Starting phenix.real_space_refine on Mon May 26 14:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu3_48618/05_2025/9mu3_48618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu3_48618/05_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_48618/05_2025/9mu3_48618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu3_48618/05_2025/9mu3_48618.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu3_48618/05_2025/9mu3_48618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu3_48618/05_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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 15.36, per 1000 atoms: 0.53 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: 6.08 Conformation dependent library (CDL) restraints added in 3.3 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: 3.64 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: 9.49 Time building geometry restraints manager: 7.22 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 57.170 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.280 ------------------------------------------------------------------------------- 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 : 3.468 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: 0.4674 time to fit residues: 788.8537 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 : 3.337 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.116271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.098865 restraints weight = 39208.576| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.15 r_work: 0.3002 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 4.55206 ( 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 : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9000 (mttt) cc_final: 0.8667 (mtpt) REVERT: A 30 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8082 (mt-10) REVERT: A 32 GLN cc_start: 0.8736 (tt0) cc_final: 0.8453 (tt0) REVERT: B 92 ILE cc_start: 0.8911 (mt) cc_final: 0.8699 (mt) REVERT: C 16 THR cc_start: 0.9071 (m) cc_final: 0.8710 (t) REVERT: C 29 ILE cc_start: 0.9135 (mp) cc_final: 0.8917 (mt) REVERT: C 89 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8791 (ttm-80) REVERT: D 13 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8230 (mt-10) REVERT: D 57 ASP cc_start: 0.7759 (t70) cc_final: 0.7459 (t70) REVERT: D 71 LEU cc_start: 0.8968 (tp) cc_final: 0.8651 (mp) REVERT: D 99 ASP cc_start: 0.8420 (t70) cc_final: 0.8078 (t0) REVERT: D 105 GLN cc_start: 0.8252 (tt0) cc_final: 0.7805 (mt0) REVERT: D 125 LYS cc_start: 0.8596 (mttt) cc_final: 0.8265 (mmtm) REVERT: E 45 THR cc_start: 0.7479 (p) cc_final: 0.7080 (t) REVERT: E 46 MET cc_start: 0.3153 (ttt) cc_final: 0.2642 (tpt) REVERT: E 71 ASP cc_start: 0.7557 (p0) cc_final: 0.7344 (p0) REVERT: F 168 ASP cc_start: 0.8598 (t0) cc_final: 0.7867 (t0) REVERT: I 10 GLN cc_start: 0.9055 (mt0) cc_final: 0.8774 (mt0) REVERT: I 16 THR cc_start: 0.8998 (m) cc_final: 0.8760 (t) REVERT: I 24 LYS cc_start: 0.7938 (ptmt) cc_final: 0.7563 (ptmt) REVERT: I 47 GLN cc_start: 0.8960 (tt0) cc_final: 0.8669 (mm-40) REVERT: I 63 LYS cc_start: 0.8597 (tptm) cc_final: 0.8240 (tptt) REVERT: J 30 GLN cc_start: 0.8830 (tt0) cc_final: 0.8571 (tt0) REVERT: J 45 ASN cc_start: 0.8851 (m-40) cc_final: 0.8554 (m-40) REVERT: J 68 SER cc_start: 0.9092 (p) cc_final: 0.8262 (p) REVERT: J 69 ASP cc_start: 0.8280 (t0) cc_final: 0.7890 (p0) REVERT: J 71 LEU cc_start: 0.8654 (tp) cc_final: 0.8436 (mp) REVERT: J 79 LYS cc_start: 0.8573 (tptp) cc_final: 0.7849 (ttpt) REVERT: J 114 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: K 37 GLU cc_start: 0.8448 (tt0) cc_final: 0.8106 (tt0) REVERT: K 40 THR cc_start: 0.8639 (p) cc_final: 0.8402 (t) REVERT: K 46 MET cc_start: 0.4706 (ttt) cc_final: 0.2860 (tpt) REVERT: K 111 GLN cc_start: 0.9214 (pt0) cc_final: 0.8189 (pt0) REVERT: K 157 THR cc_start: 0.8601 (p) cc_final: 0.8308 (t) REVERT: L 168 ASP cc_start: 0.8597 (t0) cc_final: 0.8184 (t0) REVERT: M 16 GLU cc_start: 0.8016 (mp0) cc_final: 0.7731 (mp0) REVERT: M 17 LYS cc_start: 0.9018 (mttt) cc_final: 0.8631 (mtpt) REVERT: M 32 GLN cc_start: 0.8806 (tt0) cc_final: 0.8089 (tt0) REVERT: M 87 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8003 (mt-10) REVERT: N 16 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8357 (mm-30) REVERT: N 20 GLU cc_start: 0.8373 (mp0) cc_final: 0.8005 (mp0) REVERT: N 44 ILE cc_start: 0.8935 (mp) cc_final: 0.8674 (mt) REVERT: O 24 LYS cc_start: 0.8102 (ptmt) cc_final: 0.7635 (ptmt) REVERT: P 12 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8200 (t80) REVERT: P 13 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8303 (mt-10) REVERT: P 30 GLN cc_start: 0.8729 (tt0) cc_final: 0.8263 (tt0) REVERT: P 41 MET cc_start: 0.8636 (tpt) cc_final: 0.8381 (tpp) REVERT: P 69 ASP cc_start: 0.7984 (t0) cc_final: 0.7710 (p0) REVERT: P 79 LYS cc_start: 0.8559 (tptp) cc_final: 0.8338 (tptm) REVERT: P 80 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8175 (ttp-170) REVERT: P 125 LYS cc_start: 0.8777 (mttt) cc_final: 0.8575 (mtpp) REVERT: Q 40 THR cc_start: 0.8763 (p) cc_final: 0.8464 (t) REVERT: Q 46 MET cc_start: 0.3228 (ttt) cc_final: 0.2690 (tpt) REVERT: S 17 LYS cc_start: 0.9017 (mttt) cc_final: 0.8689 (mtpt) REVERT: S 30 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8063 (mt-10) REVERT: S 32 GLN cc_start: 0.8722 (tt0) cc_final: 0.8429 (tt0) REVERT: T 92 ILE cc_start: 0.8916 (mt) cc_final: 0.8702 (mt) REVERT: U 16 THR cc_start: 0.9081 (m) cc_final: 0.8718 (t) REVERT: U 29 ILE cc_start: 0.9133 (mp) cc_final: 0.8914 (mt) REVERT: U 89 ARG cc_start: 0.9111 (ttm-80) cc_final: 0.8792 (ttm-80) REVERT: V 13 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8234 (mt-10) REVERT: V 57 ASP cc_start: 0.7748 (t70) cc_final: 0.7452 (t70) REVERT: V 71 LEU cc_start: 0.8973 (tp) cc_final: 0.8657 (mp) REVERT: V 99 ASP cc_start: 0.8444 (t70) cc_final: 0.8098 (t0) REVERT: V 105 GLN cc_start: 0.8256 (tt0) cc_final: 0.7803 (mt0) REVERT: V 125 LYS cc_start: 0.8590 (mttt) cc_final: 0.8257 (mmtm) REVERT: W 45 THR cc_start: 0.7481 (p) cc_final: 0.7078 (t) REVERT: W 46 MET cc_start: 0.3143 (ttt) cc_final: 0.2633 (tpt) REVERT: W 71 ASP cc_start: 0.7543 (p0) cc_final: 0.7330 (p0) REVERT: X 168 ASP cc_start: 0.8585 (t0) cc_final: 0.7848 (t0) REVERT: 0 10 GLN cc_start: 0.9045 (mt0) cc_final: 0.8763 (mt0) REVERT: 0 16 THR cc_start: 0.9002 (m) cc_final: 0.8765 (t) REVERT: 0 24 LYS cc_start: 0.7942 (ptmt) cc_final: 0.7574 (ptmt) REVERT: 0 47 GLN cc_start: 0.8936 (tt0) cc_final: 0.8647 (mm-40) REVERT: 0 63 LYS cc_start: 0.8597 (tptm) cc_final: 0.8242 (tptt) REVERT: 1 30 GLN cc_start: 0.8839 (tt0) cc_final: 0.8583 (tt0) REVERT: 1 45 ASN cc_start: 0.8838 (m-40) cc_final: 0.8543 (m-40) REVERT: 1 68 SER cc_start: 0.9083 (p) cc_final: 0.8254 (p) REVERT: 1 69 ASP cc_start: 0.8268 (t0) cc_final: 0.7888 (p0) REVERT: 1 71 LEU cc_start: 0.8660 (tp) cc_final: 0.8443 (mp) REVERT: 1 79 LYS cc_start: 0.8557 (tptp) cc_final: 0.7831 (ttpt) REVERT: 1 114 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: 2 37 GLU cc_start: 0.8457 (tt0) cc_final: 0.8121 (tt0) REVERT: 2 40 THR cc_start: 0.8637 (p) cc_final: 0.8405 (t) REVERT: 2 46 MET cc_start: 0.4718 (ttt) cc_final: 0.2881 (tpt) REVERT: 2 111 GLN cc_start: 0.9219 (pt0) cc_final: 0.8187 (pt0) REVERT: 2 157 THR cc_start: 0.8602 (p) cc_final: 0.8308 (t) REVERT: 3 168 ASP cc_start: 0.8589 (t0) cc_final: 0.8179 (t0) REVERT: 4 16 GLU cc_start: 0.8024 (mp0) cc_final: 0.7733 (mp0) REVERT: 4 17 LYS cc_start: 0.9029 (mttt) cc_final: 0.8643 (mtpt) REVERT: 4 32 GLN cc_start: 0.8805 (tt0) cc_final: 0.8088 (tt0) REVERT: 4 87 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7975 (mt-10) REVERT: 5 16 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8257 (mm-30) REVERT: 5 20 GLU cc_start: 0.8372 (mp0) cc_final: 0.8006 (mp0) REVERT: 5 44 ILE cc_start: 0.8938 (mp) cc_final: 0.8676 (mt) REVERT: 6 24 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7625 (ptmt) REVERT: 7 12 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8213 (t80) REVERT: 7 13 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8307 (mt-10) REVERT: 7 30 GLN cc_start: 0.8740 (tt0) cc_final: 0.8267 (tt0) REVERT: 7 41 MET cc_start: 0.8626 (tpt) cc_final: 0.8371 (tpp) REVERT: 7 69 ASP cc_start: 0.8001 (t0) cc_final: 0.7716 (p0) REVERT: 7 79 LYS cc_start: 0.8539 (tptp) cc_final: 0.8324 (tptm) REVERT: 7 80 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8174 (ttp-170) REVERT: 7 125 LYS cc_start: 0.8774 (mttt) cc_final: 0.8573 (mtpp) REVERT: 8 40 THR cc_start: 0.8764 (p) cc_final: 0.8472 (t) REVERT: 8 46 MET cc_start: 0.3219 (ttt) cc_final: 0.2679 (tpt) REVERT: 9 168 ASP cc_start: 0.8629 (t0) cc_final: 0.8423 (t0) outliers start: 62 outliers final: 30 residues processed: 969 average time/residue: 0.4263 time to fit residues: 632.5647 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 : 3.573 ------------------------------------------------------------------------------- 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: 0.9980 chunk 337 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 318 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.103572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.085880 restraints weight = 41675.216| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.25 r_work: 0.2877 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29442 Z= 0.248 Angle : 0.620 7.558 39684 Z= 0.338 Chirality : 0.045 0.149 4302 Planarity : 0.004 0.046 5190 Dihedral : 6.074 85.783 3924 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.39 % Allowed : 13.94 % Favored : 82.67 % 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: 0.47 (0.14), residues: 3486 helix: 1.13 (0.17), residues: 918 sheet: -0.16 (0.15), residues: 1134 loop : 0.39 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP W 89 HIS 0.005 0.001 HIS O 90 PHE 0.015 0.002 PHE K 110 TYR 0.022 0.002 TYR 1 8 ARG 0.008 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 1302) hydrogen bonds : angle 4.59074 ( 3942) covalent geometry : bond 0.00604 (29442) covalent geometry : angle 0.62027 (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 873 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 765 time to evaluate : 3.343 Fit side-chains REVERT: A 17 LYS cc_start: 0.9036 (mttt) cc_final: 0.8643 (mtpt) REVERT: A 27 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8687 (ttpt) REVERT: A 30 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 32 GLN cc_start: 0.8636 (tt0) cc_final: 0.8334 (tt0) REVERT: A 97 ASN cc_start: 0.6456 (m-40) cc_final: 0.6239 (m-40) REVERT: C 16 THR cc_start: 0.9182 (m) cc_final: 0.8791 (p) REVERT: C 89 ARG cc_start: 0.9147 (ttm-80) cc_final: 0.8834 (ttm-80) REVERT: D 13 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8339 (mt-10) REVERT: D 114 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: D 125 LYS cc_start: 0.8607 (mttt) cc_final: 0.8359 (mtpp) REVERT: E 46 MET cc_start: 0.2944 (ttt) cc_final: 0.2385 (tpt) REVERT: E 132 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8610 (tt0) REVERT: F 168 ASP cc_start: 0.8473 (t0) cc_final: 0.7497 (t0) REVERT: H 19 ASP cc_start: 0.8912 (m-30) cc_final: 0.8691 (m-30) REVERT: I 16 THR cc_start: 0.9068 (m) cc_final: 0.8699 (t) REVERT: I 47 GLN cc_start: 0.9087 (tt0) cc_final: 0.8684 (mm-40) REVERT: I 63 LYS cc_start: 0.8604 (tptm) cc_final: 0.8263 (tptt) REVERT: J 30 GLN cc_start: 0.8979 (tt0) cc_final: 0.8741 (tt0) REVERT: J 68 SER cc_start: 0.9041 (p) cc_final: 0.8562 (p) REVERT: J 71 LEU cc_start: 0.8751 (tp) cc_final: 0.8406 (mp) REVERT: J 79 LYS cc_start: 0.8510 (tptp) cc_final: 0.7789 (ttpt) REVERT: J 114 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: K 37 GLU cc_start: 0.8551 (tt0) cc_final: 0.8169 (tt0) REVERT: K 40 THR cc_start: 0.8683 (p) cc_final: 0.8413 (t) REVERT: K 46 MET cc_start: 0.4329 (ttt) cc_final: 0.2877 (tpt) REVERT: K 157 THR cc_start: 0.8684 (p) cc_final: 0.8341 (t) REVERT: L 168 ASP cc_start: 0.8607 (t0) cc_final: 0.7994 (t0) REVERT: M 16 GLU cc_start: 0.7971 (mp0) cc_final: 0.7758 (mp0) REVERT: M 30 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8270 (mt-10) REVERT: M 32 GLN cc_start: 0.8739 (tt0) cc_final: 0.8427 (tt0) REVERT: M 87 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8118 (mt-10) REVERT: N 44 ILE cc_start: 0.8906 (mp) cc_final: 0.8640 (mt) REVERT: N 93 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: O 24 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7945 (ptmt) REVERT: O 52 ASP cc_start: 0.9078 (m-30) cc_final: 0.8840 (m-30) REVERT: P 12 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8205 (t80) REVERT: P 13 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8397 (mt-10) REVERT: P 41 MET cc_start: 0.8754 (tpt) cc_final: 0.8487 (tpp) REVERT: P 69 ASP cc_start: 0.7712 (t0) cc_final: 0.7411 (p0) REVERT: P 79 LYS cc_start: 0.8594 (tptp) cc_final: 0.7846 (ttpt) REVERT: P 80 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8102 (ttp-170) REVERT: P 125 LYS cc_start: 0.8621 (mttt) cc_final: 0.8385 (mtpp) REVERT: Q 40 THR cc_start: 0.8791 (p) cc_final: 0.8526 (t) REVERT: Q 45 THR cc_start: 0.6242 (m) cc_final: 0.5801 (p) REVERT: Q 46 MET cc_start: 0.3490 (ttt) cc_final: 0.2742 (tpt) REVERT: S 17 LYS cc_start: 0.9061 (mttt) cc_final: 0.8675 (mtpt) REVERT: S 27 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8690 (ttpt) REVERT: S 30 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8066 (mt-10) REVERT: S 32 GLN cc_start: 0.8620 (tt0) cc_final: 0.8315 (tt0) REVERT: S 93 ASP cc_start: 0.8762 (t0) cc_final: 0.8561 (t0) REVERT: S 97 ASN cc_start: 0.6474 (m-40) cc_final: 0.6257 (m-40) REVERT: U 16 THR cc_start: 0.9181 (m) cc_final: 0.8790 (p) REVERT: U 89 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8825 (ttm-80) REVERT: V 13 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8366 (mt-10) REVERT: V 90 LYS cc_start: 0.8725 (tptm) cc_final: 0.8525 (tptp) REVERT: V 114 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: V 125 LYS cc_start: 0.8595 (mttt) cc_final: 0.8346 (mtpp) REVERT: W 46 MET cc_start: 0.2923 (ttt) cc_final: 0.2364 (tpt) REVERT: W 132 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8613 (tt0) REVERT: X 168 ASP cc_start: 0.8464 (t0) cc_final: 0.7481 (t0) REVERT: Z 19 ASP cc_start: 0.8913 (m-30) cc_final: 0.8689 (m-30) REVERT: 0 16 THR cc_start: 0.9063 (m) cc_final: 0.8690 (t) REVERT: 0 47 GLN cc_start: 0.9084 (tt0) cc_final: 0.8679 (mm-40) REVERT: 0 63 LYS cc_start: 0.8604 (tptm) cc_final: 0.8266 (tptt) REVERT: 1 30 GLN cc_start: 0.8976 (tt0) cc_final: 0.8732 (tt0) REVERT: 1 68 SER cc_start: 0.9040 (p) cc_final: 0.8558 (p) REVERT: 1 71 LEU cc_start: 0.8749 (tp) cc_final: 0.8405 (mp) REVERT: 1 79 LYS cc_start: 0.8497 (tptp) cc_final: 0.7775 (ttpt) REVERT: 1 114 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: 2 37 GLU cc_start: 0.8555 (tt0) cc_final: 0.8179 (tt0) REVERT: 2 40 THR cc_start: 0.8690 (p) cc_final: 0.8416 (t) REVERT: 2 46 MET cc_start: 0.4319 (ttt) cc_final: 0.2879 (tpt) REVERT: 2 157 THR cc_start: 0.8682 (p) cc_final: 0.8339 (t) REVERT: 3 168 ASP cc_start: 0.8611 (t0) cc_final: 0.8007 (t0) REVERT: 4 16 GLU cc_start: 0.7964 (mp0) cc_final: 0.7762 (mp0) REVERT: 4 30 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8282 (mt-10) REVERT: 4 32 GLN cc_start: 0.8752 (tt0) cc_final: 0.8440 (tt0) REVERT: 4 87 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8118 (mt-10) REVERT: 5 44 ILE cc_start: 0.8907 (mp) cc_final: 0.8639 (mt) REVERT: 5 93 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: 6 24 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7937 (ptmt) REVERT: 6 52 ASP cc_start: 0.9086 (m-30) cc_final: 0.8849 (m-30) REVERT: 7 12 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8210 (t80) REVERT: 7 13 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8390 (mt-10) REVERT: 7 41 MET cc_start: 0.8746 (tpt) cc_final: 0.8476 (tpp) REVERT: 7 69 ASP cc_start: 0.7719 (t0) cc_final: 0.7410 (p0) REVERT: 7 79 LYS cc_start: 0.8594 (tptp) cc_final: 0.7850 (ttpt) REVERT: 7 80 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8099 (ttp-170) REVERT: 7 125 LYS cc_start: 0.8606 (mttt) cc_final: 0.8375 (mtpp) REVERT: 8 40 THR cc_start: 0.8790 (p) cc_final: 0.8528 (t) REVERT: 8 45 THR cc_start: 0.6203 (m) cc_final: 0.5765 (p) REVERT: 8 46 MET cc_start: 0.3481 (ttt) cc_final: 0.2725 (tpt) outliers start: 108 outliers final: 83 residues processed: 799 average time/residue: 0.4241 time to fit residues: 522.3349 Evaluate side-chains 807 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 716 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 44 ILE 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 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 44 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS 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 39 ILE Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain T residue 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 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 82 ILE Chi-restraints excluded: chain V residue 114 GLU Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS 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 39 ILE 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: 0.9990 chunk 192 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 76 ASN M 18 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 76 ASN 4 18 GLN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.090151 restraints weight = 41266.790| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.26 r_work: 0.2955 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29442 Z= 0.114 Angle : 0.510 7.450 39684 Z= 0.279 Chirality : 0.041 0.130 4302 Planarity : 0.004 0.043 5190 Dihedral : 5.544 85.219 3924 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.26 % Allowed : 14.81 % Favored : 81.92 % 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: 0.76 (0.15), residues: 3486 helix: 1.57 (0.18), residues: 918 sheet: 0.10 (0.15), residues: 1224 loop : 0.35 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 89 HIS 0.003 0.001 HIS J 74 PHE 0.011 0.001 PHE E 110 TYR 0.012 0.001 TYR D 8 ARG 0.008 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1302) hydrogen bonds : angle 4.29527 ( 3942) covalent geometry : bond 0.00261 (29442) covalent geometry : angle 0.51048 (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 908 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 804 time to evaluate : 3.339 Fit side-chains REVERT: A 17 LYS cc_start: 0.9078 (mttt) cc_final: 0.8675 (mtpt) REVERT: A 27 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8733 (ttpt) REVERT: A 30 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8131 (mt-10) REVERT: B 19 ASP cc_start: 0.9059 (m-30) cc_final: 0.8740 (m-30) REVERT: C 16 THR cc_start: 0.9155 (m) cc_final: 0.8794 (p) REVERT: C 89 ARG cc_start: 0.9144 (ttm-80) cc_final: 0.8846 (ttm-80) REVERT: C 98 GLU cc_start: 0.8954 (tt0) cc_final: 0.8648 (tt0) REVERT: D 13 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8206 (mt-10) REVERT: D 99 ASP cc_start: 0.8514 (t70) cc_final: 0.8192 (t0) REVERT: D 114 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: D 125 LYS cc_start: 0.8734 (mttt) cc_final: 0.8294 (mmtm) REVERT: E 46 MET cc_start: 0.3676 (ttt) cc_final: 0.2786 (tpt) REVERT: E 52 THR cc_start: 0.6805 (OUTLIER) cc_final: 0.6425 (p) REVERT: E 94 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8194 (mtt90) REVERT: F 168 ASP cc_start: 0.8621 (t0) cc_final: 0.7857 (t0) REVERT: H 19 ASP cc_start: 0.8950 (m-30) cc_final: 0.8667 (m-30) REVERT: H 40 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: H 94 ASN cc_start: 0.8665 (m-40) cc_final: 0.8409 (m110) REVERT: I 10 GLN cc_start: 0.9038 (mt0) cc_final: 0.8716 (mt0) REVERT: I 16 THR cc_start: 0.8999 (m) cc_final: 0.8637 (t) REVERT: I 47 GLN cc_start: 0.9013 (tt0) cc_final: 0.8672 (mm-40) REVERT: I 56 ASP cc_start: 0.8957 (t0) cc_final: 0.8676 (t0) REVERT: I 63 LYS cc_start: 0.8594 (tptm) cc_final: 0.8230 (tptt) REVERT: I 76 ASN cc_start: 0.8428 (m-40) cc_final: 0.8191 (m110) REVERT: J 30 GLN cc_start: 0.8791 (tt0) cc_final: 0.8501 (tt0) REVERT: J 68 SER cc_start: 0.9039 (p) cc_final: 0.8541 (p) REVERT: J 71 LEU cc_start: 0.8679 (tp) cc_final: 0.8444 (mp) REVERT: J 79 LYS cc_start: 0.8466 (tptp) cc_final: 0.7733 (ttpt) REVERT: J 105 GLN cc_start: 0.8380 (mt0) cc_final: 0.8095 (mt0) REVERT: J 114 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: K 37 GLU cc_start: 0.8422 (tt0) cc_final: 0.7960 (tt0) REVERT: K 40 THR cc_start: 0.8629 (p) cc_final: 0.8422 (t) REVERT: K 46 MET cc_start: 0.4110 (ttt) cc_final: 0.2991 (tpt) REVERT: K 111 GLN cc_start: 0.9232 (pt0) cc_final: 0.8153 (pt0) REVERT: K 157 THR cc_start: 0.8683 (p) cc_final: 0.8330 (t) REVERT: L 168 ASP cc_start: 0.8623 (t0) cc_final: 0.8147 (t0) REVERT: M 16 GLU cc_start: 0.8058 (mp0) cc_final: 0.7747 (mp0) REVERT: M 32 GLN cc_start: 0.8707 (tt0) cc_final: 0.8110 (tt0) REVERT: M 50 TYR cc_start: 0.9243 (p90) cc_final: 0.8920 (p90) REVERT: M 51 MET cc_start: 0.9324 (mtt) cc_final: 0.9110 (mtt) REVERT: M 87 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7967 (mt-10) REVERT: N 20 GLU cc_start: 0.8557 (mp0) cc_final: 0.8130 (mp0) REVERT: N 44 ILE cc_start: 0.8842 (mp) cc_final: 0.8585 (mt) REVERT: O 52 ASP cc_start: 0.9046 (m-30) cc_final: 0.8833 (m-30) REVERT: P 12 TYR cc_start: 0.8993 (OUTLIER) cc_final: 0.7981 (t80) REVERT: P 13 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8276 (mt-10) REVERT: P 30 GLN cc_start: 0.8764 (tt0) cc_final: 0.8269 (tt0) REVERT: P 39 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8677 (mt) REVERT: P 52 ASP cc_start: 0.8656 (m-30) cc_final: 0.8420 (m-30) REVERT: P 79 LYS cc_start: 0.8571 (tptp) cc_final: 0.7842 (ttpt) REVERT: P 80 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.8005 (ttp-170) REVERT: Q 40 THR cc_start: 0.8774 (p) cc_final: 0.8515 (t) REVERT: Q 45 THR cc_start: 0.6253 (m) cc_final: 0.5817 (p) REVERT: Q 46 MET cc_start: 0.3765 (ttt) cc_final: 0.2996 (tpt) REVERT: S 17 LYS cc_start: 0.9095 (mttt) cc_final: 0.8699 (mtpt) REVERT: S 27 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8727 (ttpt) REVERT: S 30 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8124 (mt-10) REVERT: S 97 ASN cc_start: 0.6588 (m-40) cc_final: 0.6299 (m-40) REVERT: T 19 ASP cc_start: 0.9058 (m-30) cc_final: 0.8733 (m-30) REVERT: U 16 THR cc_start: 0.9159 (m) cc_final: 0.8796 (p) REVERT: U 89 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8843 (ttm-80) REVERT: U 98 GLU cc_start: 0.8967 (tt0) cc_final: 0.8665 (tt0) REVERT: V 13 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8232 (mt-10) REVERT: V 99 ASP cc_start: 0.8524 (t70) cc_final: 0.8205 (t0) REVERT: V 114 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: V 125 LYS cc_start: 0.8734 (mttt) cc_final: 0.8295 (mmtm) REVERT: W 46 MET cc_start: 0.3670 (ttt) cc_final: 0.2785 (tpt) REVERT: W 52 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6414 (p) REVERT: W 94 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8205 (mtt90) REVERT: X 168 ASP cc_start: 0.8616 (t0) cc_final: 0.7849 (t0) REVERT: Z 19 ASP cc_start: 0.8952 (m-30) cc_final: 0.8672 (m-30) REVERT: Z 40 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: Z 94 ASN cc_start: 0.8664 (m-40) cc_final: 0.8405 (m110) REVERT: 0 10 GLN cc_start: 0.9042 (mt0) cc_final: 0.8720 (mt0) REVERT: 0 16 THR cc_start: 0.8987 (m) cc_final: 0.8624 (t) REVERT: 0 47 GLN cc_start: 0.9018 (tt0) cc_final: 0.8682 (mm-40) REVERT: 0 56 ASP cc_start: 0.8961 (t0) cc_final: 0.8679 (t0) REVERT: 0 63 LYS cc_start: 0.8599 (tptm) cc_final: 0.8238 (tptt) REVERT: 0 76 ASN cc_start: 0.8426 (m-40) cc_final: 0.8190 (m110) REVERT: 1 30 GLN cc_start: 0.8789 (tt0) cc_final: 0.8492 (tt0) REVERT: 1 68 SER cc_start: 0.9041 (p) cc_final: 0.8558 (p) REVERT: 1 71 LEU cc_start: 0.8687 (tp) cc_final: 0.8454 (mp) REVERT: 1 79 LYS cc_start: 0.8470 (tptp) cc_final: 0.7744 (ttpt) REVERT: 1 105 GLN cc_start: 0.8385 (mt0) cc_final: 0.8103 (mt0) REVERT: 1 114 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: 2 37 GLU cc_start: 0.8435 (tt0) cc_final: 0.7978 (tt0) REVERT: 2 40 THR cc_start: 0.8626 (p) cc_final: 0.8423 (t) REVERT: 2 46 MET cc_start: 0.4124 (ttt) cc_final: 0.2996 (tpt) REVERT: 2 111 GLN cc_start: 0.9226 (pt0) cc_final: 0.8145 (pt0) REVERT: 2 157 THR cc_start: 0.8675 (p) cc_final: 0.8323 (t) REVERT: 3 168 ASP cc_start: 0.8623 (t0) cc_final: 0.8150 (t0) REVERT: 4 16 GLU cc_start: 0.8065 (mp0) cc_final: 0.7754 (mp0) REVERT: 4 32 GLN cc_start: 0.8708 (tt0) cc_final: 0.8111 (tt0) REVERT: 4 50 TYR cc_start: 0.9240 (p90) cc_final: 0.8925 (p90) REVERT: 4 51 MET cc_start: 0.9316 (mtt) cc_final: 0.9104 (mtt) REVERT: 4 87 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7969 (mt-10) REVERT: 5 19 ASP cc_start: 0.9205 (m-30) cc_final: 0.8844 (m-30) REVERT: 5 20 GLU cc_start: 0.8524 (mp0) cc_final: 0.8106 (mp0) REVERT: 5 44 ILE cc_start: 0.8844 (mp) cc_final: 0.8585 (mt) REVERT: 6 52 ASP cc_start: 0.9055 (m-30) cc_final: 0.8842 (m-30) REVERT: 7 12 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7992 (t80) REVERT: 7 13 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8271 (mt-10) REVERT: 7 30 GLN cc_start: 0.8768 (tt0) cc_final: 0.8275 (tt0) REVERT: 7 39 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8682 (mt) REVERT: 7 52 ASP cc_start: 0.8648 (m-30) cc_final: 0.8406 (m-30) REVERT: 7 79 LYS cc_start: 0.8591 (tptp) cc_final: 0.7867 (ttpt) REVERT: 7 80 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8007 (ttp-170) REVERT: 8 40 THR cc_start: 0.8777 (p) cc_final: 0.8522 (t) REVERT: 8 45 THR cc_start: 0.6215 (m) cc_final: 0.5782 (p) REVERT: 8 46 MET cc_start: 0.3766 (ttt) cc_final: 0.2985 (tpt) REVERT: 8 132 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8648 (tt0) outliers start: 104 outliers final: 68 residues processed: 844 average time/residue: 0.4201 time to fit residues: 549.6358 Evaluate side-chains 830 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 748 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 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 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 114 GLU 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 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 85 THR 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 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 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain 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 49 SER Chi-restraints excluded: chain T residue 93 ASP Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 114 GLU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 52 THR 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 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 85 THR Chi-restraints excluded: chain 1 residue 12 TYR 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 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 71 LEU Chi-restraints excluded: chain 7 residue 104 THR Chi-restraints excluded: chain 7 residue 114 GLU Chi-restraints excluded: chain 8 residue 26 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.8980 chunk 337 optimal weight: 8.9990 chunk 322 optimal weight: 0.9980 chunk 313 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS M 97 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS 4 97 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.086794 restraints weight = 41437.782| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.28 r_work: 0.2892 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29442 Z= 0.160 Angle : 0.526 5.875 39684 Z= 0.286 Chirality : 0.042 0.133 4302 Planarity : 0.004 0.040 5190 Dihedral : 5.492 83.455 3924 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.77 % Allowed : 15.38 % Favored : 80.85 % 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: 0.65 (0.15), residues: 3486 helix: 1.59 (0.18), residues: 924 sheet: -0.04 (0.15), residues: 1224 loop : 0.26 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 89 HIS 0.004 0.001 HIS J 74 PHE 0.012 0.001 PHE 2 110 TYR 0.015 0.001 TYR 1 8 ARG 0.010 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1302) hydrogen bonds : angle 4.33427 ( 3942) covalent geometry : bond 0.00384 (29442) covalent geometry : angle 0.52608 (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 869 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 749 time to evaluate : 3.173 Fit side-chains REVERT: A 17 LYS cc_start: 0.9095 (mttt) cc_final: 0.8650 (mtpt) REVERT: A 27 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8783 (ttpt) REVERT: A 30 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 41 VAL cc_start: 0.8659 (t) cc_final: 0.8302 (m) REVERT: B 59 ARG cc_start: 0.8904 (mtt180) cc_final: 0.8650 (mtt-85) REVERT: C 16 THR cc_start: 0.9213 (m) cc_final: 0.8850 (p) REVERT: C 89 ARG cc_start: 0.9168 (ttm-80) cc_final: 0.8823 (ttm-80) REVERT: C 91 GLU cc_start: 0.7881 (pm20) cc_final: 0.7096 (pm20) REVERT: C 98 GLU cc_start: 0.8935 (tt0) cc_final: 0.8599 (tt0) REVERT: D 13 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 31 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8383 (mt-10) REVERT: D 99 ASP cc_start: 0.8660 (t70) cc_final: 0.8257 (t0) REVERT: D 125 LYS cc_start: 0.8808 (mttt) cc_final: 0.8379 (mmtm) REVERT: E 46 MET cc_start: 0.3713 (ttt) cc_final: 0.2837 (tpt) REVERT: E 52 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6465 (p) REVERT: F 168 ASP cc_start: 0.8537 (t0) cc_final: 0.7520 (t0) REVERT: H 94 ASN cc_start: 0.8732 (m-40) cc_final: 0.8319 (m110) REVERT: I 10 GLN cc_start: 0.9053 (mt0) cc_final: 0.8738 (mt0) REVERT: I 16 THR cc_start: 0.9018 (m) cc_final: 0.8617 (t) REVERT: I 47 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8624 (mm-40) REVERT: I 56 ASP cc_start: 0.9064 (t0) cc_final: 0.8799 (t0) REVERT: I 63 LYS cc_start: 0.8654 (tptm) cc_final: 0.8300 (tptt) REVERT: J 30 GLN cc_start: 0.8913 (tt0) cc_final: 0.8653 (tt0) REVERT: J 68 SER cc_start: 0.9085 (p) cc_final: 0.8503 (p) REVERT: J 69 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7760 (p0) REVERT: J 71 LEU cc_start: 0.8938 (tp) cc_final: 0.8498 (mp) REVERT: J 79 LYS cc_start: 0.8468 (tptp) cc_final: 0.7745 (ttpt) REVERT: J 114 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8016 (tt0) REVERT: K 37 GLU cc_start: 0.8494 (tt0) cc_final: 0.8036 (tt0) REVERT: K 40 THR cc_start: 0.8638 (p) cc_final: 0.8433 (t) REVERT: K 46 MET cc_start: 0.4383 (ttt) cc_final: 0.3290 (tpt) REVERT: K 157 THR cc_start: 0.8679 (p) cc_final: 0.8325 (t) REVERT: L 168 ASP cc_start: 0.8623 (t0) cc_final: 0.8154 (t0) REVERT: M 16 GLU cc_start: 0.8038 (mp0) cc_final: 0.7763 (mp0) REVERT: M 32 GLN cc_start: 0.8629 (tt0) cc_final: 0.8037 (tt0) REVERT: M 50 TYR cc_start: 0.9237 (p90) cc_final: 0.8914 (p90) REVERT: N 44 ILE cc_start: 0.8855 (mp) cc_final: 0.8579 (mt) REVERT: P 12 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8021 (t80) REVERT: P 13 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8307 (mt-10) REVERT: P 30 GLN cc_start: 0.8740 (tt0) cc_final: 0.8261 (tt0) REVERT: P 69 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7577 (p0) REVERT: P 79 LYS cc_start: 0.8578 (tptp) cc_final: 0.7853 (ttpt) REVERT: P 80 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.8040 (ttp-170) REVERT: Q 40 THR cc_start: 0.8790 (p) cc_final: 0.8536 (t) REVERT: Q 45 THR cc_start: 0.6478 (m) cc_final: 0.5988 (p) REVERT: Q 46 MET cc_start: 0.3660 (ttt) cc_final: 0.2937 (tpt) REVERT: Q 132 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8654 (tt0) REVERT: S 17 LYS cc_start: 0.9107 (mttt) cc_final: 0.8666 (mtpt) REVERT: S 27 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8784 (ttpt) REVERT: S 30 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8093 (mt-10) REVERT: S 97 ASN cc_start: 0.6595 (m-40) cc_final: 0.6292 (m-40) REVERT: T 41 VAL cc_start: 0.8674 (t) cc_final: 0.8318 (m) REVERT: T 59 ARG cc_start: 0.8916 (mtt180) cc_final: 0.8655 (mtt-85) REVERT: U 16 THR cc_start: 0.9221 (m) cc_final: 0.8855 (p) REVERT: U 89 ARG cc_start: 0.9161 (ttm-80) cc_final: 0.8820 (ttm-80) REVERT: U 91 GLU cc_start: 0.7901 (pm20) cc_final: 0.7118 (pm20) REVERT: U 98 GLU cc_start: 0.8939 (tt0) cc_final: 0.8624 (tt0) REVERT: V 13 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8252 (mt-10) REVERT: V 31 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8384 (mt-10) REVERT: V 90 LYS cc_start: 0.8815 (tptm) cc_final: 0.8500 (tptp) REVERT: V 125 LYS cc_start: 0.8791 (mttt) cc_final: 0.8376 (mmtm) REVERT: W 46 MET cc_start: 0.3677 (ttt) cc_final: 0.2807 (tpt) REVERT: W 52 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6461 (p) REVERT: X 168 ASP cc_start: 0.8527 (t0) cc_final: 0.7498 (t0) REVERT: Z 19 ASP cc_start: 0.8918 (m-30) cc_final: 0.8715 (m-30) REVERT: Z 94 ASN cc_start: 0.8726 (m-40) cc_final: 0.8312 (m110) REVERT: 0 10 GLN cc_start: 0.9055 (mt0) cc_final: 0.8740 (mt0) REVERT: 0 16 THR cc_start: 0.9016 (m) cc_final: 0.8608 (t) REVERT: 0 47 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8643 (mm-40) REVERT: 0 56 ASP cc_start: 0.9061 (t0) cc_final: 0.8797 (t0) REVERT: 0 63 LYS cc_start: 0.8663 (tptm) cc_final: 0.8311 (tptt) REVERT: 1 30 GLN cc_start: 0.8898 (tt0) cc_final: 0.8635 (tt0) REVERT: 1 68 SER cc_start: 0.9089 (p) cc_final: 0.8521 (p) REVERT: 1 69 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7777 (p0) REVERT: 1 71 LEU cc_start: 0.8939 (tp) cc_final: 0.8502 (mp) REVERT: 1 79 LYS cc_start: 0.8477 (tptp) cc_final: 0.7761 (ttpt) REVERT: 1 114 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: 2 37 GLU cc_start: 0.8502 (tt0) cc_final: 0.8065 (tt0) REVERT: 2 40 THR cc_start: 0.8639 (p) cc_final: 0.8429 (t) REVERT: 2 46 MET cc_start: 0.4385 (ttt) cc_final: 0.3287 (tpt) REVERT: 2 157 THR cc_start: 0.8671 (p) cc_final: 0.8316 (t) REVERT: 3 168 ASP cc_start: 0.8629 (t0) cc_final: 0.8168 (t0) REVERT: 4 16 GLU cc_start: 0.8047 (mp0) cc_final: 0.7774 (mp0) REVERT: 4 32 GLN cc_start: 0.8630 (tt0) cc_final: 0.8050 (tt0) REVERT: 4 50 TYR cc_start: 0.9237 (p90) cc_final: 0.8923 (p90) REVERT: 5 44 ILE cc_start: 0.8858 (mp) cc_final: 0.8579 (mt) REVERT: 7 12 TYR cc_start: 0.9086 (OUTLIER) cc_final: 0.8035 (t80) REVERT: 7 13 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8313 (mt-10) REVERT: 7 30 GLN cc_start: 0.8743 (tt0) cc_final: 0.8271 (tt0) REVERT: 7 67 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8709 (t) REVERT: 7 69 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7511 (p0) REVERT: 7 79 LYS cc_start: 0.8585 (tptp) cc_final: 0.7860 (ttpt) REVERT: 7 80 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.8032 (ttp-170) REVERT: 8 40 THR cc_start: 0.8790 (p) cc_final: 0.8538 (t) REVERT: 8 45 THR cc_start: 0.6454 (m) cc_final: 0.5965 (p) REVERT: 8 46 MET cc_start: 0.3674 (ttt) cc_final: 0.2936 (tpt) REVERT: 8 132 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8651 (tt0) outliers start: 120 outliers final: 95 residues processed: 796 average time/residue: 0.4149 time to fit residues: 512.0819 Evaluate side-chains 820 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 712 time to evaluate : 3.222 ------------------------------------------------------------------------------- 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 85 THR 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 E residue 21 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 28 MET Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 114 GLU 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 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 69 ASP Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain 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 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 W residue 21 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 15 ASP Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 93 ASP Chi-restraints excluded: chain 0 residue 47 GLN Chi-restraints excluded: chain 0 residue 85 THR Chi-restraints excluded: chain 1 residue 12 TYR Chi-restraints excluded: chain 1 residue 28 MET Chi-restraints excluded: chain 1 residue 69 ASP Chi-restraints excluded: chain 1 residue 114 GLU Chi-restraints excluded: chain 2 residue 61 SER 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 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 8 residue 11 ILE Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 170 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 323 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS G 18 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 117 HIS Y 18 GLN 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.086094 restraints weight = 41675.799| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.27 r_work: 0.2860 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29442 Z= 0.197 Angle : 0.548 6.478 39684 Z= 0.298 Chirality : 0.043 0.135 4302 Planarity : 0.004 0.045 5190 Dihedral : 5.565 85.001 3924 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 4.11 % Allowed : 15.85 % Favored : 80.04 % 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: 1.59 (0.17), residues: 924 sheet: -0.21 (0.14), residues: 1236 loop : 0.11 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 89 HIS 0.004 0.001 HIS J 117 PHE 0.014 0.002 PHE K 110 TYR 0.016 0.002 TYR J 8 ARG 0.011 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1302) hydrogen bonds : angle 4.38752 ( 3942) covalent geometry : bond 0.00477 (29442) covalent geometry : angle 0.54806 (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 853 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 722 time to evaluate : 3.608 Fit side-chains REVERT: A 17 LYS cc_start: 0.9086 (mttt) cc_final: 0.8617 (mtpt) REVERT: A 27 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8724 (ttpt) REVERT: A 30 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 16 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7939 (mm-30) REVERT: B 41 VAL cc_start: 0.8766 (t) cc_final: 0.8543 (m) REVERT: C 16 THR cc_start: 0.9233 (m) cc_final: 0.8879 (p) REVERT: C 89 ARG cc_start: 0.9168 (ttm-80) cc_final: 0.8828 (ttm-80) REVERT: D 13 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8239 (mt-10) REVERT: D 125 LYS cc_start: 0.8734 (mttt) cc_final: 0.8464 (mtpp) REVERT: E 26 MET cc_start: 0.8911 (ttm) cc_final: 0.8629 (ttt) REVERT: E 46 MET cc_start: 0.3433 (ttt) cc_final: 0.2648 (tpt) REVERT: E 52 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6529 (p) REVERT: F 168 ASP cc_start: 0.8448 (t0) cc_final: 0.7412 (t0) REVERT: H 40 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: I 10 GLN cc_start: 0.9088 (mt0) cc_final: 0.8760 (mt0) REVERT: I 16 THR cc_start: 0.8991 (m) cc_final: 0.8559 (t) REVERT: I 47 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: I 56 ASP cc_start: 0.9020 (t0) cc_final: 0.8753 (t0) REVERT: I 63 LYS cc_start: 0.8682 (tptm) cc_final: 0.8351 (tptt) REVERT: I 86 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8336 (mtt180) REVERT: J 30 GLN cc_start: 0.8916 (tt0) cc_final: 0.8657 (tt0) REVERT: J 68 SER cc_start: 0.9083 (p) cc_final: 0.8456 (p) REVERT: J 69 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7937 (p0) REVERT: J 71 LEU cc_start: 0.8966 (tp) cc_final: 0.8550 (mp) REVERT: J 79 LYS cc_start: 0.8514 (tptp) cc_final: 0.7779 (ttpt) REVERT: J 114 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7977 (tt0) REVERT: K 37 GLU cc_start: 0.8516 (tt0) cc_final: 0.8114 (tt0) REVERT: K 40 THR cc_start: 0.8682 (p) cc_final: 0.8438 (t) REVERT: K 46 MET cc_start: 0.4297 (ttt) cc_final: 0.3261 (tpt) REVERT: K 157 THR cc_start: 0.8681 (p) cc_final: 0.8311 (t) REVERT: L 168 ASP cc_start: 0.8611 (t0) cc_final: 0.8122 (t0) REVERT: M 16 GLU cc_start: 0.7967 (mp0) cc_final: 0.7753 (mp0) REVERT: M 32 GLN cc_start: 0.8741 (tt0) cc_final: 0.8131 (tt0) REVERT: N 44 ILE cc_start: 0.8894 (mp) cc_final: 0.8589 (mt) REVERT: P 12 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8217 (t80) REVERT: P 13 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8292 (mt-10) REVERT: P 30 GLN cc_start: 0.8777 (tt0) cc_final: 0.8311 (tt0) REVERT: P 67 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8597 (t) REVERT: P 69 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7500 (p0) REVERT: P 79 LYS cc_start: 0.8578 (tptp) cc_final: 0.7872 (ttpt) REVERT: P 80 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.8085 (ttp-170) REVERT: Q 40 THR cc_start: 0.8785 (p) cc_final: 0.8540 (t) REVERT: Q 45 THR cc_start: 0.6535 (m) cc_final: 0.6033 (p) REVERT: Q 46 MET cc_start: 0.3680 (ttt) cc_final: 0.3008 (tpt) REVERT: S 17 LYS cc_start: 0.9088 (mttt) cc_final: 0.8621 (mtpt) REVERT: S 27 LYS cc_start: 0.9002 (ttpt) cc_final: 0.8727 (ttpt) REVERT: S 30 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8099 (mt-10) REVERT: S 93 ASP cc_start: 0.8757 (t0) cc_final: 0.8535 (t0) REVERT: T 16 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7922 (mm-30) REVERT: U 16 THR cc_start: 0.9236 (m) cc_final: 0.8882 (p) REVERT: U 89 ARG cc_start: 0.9172 (ttm-80) cc_final: 0.8836 (ttm-80) REVERT: V 13 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8245 (mt-10) REVERT: V 125 LYS cc_start: 0.8725 (mttt) cc_final: 0.8461 (mtpp) REVERT: W 26 MET cc_start: 0.8889 (ttm) cc_final: 0.8607 (ttt) REVERT: W 46 MET cc_start: 0.3385 (ttt) cc_final: 0.2613 (tpt) REVERT: W 52 THR cc_start: 0.6861 (OUTLIER) cc_final: 0.6537 (p) REVERT: X 168 ASP cc_start: 0.8437 (t0) cc_final: 0.7394 (t0) REVERT: Z 40 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: 0 10 GLN cc_start: 0.9083 (mt0) cc_final: 0.8753 (mt0) REVERT: 0 16 THR cc_start: 0.8988 (m) cc_final: 0.8554 (t) REVERT: 0 47 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: 0 56 ASP cc_start: 0.9017 (t0) cc_final: 0.8745 (t0) REVERT: 0 63 LYS cc_start: 0.8684 (tptm) cc_final: 0.8348 (tptt) REVERT: 0 86 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8340 (mtt180) REVERT: 1 30 GLN cc_start: 0.8907 (tt0) cc_final: 0.8645 (tt0) REVERT: 1 68 SER cc_start: 0.9075 (p) cc_final: 0.8459 (p) REVERT: 1 69 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.7936 (p0) REVERT: 1 71 LEU cc_start: 0.8966 (tp) cc_final: 0.8550 (mp) REVERT: 1 79 LYS cc_start: 0.8524 (tptp) cc_final: 0.7790 (ttpt) REVERT: 1 114 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: 2 37 GLU cc_start: 0.8528 (tt0) cc_final: 0.8134 (tt0) REVERT: 2 40 THR cc_start: 0.8683 (p) cc_final: 0.8439 (t) REVERT: 2 46 MET cc_start: 0.4296 (ttt) cc_final: 0.3266 (tpt) REVERT: 2 157 THR cc_start: 0.8684 (p) cc_final: 0.8312 (t) REVERT: 3 168 ASP cc_start: 0.8615 (t0) cc_final: 0.8124 (t0) REVERT: 4 16 GLU cc_start: 0.7960 (mp0) cc_final: 0.7752 (mp0) REVERT: 4 32 GLN cc_start: 0.8733 (tt0) cc_final: 0.8133 (tt0) REVERT: 5 20 GLU cc_start: 0.8482 (mp0) cc_final: 0.8131 (mp0) REVERT: 5 44 ILE cc_start: 0.8900 (mp) cc_final: 0.8590 (mt) REVERT: 7 12 TYR cc_start: 0.9160 (OUTLIER) cc_final: 0.8227 (t80) REVERT: 7 13 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8307 (mt-10) REVERT: 7 30 GLN cc_start: 0.8773 (tt0) cc_final: 0.8310 (tt0) REVERT: 7 67 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8586 (t) REVERT: 7 69 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7428 (p0) REVERT: 7 79 LYS cc_start: 0.8591 (tptp) cc_final: 0.7864 (ttpt) REVERT: 7 80 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8091 (ttp-170) REVERT: 8 40 THR cc_start: 0.8786 (p) cc_final: 0.8551 (t) REVERT: 8 45 THR cc_start: 0.6508 (m) cc_final: 0.6016 (p) REVERT: 8 46 MET cc_start: 0.3680 (ttt) cc_final: 0.3001 (tpt) outliers start: 131 outliers final: 106 residues processed: 774 average time/residue: 0.4133 time to fit residues: 494.0090 Evaluate side-chains 829 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 707 time to evaluate : 3.371 ------------------------------------------------------------------------------- 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 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 93 ASP 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 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 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 69 ASP Chi-restraints excluded: chain P residue 71 LEU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 125 LYS Chi-restraints excluded: chain P residue 126 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain 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 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 W residue 21 VAL Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 27 LYS Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 93 ASP 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 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 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 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 15 ARG Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 292 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 315 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS G 18 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS V 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.088253 restraints weight = 40981.638| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.24 r_work: 0.2861 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29442 Z= 0.179 Angle : 0.534 6.036 39684 Z= 0.290 Chirality : 0.042 0.130 4302 Planarity : 0.004 0.038 5190 Dihedral : 5.482 84.849 3924 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.58 % Allowed : 15.85 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.14), residues: 3486 helix: 1.69 (0.17), residues: 924 sheet: -0.27 (0.14), residues: 1236 loop : 0.06 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 89 HIS 0.004 0.001 HIS J 117 PHE 0.013 0.001 PHE 2 110 TYR 0.014 0.001 TYR 1 8 ARG 0.008 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 1302) hydrogen bonds : angle 4.36268 ( 3942) covalent geometry : bond 0.00431 (29442) covalent geometry : angle 0.53388 (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 878 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 732 time to evaluate : 3.343 Fit side-chains REVERT: A 17 LYS cc_start: 0.9094 (mttt) cc_final: 0.8624 (mtpt) REVERT: A 27 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8760 (ttpt) REVERT: A 30 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 13 GLN cc_start: 0.8168 (mt0) cc_final: 0.7874 (mt0) REVERT: C 16 THR cc_start: 0.9252 (m) cc_final: 0.8926 (p) REVERT: C 89 ARG cc_start: 0.9169 (ttm-80) cc_final: 0.8823 (ttm-80) REVERT: C 91 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: D 13 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 125 LYS cc_start: 0.8781 (mttt) cc_final: 0.8480 (mtpp) REVERT: E 26 MET cc_start: 0.8901 (ttm) cc_final: 0.8608 (ttt) REVERT: E 46 MET cc_start: 0.3240 (ttt) cc_final: 0.2533 (tpt) REVERT: E 146 LEU cc_start: 0.8481 (mt) cc_final: 0.8228 (mt) REVERT: F 168 ASP cc_start: 0.8535 (t0) cc_final: 0.7523 (t0) REVERT: G 62 ARG cc_start: 0.8534 (ttt180) cc_final: 0.8277 (ttm170) REVERT: H 40 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: I 10 GLN cc_start: 0.9080 (mt0) cc_final: 0.8749 (mt0) REVERT: I 16 THR cc_start: 0.9020 (m) cc_final: 0.8592 (t) REVERT: I 47 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8701 (mm-40) REVERT: I 56 ASP cc_start: 0.8996 (t0) cc_final: 0.8710 (t0) REVERT: I 63 LYS cc_start: 0.8699 (tptm) cc_final: 0.8365 (tptt) REVERT: J 30 GLN cc_start: 0.8924 (tt0) cc_final: 0.8673 (tt0) REVERT: J 69 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8059 (p0) REVERT: J 71 LEU cc_start: 0.8948 (tp) cc_final: 0.8562 (mp) REVERT: J 79 LYS cc_start: 0.8542 (tptp) cc_final: 0.7811 (ttpt) REVERT: J 114 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: K 37 GLU cc_start: 0.8491 (tt0) cc_final: 0.8071 (tt0) REVERT: K 40 THR cc_start: 0.8685 (p) cc_final: 0.8453 (t) REVERT: K 46 MET cc_start: 0.4281 (ttt) cc_final: 0.3233 (tpt) REVERT: K 157 THR cc_start: 0.8684 (p) cc_final: 0.8307 (t) REVERT: L 168 ASP cc_start: 0.8666 (t0) cc_final: 0.8189 (t0) REVERT: M 16 GLU cc_start: 0.7954 (mp0) cc_final: 0.7738 (mp0) REVERT: M 32 GLN cc_start: 0.8746 (tt0) cc_final: 0.8144 (tt0) REVERT: M 50 TYR cc_start: 0.9207 (p90) cc_final: 0.8916 (p90) REVERT: M 51 MET cc_start: 0.9282 (mtt) cc_final: 0.9030 (mtt) REVERT: N 20 GLU cc_start: 0.8553 (mp0) cc_final: 0.8226 (mp0) REVERT: N 44 ILE cc_start: 0.8897 (mp) cc_final: 0.8548 (mt) REVERT: P 12 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8219 (t80) REVERT: P 13 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8267 (mt-10) REVERT: P 30 GLN cc_start: 0.8798 (tt0) cc_final: 0.8321 (tt0) REVERT: P 67 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8687 (t) REVERT: P 69 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7466 (p0) REVERT: P 79 LYS cc_start: 0.8597 (tptp) cc_final: 0.7885 (ttpt) REVERT: P 80 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.8098 (ttp-170) REVERT: Q 40 THR cc_start: 0.8777 (p) cc_final: 0.8544 (t) REVERT: Q 45 THR cc_start: 0.6522 (m) cc_final: 0.6019 (p) REVERT: Q 46 MET cc_start: 0.3713 (ttt) cc_final: 0.3055 (tpt) REVERT: S 17 LYS cc_start: 0.9092 (mttt) cc_final: 0.8620 (mtpt) REVERT: S 27 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8764 (ttpt) REVERT: S 30 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8102 (mt-10) REVERT: U 13 GLN cc_start: 0.8172 (mt0) cc_final: 0.7878 (mt0) REVERT: U 16 THR cc_start: 0.9255 (m) cc_final: 0.8929 (p) REVERT: U 89 ARG cc_start: 0.9164 (ttm-80) cc_final: 0.8825 (ttm-80) REVERT: U 91 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: V 13 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8267 (mt-10) REVERT: V 90 LYS cc_start: 0.8871 (tptm) cc_final: 0.8543 (tptp) REVERT: V 125 LYS cc_start: 0.8770 (mttt) cc_final: 0.8481 (mtpp) REVERT: W 26 MET cc_start: 0.8915 (ttm) cc_final: 0.8626 (ttt) REVERT: W 46 MET cc_start: 0.3184 (ttt) cc_final: 0.2493 (tpt) REVERT: X 168 ASP cc_start: 0.8543 (t0) cc_final: 0.7535 (t0) REVERT: Y 62 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8276 (ttm170) REVERT: Z 40 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: 0 10 GLN cc_start: 0.9077 (mt0) cc_final: 0.8743 (mt0) REVERT: 0 16 THR cc_start: 0.9014 (m) cc_final: 0.8580 (t) REVERT: 0 47 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: 0 56 ASP cc_start: 0.9009 (t0) cc_final: 0.8728 (t0) REVERT: 0 63 LYS cc_start: 0.8710 (tptm) cc_final: 0.8374 (tptt) REVERT: 1 30 GLN cc_start: 0.8919 (tt0) cc_final: 0.8667 (tt0) REVERT: 1 69 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8061 (p0) REVERT: 1 71 LEU cc_start: 0.8952 (tp) cc_final: 0.8562 (mp) REVERT: 1 79 LYS cc_start: 0.8548 (tptp) cc_final: 0.7818 (ttpt) REVERT: 1 114 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: 2 37 GLU cc_start: 0.8506 (tt0) cc_final: 0.8094 (tt0) REVERT: 2 40 THR cc_start: 0.8688 (p) cc_final: 0.8456 (t) REVERT: 2 46 MET cc_start: 0.4291 (ttt) cc_final: 0.3241 (tpt) REVERT: 2 157 THR cc_start: 0.8684 (p) cc_final: 0.8307 (t) REVERT: 3 168 ASP cc_start: 0.8668 (t0) cc_final: 0.8190 (t0) REVERT: 4 16 GLU cc_start: 0.7957 (mp0) cc_final: 0.7743 (mp0) REVERT: 4 32 GLN cc_start: 0.8736 (tt0) cc_final: 0.8136 (tt0) REVERT: 4 50 TYR cc_start: 0.9211 (p90) cc_final: 0.8925 (p90) REVERT: 4 51 MET cc_start: 0.9277 (mtt) cc_final: 0.9023 (mtt) REVERT: 5 20 GLU cc_start: 0.8522 (mp0) cc_final: 0.8099 (mp0) REVERT: 5 44 ILE cc_start: 0.8903 (mp) cc_final: 0.8549 (mt) REVERT: 7 12 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8231 (t80) REVERT: 7 13 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8288 (mt-10) REVERT: 7 30 GLN cc_start: 0.8791 (tt0) cc_final: 0.8316 (tt0) REVERT: 7 67 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8685 (t) REVERT: 7 69 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7459 (p0) REVERT: 7 79 LYS cc_start: 0.8605 (tptp) cc_final: 0.7889 (ttpt) REVERT: 7 80 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8088 (ttp-170) REVERT: 8 40 THR cc_start: 0.8778 (p) cc_final: 0.8550 (t) REVERT: 8 45 THR cc_start: 0.6503 (m) cc_final: 0.6005 (p) REVERT: 8 46 MET cc_start: 0.3713 (ttt) cc_final: 0.3049 (tpt) outliers start: 146 outliers final: 120 residues processed: 801 average time/residue: 0.4161 time to fit residues: 513.6932 Evaluate side-chains 853 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 717 time to evaluate : 3.160 ------------------------------------------------------------------------------- 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 77 SER 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 27 THR 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 C residue 91 GLU 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 21 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 93 ASP 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 21 VAL Chi-restraints excluded: chain K residue 74 ASP 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 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 61 VAL 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 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 15 ARG Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 77 SER 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 U residue 91 GLU 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 V residue 126 THR Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 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 34 LEU Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 39 ILE Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 93 ASP 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 21 VAL Chi-restraints excluded: chain 2 residue 74 ASP 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 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 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 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 15 ARG Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 236 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 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 97 ASN I 76 ASN J 16 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 GLN P 117 HIS T 97 ASN V 117 HIS Y 97 ASN 0 76 ASN 1 16 GLN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 GLN 7 117 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.090129 restraints weight = 40818.122| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.17 r_work: 0.2855 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 29442 Z= 0.288 Angle : 0.612 8.650 39684 Z= 0.331 Chirality : 0.045 0.149 4302 Planarity : 0.004 0.057 5190 Dihedral : 5.802 87.069 3924 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.83 % Allowed : 16.35 % 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: 0.19 (0.14), residues: 3486 helix: 1.45 (0.17), residues: 924 sheet: -0.42 (0.14), residues: 1236 loop : -0.08 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP W 89 HIS 0.006 0.002 HIS J 117 PHE 0.017 0.002 PHE 2 110 TYR 0.022 0.002 TYR J 8 ARG 0.012 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 1302) hydrogen bonds : angle 4.58118 ( 3942) covalent geometry : bond 0.00703 (29442) covalent geometry : angle 0.61232 (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 865 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 711 time to evaluate : 3.307 Fit side-chains REVERT: A 16 GLU cc_start: 0.8081 (mp0) cc_final: 0.7826 (mp0) REVERT: A 17 LYS cc_start: 0.9108 (mttt) cc_final: 0.8671 (mtpt) REVERT: A 27 LYS cc_start: 0.9058 (ttpt) cc_final: 0.8780 (ttpt) REVERT: A 30 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8211 (mt-10) REVERT: C 16 THR cc_start: 0.9276 (m) cc_final: 0.8974 (p) REVERT: C 89 ARG cc_start: 0.9152 (ttm-80) cc_final: 0.8821 (ttm-80) REVERT: C 98 GLU cc_start: 0.8838 (tt0) cc_final: 0.8537 (tt0) REVERT: D 13 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8279 (mt-10) REVERT: D 125 LYS cc_start: 0.8795 (mttt) cc_final: 0.8530 (mtpp) REVERT: E 26 MET cc_start: 0.8839 (ttm) cc_final: 0.8542 (ttt) REVERT: E 46 MET cc_start: 0.3170 (ttt) cc_final: 0.2648 (tpt) REVERT: F 168 ASP cc_start: 0.8497 (t0) cc_final: 0.7561 (t0) REVERT: H 40 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: H 66 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: I 16 THR cc_start: 0.9030 (m) cc_final: 0.8589 (t) REVERT: I 47 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8739 (mm-40) REVERT: I 56 ASP cc_start: 0.9006 (t0) cc_final: 0.8759 (t0) REVERT: J 69 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8143 (p0) REVERT: J 71 LEU cc_start: 0.8795 (tp) cc_final: 0.8593 (mp) REVERT: J 79 LYS cc_start: 0.8639 (tptp) cc_final: 0.7855 (ttpt) REVERT: K 40 THR cc_start: 0.8776 (p) cc_final: 0.8437 (t) REVERT: K 46 MET cc_start: 0.4339 (ttt) cc_final: 0.3216 (tpt) REVERT: K 111 GLN cc_start: 0.9363 (pt0) cc_final: 0.8745 (pt0) REVERT: K 157 THR cc_start: 0.8704 (p) cc_final: 0.8307 (t) REVERT: L 168 ASP cc_start: 0.8663 (t0) cc_final: 0.7930 (t0) REVERT: M 16 GLU cc_start: 0.7989 (mp0) cc_final: 0.7780 (mp0) REVERT: M 32 GLN cc_start: 0.8838 (tt0) cc_final: 0.8181 (tt0) REVERT: M 61 ASN cc_start: 0.8641 (m-40) cc_final: 0.8330 (m110) REVERT: N 20 GLU cc_start: 0.8539 (mp0) cc_final: 0.8133 (mp0) REVERT: N 44 ILE cc_start: 0.8927 (mp) cc_final: 0.8600 (mt) REVERT: O 13 GLN cc_start: 0.8470 (mt0) cc_final: 0.8244 (mt0) REVERT: P 6 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8895 (mt0) REVERT: P 12 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8227 (t80) REVERT: P 13 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8291 (mt-10) REVERT: P 15 LEU cc_start: 0.9178 (mt) cc_final: 0.8867 (mm) REVERT: P 67 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8685 (t) REVERT: P 69 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7504 (p0) REVERT: P 79 LYS cc_start: 0.8656 (tptp) cc_final: 0.7980 (ttpt) REVERT: Q 40 THR cc_start: 0.8813 (p) cc_final: 0.8542 (t) REVERT: Q 45 THR cc_start: 0.6641 (m) cc_final: 0.6131 (p) REVERT: Q 46 MET cc_start: 0.3937 (ttt) cc_final: 0.3225 (tpt) REVERT: S 16 GLU cc_start: 0.8096 (mp0) cc_final: 0.7834 (mp0) REVERT: S 17 LYS cc_start: 0.9111 (mttt) cc_final: 0.8675 (mtpt) REVERT: S 27 LYS cc_start: 0.9059 (ttpt) cc_final: 0.8780 (ttpt) REVERT: S 30 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8195 (mt-10) REVERT: U 16 THR cc_start: 0.9281 (m) cc_final: 0.8975 (p) REVERT: U 89 ARG cc_start: 0.9142 (ttm-80) cc_final: 0.8828 (ttm-80) REVERT: U 98 GLU cc_start: 0.8834 (tt0) cc_final: 0.8533 (tt0) REVERT: V 13 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8278 (mt-10) REVERT: V 90 LYS cc_start: 0.8840 (tptm) cc_final: 0.8635 (tptp) REVERT: V 125 LYS cc_start: 0.8786 (mttt) cc_final: 0.8525 (mtpp) REVERT: W 26 MET cc_start: 0.8843 (ttm) cc_final: 0.8547 (ttt) REVERT: W 46 MET cc_start: 0.3112 (ttt) cc_final: 0.2598 (tpt) REVERT: X 168 ASP cc_start: 0.8495 (t0) cc_final: 0.7560 (t0) REVERT: Z 40 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: Z 66 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: 0 16 THR cc_start: 0.9035 (m) cc_final: 0.8590 (t) REVERT: 0 47 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8724 (mm-40) REVERT: 0 56 ASP cc_start: 0.9019 (t0) cc_final: 0.8771 (t0) REVERT: 1 69 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8147 (p0) REVERT: 1 79 LYS cc_start: 0.8640 (tptp) cc_final: 0.7852 (ttpt) REVERT: 2 40 THR cc_start: 0.8783 (p) cc_final: 0.8448 (t) REVERT: 2 46 MET cc_start: 0.4356 (ttt) cc_final: 0.3232 (tpt) REVERT: 2 111 GLN cc_start: 0.9363 (pt0) cc_final: 0.8748 (pt0) REVERT: 2 157 THR cc_start: 0.8696 (p) cc_final: 0.8298 (t) REVERT: 3 168 ASP cc_start: 0.8668 (t0) cc_final: 0.7938 (t0) REVERT: 4 32 GLN cc_start: 0.8838 (tt0) cc_final: 0.8179 (tt0) REVERT: 4 61 ASN cc_start: 0.8646 (m-40) cc_final: 0.8334 (m110) REVERT: 5 20 GLU cc_start: 0.8529 (mp0) cc_final: 0.8107 (mp0) REVERT: 5 44 ILE cc_start: 0.8929 (mp) cc_final: 0.8598 (mt) REVERT: 7 6 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8899 (mt0) REVERT: 7 12 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8225 (t80) REVERT: 7 13 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8294 (mt-10) REVERT: 7 15 LEU cc_start: 0.9157 (mt) cc_final: 0.8843 (mm) REVERT: 7 67 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8682 (t) REVERT: 7 69 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7507 (p0) REVERT: 7 79 LYS cc_start: 0.8674 (tptp) cc_final: 0.7997 (ttpt) REVERT: 8 40 THR cc_start: 0.8814 (p) cc_final: 0.8552 (t) REVERT: 8 45 THR cc_start: 0.6637 (m) cc_final: 0.6127 (p) REVERT: 8 46 MET cc_start: 0.3943 (ttt) cc_final: 0.3227 (tpt) outliers start: 154 outliers final: 116 residues processed: 784 average time/residue: 0.4110 time to fit residues: 497.1573 Evaluate side-chains 833 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 701 time to evaluate : 3.166 ------------------------------------------------------------------------------- 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 27 THR 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 21 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 93 ASP 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 69 ASP 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 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 27 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 6 GLN Chi-restraints excluded: chain P residue 12 TYR Chi-restraints excluded: chain P residue 39 ILE 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 15 ARG Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 26 MET Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain S residue 9 LYS Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain 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 21 VAL 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 26 ILE Chi-restraints excluded: chain Y residue 27 LYS Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 93 ASP 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 69 ASP 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 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 27 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 6 GLN Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 39 ILE 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 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 15 ARG Chi-restraints excluded: chain 8 residue 21 VAL Chi-restraints excluded: chain 8 residue 26 MET Chi-restraints excluded: chain 8 residue 61 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 216 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 282 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN G 18 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS P 117 HIS W 111 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095860 restraints weight = 39659.995| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.16 r_work: 0.2944 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3918 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= 0.114 Angle : 0.503 6.786 39684 Z= 0.273 Chirality : 0.041 0.125 4302 Planarity : 0.004 0.040 5190 Dihedral : 5.291 84.187 3924 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.23 % Allowed : 18.46 % Favored : 78.31 % 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: 0.48 (0.15), residues: 3486 helix: 1.89 (0.17), residues: 924 sheet: -0.34 (0.14), residues: 1236 loop : 0.02 (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 J 74 PHE 0.010 0.001 PHE A 96 TYR 0.013 0.001 TYR P 8 ARG 0.009 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1302) hydrogen bonds : angle 4.26634 ( 3942) covalent geometry : bond 0.00262 (29442) covalent geometry : angle 0.50304 (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 849 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 746 time to evaluate : 3.111 Fit side-chains REVERT: A 16 GLU cc_start: 0.8113 (mp0) cc_final: 0.7824 (mp0) REVERT: A 17 LYS cc_start: 0.9111 (mttt) cc_final: 0.8660 (mtmt) REVERT: A 27 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8715 (ttpt) REVERT: A 30 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 40 GLU cc_start: 0.7711 (mp0) cc_final: 0.7470 (pt0) REVERT: C 1 MET cc_start: 0.8536 (tpp) cc_final: 0.8226 (mmt) REVERT: C 16 THR cc_start: 0.9241 (m) cc_final: 0.8983 (p) REVERT: D 13 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8261 (mt-10) REVERT: D 125 LYS cc_start: 0.8782 (mttt) cc_final: 0.8542 (mmtm) REVERT: E 26 MET cc_start: 0.8799 (ttm) cc_final: 0.8513 (ttt) REVERT: E 46 MET cc_start: 0.3187 (ttt) cc_final: 0.2571 (tpt) REVERT: F 168 ASP cc_start: 0.8680 (t0) cc_final: 0.7845 (t0) REVERT: H 40 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: H 95 TYR cc_start: 0.8400 (t80) cc_final: 0.7781 (t80) REVERT: I 10 GLN cc_start: 0.9092 (mt0) cc_final: 0.8775 (mt0) REVERT: I 16 THR cc_start: 0.8993 (m) cc_final: 0.8669 (p) REVERT: I 20 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8295 (mmmt) REVERT: I 47 GLN cc_start: 0.9005 (tt0) cc_final: 0.8734 (mm-40) REVERT: I 86 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8343 (mtt180) REVERT: J 30 GLN cc_start: 0.8896 (tt0) cc_final: 0.8628 (tt0) REVERT: J 69 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7833 (p0) REVERT: J 71 LEU cc_start: 0.8883 (tp) cc_final: 0.8536 (mp) REVERT: J 79 LYS cc_start: 0.8600 (tptp) cc_final: 0.7862 (ttpt) REVERT: K 37 GLU cc_start: 0.8466 (tt0) cc_final: 0.8060 (tt0) REVERT: K 40 THR cc_start: 0.8700 (p) cc_final: 0.8462 (t) REVERT: K 46 MET cc_start: 0.4150 (ttt) cc_final: 0.3256 (tpt) REVERT: K 111 GLN cc_start: 0.9299 (pt0) cc_final: 0.8460 (pt0) REVERT: K 157 THR cc_start: 0.8714 (p) cc_final: 0.8328 (t) REVERT: L 168 ASP cc_start: 0.8620 (t0) cc_final: 0.8223 (t0) REVERT: M 30 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8302 (mt-10) REVERT: M 32 GLN cc_start: 0.8743 (tt0) cc_final: 0.8190 (tt0) REVERT: N 20 GLU cc_start: 0.8476 (mp0) cc_final: 0.8059 (mp0) REVERT: N 44 ILE cc_start: 0.8832 (mp) cc_final: 0.8525 (mt) REVERT: P 12 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8034 (t80) REVERT: P 13 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8055 (mt-10) REVERT: P 15 LEU cc_start: 0.9037 (mt) cc_final: 0.8700 (mm) REVERT: P 30 GLN cc_start: 0.8775 (tt0) cc_final: 0.8241 (tt0) REVERT: P 52 ASP cc_start: 0.8653 (m-30) cc_final: 0.8413 (m-30) REVERT: P 67 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8680 (t) REVERT: P 69 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7553 (p0) REVERT: P 79 LYS cc_start: 0.8624 (tptp) cc_final: 0.7929 (ttpt) REVERT: Q 40 THR cc_start: 0.8813 (p) cc_final: 0.8553 (t) REVERT: Q 45 THR cc_start: 0.6617 (m) cc_final: 0.6067 (p) REVERT: Q 46 MET cc_start: 0.3520 (ttt) cc_final: 0.2969 (tpt) REVERT: Q 132 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8728 (tt0) REVERT: S 16 GLU cc_start: 0.8136 (mp0) cc_final: 0.7837 (mp0) REVERT: S 17 LYS cc_start: 0.9101 (mttt) cc_final: 0.8644 (mtmt) REVERT: S 27 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8719 (ttpt) REVERT: S 30 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8106 (mt-10) REVERT: U 1 MET cc_start: 0.8539 (tpp) cc_final: 0.8229 (mmt) REVERT: U 16 THR cc_start: 0.9240 (m) cc_final: 0.8979 (p) REVERT: V 13 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8250 (mt-10) REVERT: V 90 LYS cc_start: 0.8822 (tptm) cc_final: 0.8497 (tptp) REVERT: V 125 LYS cc_start: 0.8762 (mttt) cc_final: 0.8538 (mmtm) REVERT: W 26 MET cc_start: 0.8829 (ttm) cc_final: 0.8552 (ttt) REVERT: W 46 MET cc_start: 0.3158 (ttt) cc_final: 0.2555 (tpt) REVERT: X 168 ASP cc_start: 0.8713 (t0) cc_final: 0.7909 (t0) REVERT: Z 40 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: Z 95 TYR cc_start: 0.8403 (t80) cc_final: 0.7785 (t80) REVERT: 0 10 GLN cc_start: 0.9093 (mt0) cc_final: 0.8773 (mt0) REVERT: 0 16 THR cc_start: 0.8994 (m) cc_final: 0.8673 (p) REVERT: 0 20 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8291 (mmmt) REVERT: 0 47 GLN cc_start: 0.9005 (tt0) cc_final: 0.8736 (mm-40) REVERT: 0 86 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8347 (mtt180) REVERT: 1 30 GLN cc_start: 0.8892 (tt0) cc_final: 0.8622 (tt0) REVERT: 1 69 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7912 (p0) REVERT: 1 79 LYS cc_start: 0.8598 (tptp) cc_final: 0.7862 (ttpt) REVERT: 2 37 GLU cc_start: 0.8481 (tt0) cc_final: 0.8080 (tt0) REVERT: 2 40 THR cc_start: 0.8703 (p) cc_final: 0.8467 (t) REVERT: 2 46 MET cc_start: 0.4137 (ttt) cc_final: 0.3260 (tpt) REVERT: 2 111 GLN cc_start: 0.9287 (pt0) cc_final: 0.8448 (pt0) REVERT: 2 157 THR cc_start: 0.8716 (p) cc_final: 0.8333 (t) REVERT: 3 168 ASP cc_start: 0.8612 (t0) cc_final: 0.8219 (t0) REVERT: 4 30 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8311 (mt-10) REVERT: 4 32 GLN cc_start: 0.8727 (tt0) cc_final: 0.8178 (tt0) REVERT: 5 44 ILE cc_start: 0.8838 (mp) cc_final: 0.8528 (mt) REVERT: 6 13 GLN cc_start: 0.8426 (mt0) cc_final: 0.8212 (mt0) REVERT: 7 12 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8027 (t80) REVERT: 7 13 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8070 (mt-10) REVERT: 7 15 LEU cc_start: 0.9039 (mt) cc_final: 0.8718 (mm) REVERT: 7 30 GLN cc_start: 0.8779 (tt0) cc_final: 0.8254 (tt0) REVERT: 7 52 ASP cc_start: 0.8650 (m-30) cc_final: 0.8405 (m-30) REVERT: 7 69 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7555 (p0) REVERT: 7 79 LYS cc_start: 0.8624 (tptp) cc_final: 0.7924 (ttpt) REVERT: 8 40 THR cc_start: 0.8820 (p) cc_final: 0.8566 (t) REVERT: 8 45 THR cc_start: 0.6587 (m) cc_final: 0.6047 (p) REVERT: 8 46 MET cc_start: 0.3506 (ttt) cc_final: 0.2951 (tpt) REVERT: 8 132 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8718 (tt0) outliers start: 103 outliers final: 81 residues processed: 795 average time/residue: 0.4004 time to fit residues: 495.7160 Evaluate side-chains 807 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 717 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 85 THR Chi-restraints excluded: chain C residue 92 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 E residue 21 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 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 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 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 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 Q residue 61 SER 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 U residue 92 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 W residue 21 VAL 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 26 ILE Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain 0 residue 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 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 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 69 ASP 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 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 245 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 HIS G 18 GLN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 HIS V 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094594 restraints weight = 39935.561| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.18 r_work: 0.2929 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29442 Z= 0.126 Angle : 0.513 7.072 39684 Z= 0.277 Chirality : 0.041 0.125 4302 Planarity : 0.004 0.058 5190 Dihedral : 5.187 82.196 3924 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.11 % Allowed : 18.49 % Favored : 78.41 % 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: 1.97 (0.17), residues: 924 sheet: -0.28 (0.14), residues: 1236 loop : 0.03 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 89 HIS 0.003 0.001 HIS D 74 PHE 0.012 0.001 PHE E 14 TYR 0.014 0.001 TYR 1 124 ARG 0.013 0.001 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1302) hydrogen bonds : angle 4.26095 ( 3942) covalent geometry : bond 0.00297 (29442) covalent geometry : angle 0.51289 (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 825 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 726 time to evaluate : 3.154 Fit side-chains REVERT: A 17 LYS cc_start: 0.9143 (mttt) cc_final: 0.8689 (mtpt) REVERT: A 27 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8732 (ttpt) REVERT: A 30 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 1 MET cc_start: 0.8548 (tpp) cc_final: 0.8193 (mmt) REVERT: C 16 THR cc_start: 0.9252 (m) cc_final: 0.9019 (p) REVERT: D 13 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8265 (mt-10) REVERT: D 99 ASP cc_start: 0.8617 (t70) cc_final: 0.8266 (t0) REVERT: D 125 LYS cc_start: 0.8765 (mttt) cc_final: 0.8534 (mmtm) REVERT: E 26 MET cc_start: 0.8779 (ttm) cc_final: 0.8535 (ttt) REVERT: E 46 MET cc_start: 0.3172 (ttt) cc_final: 0.2365 (tpt) REVERT: E 94 ARG cc_start: 0.8960 (mtt-85) cc_final: 0.8602 (mmm160) REVERT: F 168 ASP cc_start: 0.8673 (t0) cc_final: 0.7848 (t0) REVERT: H 40 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: H 95 TYR cc_start: 0.8401 (t80) cc_final: 0.7794 (t80) REVERT: I 10 GLN cc_start: 0.9085 (mt0) cc_final: 0.8791 (mt0) REVERT: I 13 GLN cc_start: 0.8444 (mt0) cc_final: 0.8111 (mp10) REVERT: I 16 THR cc_start: 0.8973 (m) cc_final: 0.8653 (p) REVERT: I 20 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8303 (mmmt) REVERT: I 47 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8655 (mm-40) REVERT: I 56 ASP cc_start: 0.8945 (t0) cc_final: 0.8655 (t0) REVERT: I 86 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8330 (mtt180) REVERT: J 69 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8008 (p0) REVERT: J 71 LEU cc_start: 0.8880 (tp) cc_final: 0.8539 (mp) REVERT: J 79 LYS cc_start: 0.8601 (tptp) cc_final: 0.7894 (ttpt) REVERT: K 37 GLU cc_start: 0.8491 (tt0) cc_final: 0.8073 (tt0) REVERT: K 46 MET cc_start: 0.4120 (ttt) cc_final: 0.3275 (tpt) REVERT: K 111 GLN cc_start: 0.9322 (pt0) cc_final: 0.8502 (pt0) REVERT: K 157 THR cc_start: 0.8662 (p) cc_final: 0.8254 (t) REVERT: L 168 ASP cc_start: 0.8631 (t0) cc_final: 0.8228 (t0) REVERT: M 30 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8312 (mt-10) REVERT: M 32 GLN cc_start: 0.8764 (tt0) cc_final: 0.8187 (tt0) REVERT: M 89 GLU cc_start: 0.8145 (pt0) cc_final: 0.7786 (pt0) REVERT: N 20 GLU cc_start: 0.8523 (mp0) cc_final: 0.8068 (mp0) REVERT: N 44 ILE cc_start: 0.8819 (mp) cc_final: 0.8525 (mt) REVERT: O 16 THR cc_start: 0.9169 (m) cc_final: 0.8831 (p) REVERT: P 12 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8004 (t80) REVERT: P 13 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8091 (mt-10) REVERT: P 30 GLN cc_start: 0.8842 (tt0) cc_final: 0.8394 (tt0) REVERT: P 52 ASP cc_start: 0.8661 (m-30) cc_final: 0.8420 (m-30) REVERT: P 67 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8686 (t) REVERT: P 69 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7652 (p0) REVERT: P 79 LYS cc_start: 0.8621 (tptp) cc_final: 0.7928 (ttpt) REVERT: Q 45 THR cc_start: 0.6612 (m) cc_final: 0.6062 (p) REVERT: Q 46 MET cc_start: 0.3509 (ttt) cc_final: 0.2980 (tpt) REVERT: Q 132 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8752 (tt0) REVERT: S 17 LYS cc_start: 0.9129 (mttt) cc_final: 0.8668 (mtpt) REVERT: S 27 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8735 (ttpt) REVERT: S 30 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8189 (mt-10) REVERT: U 1 MET cc_start: 0.8534 (tpp) cc_final: 0.8185 (mmt) REVERT: U 16 THR cc_start: 0.9257 (m) cc_final: 0.9025 (p) REVERT: V 13 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8265 (mt-10) REVERT: V 90 LYS cc_start: 0.8836 (tptm) cc_final: 0.8522 (tptp) REVERT: V 125 LYS cc_start: 0.8726 (mttt) cc_final: 0.8486 (mtpp) REVERT: W 26 MET cc_start: 0.8801 (ttm) cc_final: 0.8570 (ttt) REVERT: W 46 MET cc_start: 0.3136 (ttt) cc_final: 0.2564 (tpt) REVERT: W 94 ARG cc_start: 0.8942 (mtt-85) cc_final: 0.8582 (mmm160) REVERT: X 168 ASP cc_start: 0.8677 (t0) cc_final: 0.7853 (t0) REVERT: Z 40 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: Z 95 TYR cc_start: 0.8406 (t80) cc_final: 0.7801 (t80) REVERT: 0 10 GLN cc_start: 0.9089 (mt0) cc_final: 0.8793 (mt0) REVERT: 0 13 GLN cc_start: 0.8430 (mt0) cc_final: 0.8026 (mp10) REVERT: 0 16 THR cc_start: 0.8971 (m) cc_final: 0.8645 (p) REVERT: 0 20 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8278 (mmmt) REVERT: 0 47 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8666 (mm-40) REVERT: 0 56 ASP cc_start: 0.8960 (t0) cc_final: 0.8674 (t0) REVERT: 0 86 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8314 (mtt180) REVERT: 1 69 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8175 (p0) REVERT: 1 79 LYS cc_start: 0.8606 (tptp) cc_final: 0.7902 (ttpt) REVERT: 2 37 GLU cc_start: 0.8503 (tt0) cc_final: 0.8171 (tt0) REVERT: 2 46 MET cc_start: 0.4118 (ttt) cc_final: 0.3285 (tpt) REVERT: 2 111 GLN cc_start: 0.9311 (pt0) cc_final: 0.8496 (pt0) REVERT: 2 157 THR cc_start: 0.8661 (p) cc_final: 0.8255 (t) REVERT: 3 168 ASP cc_start: 0.8623 (t0) cc_final: 0.8225 (t0) REVERT: 4 30 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8315 (mt-10) REVERT: 4 32 GLN cc_start: 0.8741 (tt0) cc_final: 0.8194 (tt0) REVERT: 4 89 GLU cc_start: 0.8161 (pt0) cc_final: 0.7793 (pt0) REVERT: 5 44 ILE cc_start: 0.8823 (mp) cc_final: 0.8524 (mt) REVERT: 6 13 GLN cc_start: 0.8384 (mt0) cc_final: 0.8184 (mt0) REVERT: 6 16 THR cc_start: 0.9163 (m) cc_final: 0.8834 (p) REVERT: 7 12 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.7982 (t80) REVERT: 7 13 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8092 (mt-10) REVERT: 7 30 GLN cc_start: 0.8845 (tt0) cc_final: 0.8389 (tt0) REVERT: 7 52 ASP cc_start: 0.8656 (m-30) cc_final: 0.8405 (m-30) REVERT: 7 69 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7673 (p0) REVERT: 7 79 LYS cc_start: 0.8634 (tptp) cc_final: 0.7934 (ttpt) REVERT: 8 45 THR cc_start: 0.6613 (m) cc_final: 0.6064 (p) REVERT: 8 46 MET cc_start: 0.3509 (ttt) cc_final: 0.2981 (tpt) REVERT: 8 132 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8744 (tt0) outliers start: 99 outliers final: 81 residues processed: 773 average time/residue: 0.4099 time to fit residues: 496.0028 Evaluate side-chains 797 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 705 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 49 SER Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 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 110 PHE 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 34 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain I residue 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 69 ASP Chi-restraints excluded: chain K residue 8 ASN Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 110 PHE Chi-restraints excluded: chain M residue 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 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 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 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 61 SER Chi-restraints excluded: chain W residue 110 PHE Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 40 GLU Chi-restraints excluded: chain Z residue 49 SER 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 69 ASP Chi-restraints excluded: chain 2 residue 8 ASN 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 86 LYS Chi-restraints excluded: chain 5 residue 15 ASP Chi-restraints excluded: chain 5 residue 35 SER Chi-restraints excluded: chain 5 residue 49 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 THR Chi-restraints excluded: chain 7 residue 12 TYR Chi-restraints excluded: chain 7 residue 69 ASP Chi-restraints excluded: chain 7 residue 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: 6.9990 chunk 242 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 145 optimal weight: 0.0770 chunk 128 optimal weight: 5.9990 chunk 253 optimal weight: 0.0170 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 26 ASN I 76 ASN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN P 117 HIS V 117 HIS Y 18 GLN Y 32 GLN Y 97 ASN 0 26 ASN 0 76 ASN ** 6 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 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 = 0.3366 r_free = 0.3366 target = 0.115956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098499 restraints weight = 39570.245| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.19 r_work: 0.2983 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29442 Z= 0.100 Angle : 0.493 6.609 39684 Z= 0.266 Chirality : 0.040 0.125 4302 Planarity : 0.004 0.059 5190 Dihedral : 4.939 78.559 3924 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.92 % Allowed : 18.96 % Favored : 78.12 % 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: 0.67 (0.15), residues: 3486 helix: 2.12 (0.17), residues: 924 sheet: -0.19 (0.14), residues: 1236 loop : 0.04 (0.18), residues: 1326 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 0.010 0.001 PHE E 14 TYR 0.012 0.001 TYR 7 54 ARG 0.014 0.001 ARG 9 160 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 1302) hydrogen bonds : angle 4.17662 ( 3942) covalent geometry : bond 0.00229 (29442) covalent geometry : angle 0.49297 (39684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15191.24 seconds wall clock time: 263 minutes 39.03 seconds (15819.03 seconds total)