30 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 42 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7579 (tp30) REVERT: B 40 GLU cc_start: 0.7768 (mp0) cc_final: 0.7548 (pt0) REVERT: C 13 GLN cc_start: 0.8194 (mt0) cc_final: 0.7909 (mt0) REVERT: C 16 THR cc_start: 0.9234 (m) cc_final: 0.8947 (p) REVERT: C 89 ARG cc_start: 0.9128 (ttm-80) cc_final: 0.8907 (ttm-80) REVERT: D 13 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8261 (mt-10) REVERT: D 90 LYS cc_start: 0.8823 (tptm) cc_final: 0.8481 (tptp) REVERT: D 125 LYS cc_start: 0.8777 (mttt) cc_final: 0.8485 (mtpp) REVERT: E 46 MET cc_start: 0.3213 (ttt) cc_final: 0.2570 (tpt) REVERT: E 94 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8613 (mmm160) REVERT: F 168 ASP cc_start: 0.8635 (t0) cc_final: 0.7877 (t0) REVERT: H 40 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: H 95 TYR cc_start: 0.8346 (t80) cc_final: 0.7724 (t80) REVERT: I 10 GLN cc_start: 0.9051 (mt0) cc_final: 0.8734 (mt0) REVERT: I 16 THR cc_start: 0.9020 (m) cc_final: 0.8665 (p) REVERT: I 56 ASP cc_start: 0.8989 (t0) cc_final: 0.8723 (t0) REVERT: I 86 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8315 (mtt180) REVERT: J 13 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8590 (mt-10) REVERT: J 30 GLN cc_start: 0.8885 (tt0) cc_final: 0.8612 (tt0) REVERT: J 69 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8099 (p0) REVERT: J 79 LYS cc_start: 0.8501 (tptp) cc_final: 0.7782 (ttpt) REVERT: J 114 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: K 37 GLU cc_start: 0.8500 (tt0) cc_final: 0.8066 (tt0) REVERT: K 46 MET cc_start: 0.4238 (ttt) cc_final: 0.3242 (tpt) REVERT: K 111 GLN cc_start: 0.9330 (pt0) cc_final: 0.8588 (pt0) REVERT: K 157 THR cc_start: 0.8626 (p) cc_final: 0.8217 (t) REVERT: L 168 ASP cc_start: 0.8635 (t0) cc_final: 0.8189 (t0) REVERT: M 32 GLN cc_start: 0.8732 (tt0) cc_final: 0.8159 (tt0) REVERT: M 50 TYR cc_start: 0.9233 (p90) cc_final: 0.8941 (p90) REVERT: N 20 GLU cc_start: 0.8499 (mp0) cc_final: 0.8134 (mp0) REVERT: N 44 ILE cc_start: 0.8825 (mp) cc_final: 0.8512 (mt) REVERT: O 91 GLU cc_start: 0.7956 (tt0) cc_final: 0.7679 (tt0) REVERT: P 12 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8011 (t80) REVERT: P 13 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8238 (mt-10) REVERT: P 15 LEU cc_start: 0.9032 (mt) cc_final: 0.8675 (mm) REVERT: P 30 GLN cc_start: 0.8753 (tt0) cc_final: 0.8250 (tt0) REVERT: P 52 ASP cc_start: 0.8702 (m-30) cc_final: 0.8454 (m-30) REVERT: P 67 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8600 (t) REVERT: P 69 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7537 (p0) REVERT: P 79 LYS cc_start: 0.8595 (tptp) cc_final: 0.7874 (ttpt) REVERT: P 80 ARG cc_start: 0.8308 (ttm-80) cc_final: 0.8073 (ttp-170) REVERT: Q 40 THR cc_start: 0.8817 (p) cc_final: 0.8530 (t) REVERT: Q 45 THR cc_start: 0.6570 (m) cc_final: 0.6052 (p) REVERT: Q 46 MET cc_start: 0.3552 (ttt) cc_final: 0.2957 (tpt) REVERT: Q 132 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8722 (tt0) REVERT: S 17 LYS cc_start: 0.9088 (mttt) cc_final: 0.8670 (mtpt) REVERT: S 27 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8705 (ttpt) REVERT: S 30 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8112 (mt-10) REVERT: S 42 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7585 (tp30) REVERT: T 40 GLU cc_start: 0.7739 (mp0) cc_final: 0.7533 (pt0) REVERT: U 13 GLN cc_start: 0.8191 (mt0) cc_final: 0.7904 (mt0) REVERT: U 16 THR cc_start: 0.9244 (m) cc_final: 0.8953 (p) REVERT: U 89 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8900 (ttm-80) REVERT: V 13 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8259 (mt-10) REVERT: V 125 LYS cc_start: 0.8761 (mttt) cc_final: 0.8472 (mtpp) REVERT: W 46 MET cc_start: 0.3148 (ttt) cc_final: 0.2528 (tpt) REVERT: X 168 ASP cc_start: 0.8637 (t0) cc_final: 0.7877 (t0) REVERT: Z 40 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: Z 95 TYR cc_start: 0.8349 (t80) cc_final: 0.7725 (t80) REVERT: 0 10 GLN cc_start: 0.9047 (mt0) cc_final: 0.8729 (mt0) REVERT: 0 16 THR cc_start: 0.9019 (m) cc_final: 0.8661 (p) REVERT: 0 56 ASP cc_start: 0.9018 (t0) cc_final: 0.8761 (t0) REVERT: 0 86 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8389 (mtt180) REVERT: 1 13 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8567 (mt-10) REVERT: 1 30 GLN cc_start: 0.8887 (tt0) cc_final: 0.8608 (tt0) REVERT: 1 68 SER cc_start: 0.9031 (p) cc_final: 0.8330 (p) REVERT: 1 69 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7861 (p0) REVERT: 1 79 LYS cc_start: 0.8498 (tptp) cc_final: 0.7778 (ttpt) REVERT: 1 114 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7996 (tt0) REVERT: 2 37 GLU cc_start: 0.8528 (tt0) cc_final: 0.8108 (tt0) REVERT: 2 46 MET cc_start: 0.4221 (ttt) cc_final: 0.3238 (tpt) REVERT: 2 111 GLN cc_start: 0.9319 (pt0) cc_final: 0.8576 (pt0) REVERT: 2 157 THR cc_start: 0.8624 (p) cc_final: 0.8217 (t) REVERT: 3 168 ASP cc_start: 0.8633 (t0) cc_final: 0.8183 (t0) REVERT: 4 32 GLN cc_start: 0.8711 (tt0) cc_final: 0.8147 (tt0) REVERT: 4 50 TYR cc_start: 0.9190 (p90) cc_final: 0.8793 (p90) REVERT: 4 51 MET cc_start: 0.9234 (mtt) cc_final: 0.8987 (mtt) REVERT: 5 44 ILE cc_start: 0.8825 (mp) cc_final: 0.8512 (mt) REVERT: 6 91 GLU cc_start: 0.7965 (tt0) cc_final: 0.7691 (tt0) REVERT: 7 12 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8024 (t80) REVERT: 7 13 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8235 (mt-10) REVERT: 7 15 LEU cc_start: 0.9036 (mt) cc_final: 0.8684 (mm) REVERT: 7 28 MET cc_start: 0.9363 (ttp) cc_final: 0.9051 (ttt) REVERT: 7 30 GLN cc_start: 0.8765 (tt0) cc_final: 0.8257 (tt0) REVERT: 7 52 ASP cc_start: 0.8690 (m-30) cc_final: 0.8436 (m-30) REVERT: 7 67 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8588 (t) REVERT: 7 69 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7473 (p0) REVERT: 7 79 LYS cc_start: 0.8597 (tptp) cc_final: 0.7873 (ttpt) REVERT: 7 80 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8055 (ttp-170) REVERT: 8 40 THR cc_start: 0.8821 (p) cc_final: 0.8538 (t) REVERT: 8 45 THR cc_start: 0.6557 (m) cc_final: 0.6047 (p) REVERT: 8 46 MET cc_start: 0.3552 (ttt) cc_final: 0.2952 (tpt) REVERT: 8 132 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8723 (tt0) outliers start: 129 outliers final: 95 residues processed: 799 average time/residue: 0.4427 time to fit residues: 555.2031 Evaluate side-chains 824 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 716 time to evaluate : 3.627 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain B 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 42 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 THR 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 126 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 27 LYS 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 49 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 1 MET 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 110 PHE Chi-restraints excluded: chain M residue 9 LYS 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 58 SER Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ASP 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 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 34 LEU Chi-restraints excluded: chain T 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 58 SER Chi-restraints excluded: chain U residue 85 THR 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 126 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 27 LYS 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 49 SER Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 1 MET 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 9 LYS 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 58 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 55 SER Chi-restraints excluded: chain 7 residue 67 VAL 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 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 216 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN I 76 ASN M 97 ASN N 61 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS Y 18 GLN 0 76 ASN 4 97 ASN 5 61 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.089666 restraints weight = 40909.038| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.25 r_work: 0.2879 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29442 Z= 0.147 Angle : 0.519 6.110 39684 Z= 0.282 Chirality : 0.041 0.125 4302 Planarity : 0.004 0.058 5190 Dihedral : 5.284 82.953 3924 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.83 % Allowed : 16.95 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3486 helix: 1.89 (0.17), residues: 924 sheet: -0.40 (0.15), residues: 1140 loop : 0.18 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 89 HIS 0.004 0.001 HIS V 74 PHE 0.012 0.001 PHE K 110 TYR 0.014 0.001 TYR A 95 ARG 0.013 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1302) hydrogen bonds : angle 4.31126 ( 3942) covalent geometry : bond 0.00353 (29442) covalent geometry : angle 0.51898 (39684) *********************** 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 851 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 729 time to evaluate : 3.459 Fit side-chains REVERT: A 17 LYS cc_start: 0.9125 (mttt) cc_final: 0.8699 (mtpt) REVERT: A 27 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8745 (ttpt) REVERT: A 30 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 42 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7741 (tp30) REVERT: B 19 ASP cc_start: 0.9052 (m-30) cc_final: 0.8825 (m-30) REVERT: C 13 GLN cc_start: 0.8219 (mt0) cc_final: 0.7940 (mt0) REVERT: C 16 THR cc_start: 0.9240 (m) cc_final: 0.8956 (p) REVERT: C 89 ARG cc_start: 0.9127 (ttm-80) cc_final: 0.8909 (ttm-80) REVERT: D 13 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8246 (mt-10) REVERT: D 90 LYS cc_start: 0.8814 (tptm) cc_final: 0.8492 (tptp) REVERT: D 99 ASP cc_start: 0.8666 (t70) cc_final: 0.8303 (t0) REVERT: D 125 LYS cc_start: 0.8767 (mttt) cc_final: 0.8480 (mtpp) REVERT: E 46 MET cc_start: 0.3209 (ttt) cc_final: 0.2589 (tpt) REVERT: E 94 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8587 (mmm160) REVERT: F 168 ASP cc_start: 0.8630 (t0) cc_final: 0.7864 (t0) REVERT: H 40 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: H 95 TYR cc_start: 0.8379 (t80) cc_final: 0.7763 (t80) REVERT: I 10 GLN cc_start: 0.9067 (mt0) cc_final: 0.8764 (mt0) REVERT: I 16 THR cc_start: 0.9014 (m) cc_final: 0.8672 (p) REVERT: I 20 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8335 (mmmt) REVERT: I 47 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8626 (mm110) REVERT: I 56 ASP cc_start: 0.9026 (t0) cc_final: 0.8783 (t0) REVERT: I 86 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8330 (mtt180) REVERT: J 13 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8609 (mt-10) REVERT: J 30 GLN cc_start: 0.8921 (tt0) cc_final: 0.8714 (tt0) REVERT: J 40 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8791 (mtmt) REVERT: J 69 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8124 (p0) REVERT: J 79 LYS cc_start: 0.8526 (tptp) cc_final: 0.7798 (ttpt) REVERT: J 114 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: K 37 GLU cc_start: 0.8492 (tt0) cc_final: 0.8041 (tt0) REVERT: K 46 MET cc_start: 0.4225 (ttt) cc_final: 0.3268 (tpt) REVERT: K 111 GLN cc_start: 0.9337 (pt0) cc_final: 0.8631 (pt0) REVERT: K 157 THR cc_start: 0.8623 (p) cc_final: 0.8209 (t) REVERT: L 168 ASP cc_start: 0.8630 (t0) cc_final: 0.8182 (t0) REVERT: M 32 GLN cc_start: 0.8756 (tt0) cc_final: 0.8158 (tt0) REVERT: M 50 TYR cc_start: 0.9256 (p90) cc_final: 0.8949 (p90) REVERT: M 89 GLU cc_start: 0.8142 (pt0) cc_final: 0.7791 (pt0) REVERT: N 20 GLU cc_start: 0.8529 (mp0) cc_final: 0.8083 (mp0) REVERT: N 44 ILE cc_start: 0.8823 (mp) cc_final: 0.8517 (mt) REVERT: O 91 GLU cc_start: 0.8037 (tt0) cc_final: 0.7778 (tt0) REVERT: P 12 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8003 (t80) REVERT: P 13 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8163 (mt-10) REVERT: P 30 GLN cc_start: 0.8790 (tt0) cc_final: 0.8345 (tt0) REVERT: P 52 ASP cc_start: 0.8708 (m-30) cc_final: 0.8462 (m-30) REVERT: P 67 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8613 (t) REVERT: P 69 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7525 (p0) REVERT: P 79 LYS cc_start: 0.8595 (tptp) cc_final: 0.7884 (ttpt) REVERT: P 80 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.8102 (ttp80) REVERT: Q 40 THR cc_start: 0.8811 (p) cc_final: 0.8529 (t) REVERT: Q 45 THR cc_start: 0.6656 (m) cc_final: 0.6088 (p) REVERT: Q 46 MET cc_start: 0.3579 (ttt) cc_final: 0.2993 (tpt) REVERT: R 168 ASP cc_start: 0.8555 (t0) cc_final: 0.8276 (t0) REVERT: S 17 LYS cc_start: 0.9123 (mttt) cc_final: 0.8695 (mtpt) REVERT: S 27 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8745 (ttpt) REVERT: S 30 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8145 (mt-10) REVERT: S 42 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7745 (tp30) REVERT: T 19 ASP cc_start: 0.9049 (m-30) cc_final: 0.8819 (m-30) REVERT: U 13 GLN cc_start: 0.8227 (mt0) cc_final: 0.7947 (mt0) REVERT: U 16 THR cc_start: 0.9248 (m) cc_final: 0.8963 (p) REVERT: U 89 ARG cc_start: 0.9111 (ttm-80) cc_final: 0.8905 (ttm-80) REVERT: V 13 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8231 (mt-10) REVERT: V 99 ASP cc_start: 0.8663 (t70) cc_final: 0.8296 (t0) REVERT: V 125 LYS cc_start: 0.8749 (mttt) cc_final: 0.8472 (mtpp) REVERT: W 46 MET cc_start: 0.3151 (ttt) cc_final: 0.2557 (tpt) REVERT: X 168 ASP cc_start: 0.8648 (t0) cc_final: 0.7885 (t0) REVERT: Z 40 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: Z 94 ASN cc_start: 0.8574 (m-40) cc_final: 0.8042 (m110) REVERT: Z 95 TYR cc_start: 0.8376 (t80) cc_final: 0.7750 (t80) REVERT: 0 10 GLN cc_start: 0.9072 (mt0) cc_final: 0.8764 (mt0) REVERT: 0 16 THR cc_start: 0.9011 (m) cc_final: 0.8663 (p) REVERT: 0 20 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8318 (mmmt) REVERT: 0 47 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8613 (mm110) REVERT: 0 56 ASP cc_start: 0.9055 (t0) cc_final: 0.8818 (t0) REVERT: 0 86 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8401 (mtt180) REVERT: 1 13 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8594 (mt-10) REVERT: 1 30 GLN cc_start: 0.8915 (tt0) cc_final: 0.8705 (tt0) REVERT: 1 40 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8798 (mtmt) REVERT: 1 68 SER cc_start: 0.9029 (p) cc_final: 0.8307 (p) REVERT: 1 69 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8074 (p0) REVERT: 1 79 LYS cc_start: 0.8533 (tptp) cc_final: 0.7805 (ttpt) REVERT: 1 114 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: 2 37 GLU cc_start: 0.8520 (tt0) cc_final: 0.8086 (tt0) REVERT: 2 46 MET cc_start: 0.4155 (ttt) cc_final: 0.3203 (tpt) REVERT: 2 111 GLN cc_start: 0.9337 (pt0) cc_final: 0.8641 (pt0) REVERT: 2 157 THR cc_start: 0.8618 (p) cc_final: 0.8207 (t) REVERT: 3 168 ASP cc_start: 0.8627 (t0) cc_final: 0.8180 (t0) REVERT: 4 32 GLN cc_start: 0.8732 (tt0) cc_final: 0.8144 (tt0) REVERT: 4 50 TYR cc_start: 0.9188 (p90) cc_final: 0.8942 (p90) REVERT: 4 89 GLU cc_start: 0.8187 (pt0) cc_final: 0.7763 (pt0) REVERT: 5 44 ILE cc_start: 0.8831 (mp) cc_final: 0.8519 (mt) REVERT: 6 91 GLU cc_start: 0.8047 (tt0) cc_final: 0.7796 (tt0) REVERT: 7 12 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8016 (t80) REVERT: 7 13 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8157 (mt-10) REVERT: 7 30 GLN cc_start: 0.8785 (tt0) cc_final: 0.8333 (tt0) REVERT: 7 52 ASP cc_start: 0.8741 (m-30) cc_final: 0.8488 (m-30) REVERT: 7 67 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8598 (t) REVERT: 7 69 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7527 (p0) REVERT: 7 79 LYS cc_start: 0.8607 (tptp) cc_final: 0.7893 (ttpt) REVERT: 7 80 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8108 (ttp80) REVERT: 8 40 THR cc_start: 0.8812 (p) cc_final: 0.8534 (t) REVERT: 8 45 THR cc_start: 0.6629 (m) cc_final: 0.6069 (p) REVERT: 8 46 MET cc_start: 0.3569 (ttt) cc_final: 0.2984 (tpt) REVERT: 9 168 ASP cc_start: 0.8548 (t0) cc_final: 0.8264 (t0) outliers start: 122 outliers final: 102 residues processed: 791 average time/residue: 0.4190 time to fit residues: 517.5572 Evaluate side-chains 832 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 717 time to evaluate : 3.151 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain B 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 42 SER Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 85 THR 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 126 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 26 ILE Chi-restraints excluded: chain G residue 27 LYS 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 49 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 1 MET 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 110 PHE Chi-restraints excluded: chain M residue 9 LYS 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 58 SER 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 55 SER Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ASP 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 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 34 LEU Chi-restraints excluded: chain T 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 58 SER Chi-restraints excluded: chain U residue 85 THR 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 126 THR Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS 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 49 SER Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 1 MET 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 9 LYS 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 58 SER 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 67 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 86 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 172 optimal weight: 0.2980 chunk 158 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN I 76 ASN M 97 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS Y 18 GLN 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.089152 restraints weight = 41139.476| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.37 r_work: 0.2860 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29442 Z= 0.118 Angle : 0.497 6.445 39684 Z= 0.270 Chirality : 0.041 0.124 4302 Planarity : 0.004 0.058 5190 Dihedral : 5.117 80.466 3924 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.58 % Allowed : 17.45 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3486 helix: 2.02 (0.17), residues: 924 sheet: -0.36 (0.15), residues: 1140 loop : 0.17 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 89 HIS 0.003 0.001 HIS 1 74 PHE 0.011 0.001 PHE E 110 TYR 0.012 0.001 TYR 1 124 ARG 0.013 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 1302) hydrogen bonds : angle 4.24975 ( 3942) covalent geometry : bond 0.00279 (29442) covalent geometry : angle 0.49749 (39684) ********************** 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 832 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 718 time to evaluate : 3.457 Fit side-chains REVERT: A 17 LYS cc_start: 0.9127 (mttt) cc_final: 0.8709 (mtpt) REVERT: A 27 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8672 (ttpt) REVERT: A 30 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 42 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7711 (tp30) REVERT: B 19 ASP cc_start: 0.8978 (m-30) cc_final: 0.8696 (m-30) REVERT: C 13 GLN cc_start: 0.8183 (mt0) cc_final: 0.7835 (mt0) REVERT: C 16 THR cc_start: 0.9260 (m) cc_final: 0.8994 (p) REVERT: D 13 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 90 LYS cc_start: 0.8828 (tptm) cc_final: 0.8504 (tptp) REVERT: D 99 ASP cc_start: 0.8646 (t70) cc_final: 0.8298 (t0) REVERT: D 125 LYS cc_start: 0.8699 (mttt) cc_final: 0.8384 (mmtm) REVERT: E 46 MET cc_start: 0.3122 (ttt) cc_final: 0.2313 (tpt) REVERT: E 94 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8538 (mmm160) REVERT: F 168 ASP cc_start: 0.8632 (t0) cc_final: 0.7711 (t0) REVERT: H 40 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: H 94 ASN cc_start: 0.8543 (m-40) cc_final: 0.8073 (m-40) REVERT: H 95 TYR cc_start: 0.8310 (t80) cc_final: 0.7696 (t80) REVERT: I 10 GLN cc_start: 0.9053 (mt0) cc_final: 0.8740 (mt0) REVERT: I 13 GLN cc_start: 0.8331 (mt0) cc_final: 0.7440 (mp10) REVERT: I 16 THR cc_start: 0.8976 (m) cc_final: 0.8621 (p) REVERT: I 20 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8309 (mmmt) REVERT: I 47 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8573 (mm110) REVERT: I 56 ASP cc_start: 0.9002 (t0) cc_final: 0.8735 (t0) REVERT: I 86 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8298 (mtt180) REVERT: J 13 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8585 (mt-10) REVERT: J 69 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8031 (p0) REVERT: J 79 LYS cc_start: 0.8406 (tptp) cc_final: 0.7671 (ttpt) REVERT: J 114 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: K 8 ASN cc_start: 0.8898 (p0) cc_final: 0.8488 (p0) REVERT: K 37 GLU cc_start: 0.8447 (tt0) cc_final: 0.7969 (tt0) REVERT: K 46 MET cc_start: 0.4102 (ttt) cc_final: 0.3185 (tpt) REVERT: K 111 GLN cc_start: 0.9322 (pt0) cc_final: 0.8586 (pt0) REVERT: L 168 ASP cc_start: 0.8642 (t0) cc_final: 0.7997 (t0) REVERT: M 32 GLN cc_start: 0.8650 (tt0) cc_final: 0.8072 (tt0) REVERT: M 50 TYR cc_start: 0.9208 (p90) cc_final: 0.8903 (p90) REVERT: M 89 GLU cc_start: 0.8147 (pt0) cc_final: 0.7754 (pt0) REVERT: N 20 GLU cc_start: 0.8545 (mp0) cc_final: 0.8058 (mp0) REVERT: N 44 ILE cc_start: 0.8761 (mp) cc_final: 0.8472 (mt) REVERT: O 91 GLU cc_start: 0.8083 (tt0) cc_final: 0.7766 (tt0) REVERT: P 12 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.7914 (t80) REVERT: P 13 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8163 (mt-10) REVERT: P 30 GLN cc_start: 0.8713 (tt0) cc_final: 0.8224 (tt0) REVERT: P 52 ASP cc_start: 0.8617 (m-30) cc_final: 0.8370 (m-30) REVERT: P 67 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8656 (t) REVERT: P 69 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7451 (p0) REVERT: P 79 LYS cc_start: 0.8487 (tptp) cc_final: 0.7747 (ttpt) REVERT: P 80 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.8018 (ttp80) REVERT: Q 45 THR cc_start: 0.6542 (m) cc_final: 0.5989 (p) REVERT: Q 46 MET cc_start: 0.3508 (ttt) cc_final: 0.2954 (tpt) REVERT: Q 132 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8719 (tt0) REVERT: R 168 ASP cc_start: 0.8491 (t0) cc_final: 0.8184 (t0) REVERT: S 17 LYS cc_start: 0.9119 (mttt) cc_final: 0.8698 (mtpt) REVERT: S 27 LYS cc_start: 0.8926 (ttpt) cc_final: 0.8672 (ttpt) REVERT: S 30 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8081 (mt-10) REVERT: S 42 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7721 (tp30) REVERT: T 19 ASP cc_start: 0.8967 (m-30) cc_final: 0.8680 (m-30) REVERT: U 13 GLN cc_start: 0.8198 (mt0) cc_final: 0.7850 (mt0) REVERT: U 16 THR cc_start: 0.9263 (m) cc_final: 0.8998 (p) REVERT: V 13 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8250 (mt-10) REVERT: V 99 ASP cc_start: 0.8648 (t70) cc_final: 0.8284 (t0) REVERT: V 125 LYS cc_start: 0.8690 (mttt) cc_final: 0.8390 (mmtm) REVERT: W 46 MET cc_start: 0.3067 (ttt) cc_final: 0.2509 (tpt) REVERT: X 168 ASP cc_start: 0.8633 (t0) cc_final: 0.7717 (t0) REVERT: Z 40 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: Z 94 ASN cc_start: 0.8550 (m-40) cc_final: 0.8080 (m-40) REVERT: Z 95 TYR cc_start: 0.8308 (t80) cc_final: 0.7686 (t80) REVERT: 0 10 GLN cc_start: 0.9027 (mt0) cc_final: 0.8726 (mt0) REVERT: 0 13 GLN cc_start: 0.8319 (mt0) cc_final: 0.7430 (mp10) REVERT: 0 16 THR cc_start: 0.8976 (m) cc_final: 0.8618 (p) REVERT: 0 20 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8291 (mmmt) REVERT: 0 47 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8571 (mm110) REVERT: 0 56 ASP cc_start: 0.9027 (t0) cc_final: 0.8765 (t0) REVERT: 0 86 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8293 (mtt180) REVERT: 1 13 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8569 (mt-10) REVERT: 1 30 GLN cc_start: 0.8869 (tt0) cc_final: 0.8668 (tt0) REVERT: 1 68 SER cc_start: 0.9010 (p) cc_final: 0.8297 (p) REVERT: 1 69 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7980 (p0) REVERT: 1 79 LYS cc_start: 0.8407 (tptp) cc_final: 0.7677 (ttpt) REVERT: 1 114 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: 2 8 ASN cc_start: 0.8893 (p0) cc_final: 0.8482 (p0) REVERT: 2 37 GLU cc_start: 0.8475 (tt0) cc_final: 0.8014 (tt0) REVERT: 2 46 MET cc_start: 0.4105 (ttt) cc_final: 0.3182 (tpt) REVERT: 2 111 GLN cc_start: 0.9307 (pt0) cc_final: 0.8578 (pt0) REVERT: 3 168 ASP cc_start: 0.8635 (t0) cc_final: 0.7989 (t0) REVERT: 4 32 GLN cc_start: 0.8608 (tt0) cc_final: 0.8040 (tt0) REVERT: 4 50 TYR cc_start: 0.9165 (p90) cc_final: 0.8895 (p90) REVERT: 4 51 MET cc_start: 0.9267 (mtt) cc_final: 0.9031 (mtt) REVERT: 5 44 ILE cc_start: 0.8753 (mp) cc_final: 0.8452 (mt) REVERT: 6 91 GLU cc_start: 0.8108 (tt0) cc_final: 0.7785 (tt0) REVERT: 7 12 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.7923 (t80) REVERT: 7 13 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8164 (mt-10) REVERT: 7 30 GLN cc_start: 0.8721 (tt0) cc_final: 0.8225 (tt0) REVERT: 7 52 ASP cc_start: 0.8624 (m-30) cc_final: 0.8370 (m-30) REVERT: 7 67 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8541 (t) REVERT: 7 69 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7468 (p0) REVERT: 7 79 LYS cc_start: 0.8505 (tptp) cc_final: 0.7765 (ttpt) REVERT: 7 80 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.8028 (ttp80) REVERT: 8 45 THR cc_start: 0.6507 (m) cc_final: 0.5960 (p) REVERT: 8 46 MET cc_start: 0.3487 (ttt) cc_final: 0.2928 (tpt) REVERT: 8 132 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8717 (tt0) REVERT: 9 168 ASP cc_start: 0.8493 (t0) cc_final: 0.8183 (t0) outliers start: 114 outliers final: 98 residues processed: 773 average time/residue: 0.4400 time to fit residues: 535.5919 Evaluate side-chains 817 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 706 time to evaluate : 3.134 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain B residue 35 SER 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 58 SER Chi-restraints excluded: chain C residue 85 THR 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 D residue 126 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 26 ILE Chi-restraints excluded: chain G residue 27 LYS 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 49 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 1 MET 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 110 PHE Chi-restraints excluded: chain M residue 9 LYS 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 58 SER Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 69 ASP 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 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 34 LEU Chi-restraints excluded: chain T 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 58 SER Chi-restraints excluded: chain U residue 85 THR 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 126 THR Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS 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 49 SER Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 58 SER Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 1 MET 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 9 LYS 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 58 SER Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 67 VAL 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 11 ILE 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 172 optimal weight: 3.9990 chunk 304 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 145 optimal weight: 0.2980 chunk 128 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 97 ASN I 26 ASN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS Y 18 GLN Y 97 ASN 0 26 ASN 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 117 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.094873 restraints weight = 40290.722| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.21 r_work: 0.2987 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29442 Z= 0.097 Angle : 0.480 6.518 39684 Z= 0.260 Chirality : 0.040 0.126 4302 Planarity : 0.003 0.060 5190 Dihedral : 4.853 76.498 3924 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.23 % Allowed : 17.95 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 3486 helix: 2.18 (0.18), residues: 924 sheet: -0.29 (0.15), residues: 1152 loop : 0.16 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 89 HIS 0.003 0.001 HIS J 74 PHE 0.011 0.001 PHE E 14 TYR 0.011 0.001 TYR 7 8 ARG 0.014 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 1302) hydrogen bonds : angle 4.15203 ( 3942) covalent geometry : bond 0.00222 (29442) covalent geometry : angle 0.48046 (39684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18178.66 seconds wall clock time: 321 minutes 37.84 seconds (19297.84 seconds total)