Starting phenix.real_space_refine on Mon Aug 25 21:14:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu2_48617/08_2025/9mu2_48617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu2_48617/08_2025/9mu2_48617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2025/9mu2_48617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2025/9mu2_48617.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2025/9mu2_48617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2025/9mu2_48617.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.013 sd= 0.139 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 121 5.16 5 C 19681 2.51 5 N 5207 2.21 5 O 6355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31396 Number of models: 1 Model: "" Number of chains: 42 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: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 306 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "N" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "O" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "P" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 904 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "Q" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 324 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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: "a" 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: "b" 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: "c" 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: "d" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "e" 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: "f" 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: "g" 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: "h" 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: "i" 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: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "k" 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: "l" 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: "m" 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: "n" 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: "o" 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: "p" 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: 6.37, per 1000 atoms: 0.20 Number of scatterers: 31396 At special positions: 0 Unit cell: (115.71, 118.37, 190.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 32 15.00 O 6355 8.00 N 5207 7.00 C 19681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7188 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 22 sheets defined 32.8% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.323A pdb=" N VAL A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.665A 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 63 removed outlier: 4.262A pdb=" N ILE A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 removed outlier: 4.127A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.022A pdb=" N VAL B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 3.692A 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: 4.132A pdb=" N ILE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 removed outlier: 4.174A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.587A 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: 3.622A 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: 3.743A 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: 4.324A pdb=" N VAL G 7 " --> pdb=" O THR G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 37 removed outlier: 3.658A 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 63 removed outlier: 4.210A pdb=" N ILE G 52 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 97 removed outlier: 4.145A pdb=" N ALA G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 removed outlier: 4.040A pdb=" N VAL H 7 " --> pdb=" O THR H 3 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.685A 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: 4.135A pdb=" N ILE H 52 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 4.203A pdb=" N ALA H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.582A 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 17 through 19 No H-bonds generated for 'chain 'J' and resid 17 through 19' Processing helix chain 'J' and resid 70 through 86 removed outlier: 3.650A 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: 3.700A 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 14 through 37 removed outlier: 3.744A pdb=" N GLN M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 37 removed outlier: 4.433A pdb=" N PHE N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG N 30 " --> pdb=" O LYS N 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 37 removed outlier: 3.983A pdb=" N PHE O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG O 19 " --> pdb=" O ALA O 15 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP O 36 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN O 37 " --> pdb=" O ARG O 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 47 removed outlier: 4.117A pdb=" N GLN P 12 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP P 21 " --> pdb=" O LYS P 17 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 58 No H-bonds generated for 'chain 'P' and resid 56 through 58' Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 95 through 113 removed outlier: 3.700A pdb=" N VAL P 101 " --> pdb=" O PRO P 97 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.301A pdb=" N VAL S 7 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 37 removed outlier: 3.668A 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 63 removed outlier: 4.206A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 97 removed outlier: 4.133A pdb=" N ALA S 90 " --> pdb=" O LYS S 86 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.039A pdb=" N VAL T 7 " --> pdb=" O THR T 3 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 37 removed outlier: 3.709A 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: 4.135A pdb=" N ILE T 52 " --> pdb=" O PHE T 48 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS T 53 " --> pdb=" O SER T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 97 removed outlier: 4.172A pdb=" N ALA T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE T 91 " --> pdb=" O GLU T 87 " (cutoff:3.500A) removed outlier: 3.580A 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 85 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: 3.687A 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: 4.330A pdb=" N VAL Y 7 " --> pdb=" O THR Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 37 removed outlier: 3.669A 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 63 removed outlier: 4.200A pdb=" N ILE Y 52 " --> pdb=" O PHE Y 48 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 97 removed outlier: 4.019A pdb=" N ALA Y 90 " --> pdb=" O LYS Y 86 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE Y 91 " --> pdb=" O GLU Y 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 11 removed outlier: 4.062A pdb=" N VAL Z 7 " --> pdb=" O THR Z 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG Z 10 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 37 removed outlier: 3.683A 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: 4.119A pdb=" N ILE Z 52 " --> pdb=" O PHE Z 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 97 removed outlier: 4.085A pdb=" N ALA Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE Z 91 " --> pdb=" O GLU Z 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 16 Processing helix chain 'b' and resid 17 through 19 No H-bonds generated for 'chain 'b' and resid 17 through 19' Processing helix chain 'b' and resid 70 through 86 removed outlier: 3.641A pdb=" N HIS b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 8 No H-bonds generated for 'chain 'c' and resid 6 through 8' Processing helix chain 'c' and resid 71 through 83 removed outlier: 3.678A pdb=" N VAL c 81 " --> pdb=" O GLU c 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 147 through 152 Processing helix chain 'd' and resid 165 through 169 Processing helix chain 'e' and resid 3 through 11 removed outlier: 4.355A pdb=" N VAL e 7 " --> pdb=" O THR e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 37 removed outlier: 3.654A pdb=" N GLU e 24 " --> pdb=" O GLU e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 47 No H-bonds generated for 'chain 'e' and resid 45 through 47' Processing helix chain 'e' and resid 48 through 63 removed outlier: 4.197A pdb=" N ILE e 52 " --> pdb=" O PHE e 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS e 53 " --> pdb=" O SER e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 97 removed outlier: 4.067A pdb=" N ALA e 90 " --> pdb=" O LYS e 86 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE e 91 " --> pdb=" O GLU e 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 11 removed outlier: 4.027A pdb=" N VAL f 7 " --> pdb=" O THR f 3 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG f 10 " --> pdb=" O ASP f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 37 removed outlier: 3.701A pdb=" N GLU f 24 " --> pdb=" O GLU f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 47 No H-bonds generated for 'chain 'f' and resid 45 through 47' Processing helix chain 'f' and resid 48 through 63 removed outlier: 4.146A pdb=" N ILE f 52 " --> pdb=" O PHE f 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS f 53 " --> pdb=" O SER f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 97 removed outlier: 4.122A pdb=" N ALA f 90 " --> pdb=" O LYS f 86 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE f 91 " --> pdb=" O GLU f 87 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN f 94 " --> pdb=" O ALA f 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 16 Processing helix chain 'h' and resid 70 through 86 removed outlier: 3.507A pdb=" N HIS h 74 " --> pdb=" O ASP h 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 8 No H-bonds generated for 'chain 'i' and resid 6 through 8' Processing helix chain 'i' and resid 71 through 83 removed outlier: 3.727A pdb=" N VAL i 81 " --> pdb=" O GLU i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 147 through 152 Processing helix chain 'j' and resid 165 through 169 Processing helix chain 'k' and resid 3 through 11 removed outlier: 4.310A pdb=" N VAL k 7 " --> pdb=" O THR k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 18 through 37 removed outlier: 3.634A pdb=" N GLU k 24 " --> pdb=" O GLU k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 47 No H-bonds generated for 'chain 'k' and resid 45 through 47' Processing helix chain 'k' and resid 48 through 63 removed outlier: 4.228A pdb=" N ILE k 52 " --> pdb=" O PHE k 48 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS k 53 " --> pdb=" O SER k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 97 removed outlier: 4.068A pdb=" N ALA k 90 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE k 91 " --> pdb=" O GLU k 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 4.053A pdb=" N VAL l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG l 10 " --> pdb=" O ASP l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 18 through 37 removed outlier: 3.690A pdb=" N GLU l 24 " --> pdb=" O GLU l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 45 through 47 No H-bonds generated for 'chain 'l' and resid 45 through 47' Processing helix chain 'l' and resid 48 through 63 removed outlier: 4.172A pdb=" N ILE l 52 " --> pdb=" O PHE l 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS l 53 " --> pdb=" O SER l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 97 removed outlier: 4.135A pdb=" N ALA l 90 " --> pdb=" O LYS l 86 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE l 91 " --> pdb=" O GLU l 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 16 Processing helix chain 'n' and resid 17 through 19 No H-bonds generated for 'chain 'n' and resid 17 through 19' Processing helix chain 'n' and resid 70 through 86 removed outlier: 3.597A pdb=" N HIS n 74 " --> pdb=" O ASP n 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 6 through 8 No H-bonds generated for 'chain 'o' and resid 6 through 8' Processing helix chain 'o' and resid 71 through 83 removed outlier: 3.731A pdb=" N VAL o 81 " --> pdb=" O GLU o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 152 Processing helix chain 'p' and resid 165 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 73 removed outlier: 5.934A pdb=" N THR A 69 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR B 69 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR k 69 " --> pdb=" O TYR k 80 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER k 77 " --> pdb=" O GLU l 71 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU l 71 " --> pdb=" O SER k 77 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA k 79 " --> pdb=" O THR l 69 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR l 69 " --> pdb=" O TYR l 80 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR e 69 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER f 70 " --> pdb=" O ALA e 79 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR f 69 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR Y 69 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER Y 77 " --> pdb=" O GLU Z 71 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU Z 71 " --> pdb=" O SER Y 77 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA Y 79 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR Z 69 " --> pdb=" O TYR Z 80 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR S 69 " --> pdb=" O TYR S 80 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER S 77 " --> pdb=" O GLU T 71 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU T 71 " --> pdb=" O SER S 77 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA S 79 " --> pdb=" O THR T 69 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR T 69 " --> pdb=" O TYR T 80 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR G 69 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR H 69 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.386A pdb=" N ILE C 82 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 97 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS C 63 " --> pdb=" O PRO C 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.239A pdb=" N VAL D 61 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN D 59 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER D 44 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP D 57 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG D 46 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER D 55 " --> pdb=" O ARG D 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 67 current: chain 'D' and resid 95 through 108 removed outlier: 6.800A pdb=" N SER D 123 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 101 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR D 121 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE D 103 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 119 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN D 105 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 117 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 107 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 115 " --> pdb=" O VAL D 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 115 through 127 current: chain 'J' and resid 36 through 48 removed outlier: 4.229A pdb=" N VAL J 61 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN J 59 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER J 44 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP J 57 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG J 46 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER J 55 " --> pdb=" O ARG J 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 67 current: chain 'J' and resid 95 through 108 removed outlier: 6.819A pdb=" N SER J 123 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR J 101 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR J 121 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE J 103 " --> pdb=" O SER J 119 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER J 119 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN J 105 " --> pdb=" O HIS J 117 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS J 117 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL J 107 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU J 115 " --> pdb=" O VAL J 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 115 through 127 current: chain 'V' and resid 36 through 48 removed outlier: 4.220A pdb=" N VAL V 61 " --> pdb=" O LYS V 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN V 59 " --> pdb=" O PRO V 42 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER V 44 " --> pdb=" O ASP V 57 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP V 57 " --> pdb=" O SER V 44 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG V 46 " --> pdb=" O SER V 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER V 55 " --> pdb=" O ARG V 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 54 through 67 current: chain 'V' and resid 95 through 108 removed outlier: 6.547A pdb=" N SER V 123 " --> pdb=" O ASP V 99 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR V 101 " --> pdb=" O THR V 121 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR V 121 " --> pdb=" O THR V 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE V 103 " --> pdb=" O SER V 119 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER V 119 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN V 105 " --> pdb=" O HIS V 117 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS V 117 " --> pdb=" O GLN V 105 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL V 107 " --> pdb=" O LEU V 115 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU V 115 " --> pdb=" O VAL V 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 115 through 127 current: chain 'b' and resid 36 through 48 removed outlier: 4.109A pdb=" N VAL b 61 " --> pdb=" O LYS b 40 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN b 59 " --> pdb=" O PRO b 42 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER b 44 " --> pdb=" O ASP b 57 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP b 57 " --> pdb=" O SER b 44 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG b 46 " --> pdb=" O SER b 55 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER b 55 " --> pdb=" O ARG b 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 54 through 67 current: chain 'b' and resid 95 through 108 removed outlier: 5.636A pdb=" N PHE b 96 " --> pdb=" O PHE b 127 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE b 127 " --> pdb=" O PHE b 96 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU b 98 " --> pdb=" O LYS b 125 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS b 125 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP b 100 " --> pdb=" O SER b 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 115 through 127 current: chain 'h' and resid 36 through 48 removed outlier: 4.252A pdb=" N VAL h 61 " --> pdb=" O LYS h 40 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN h 59 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER h 44 " --> pdb=" O ASP h 57 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP h 57 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG h 46 " --> pdb=" O SER h 55 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER h 55 " --> pdb=" O ARG h 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 54 through 67 current: chain 'h' and resid 95 through 108 removed outlier: 6.788A pdb=" N SER h 123 " --> pdb=" O ASP h 99 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR h 101 " --> pdb=" O THR h 121 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR h 121 " --> pdb=" O THR h 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE h 103 " --> pdb=" O SER h 119 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER h 119 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN h 105 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS h 117 " --> pdb=" O GLN h 105 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL h 107 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU h 115 " --> pdb=" O VAL h 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 115 through 127 current: chain 'n' and resid 36 through 48 removed outlier: 5.516A pdb=" N PHE n 37 " --> pdb=" O TRP n 65 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TRP n 65 " --> pdb=" O PHE n 37 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE n 39 " --> pdb=" O ASP n 63 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASP n 63 " --> pdb=" O ILE n 39 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N MET n 41 " --> pdb=" O VAL n 61 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL n 61 " --> pdb=" O MET n 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 54 through 67 current: chain 'n' and resid 95 through 108 removed outlier: 6.843A pdb=" N SER n 123 " --> pdb=" O ASP n 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR n 101 " --> pdb=" O THR n 121 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR n 121 " --> pdb=" O THR n 101 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE n 103 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER n 119 " --> pdb=" O ILE n 103 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN n 105 " --> pdb=" O HIS n 117 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS n 117 " --> pdb=" O GLN n 105 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL n 107 " --> pdb=" O LEU n 115 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU n 115 " --> pdb=" O VAL n 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 25 current: chain 'E' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 65 current: chain 'E' and resid 105 through 122 removed outlier: 6.015A pdb=" N GLU E 132 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 117 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU E 130 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU E 119 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU E 128 " --> pdb=" O LEU E 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 128 through 135 current: chain 'K' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 24 through 25 current: chain 'K' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 56 through 65 current: chain 'K' and resid 105 through 122 removed outlier: 6.033A pdb=" N GLU K 132 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE K 117 " --> pdb=" O GLU K 130 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU K 130 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU K 119 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU K 128 " --> pdb=" O LEU K 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 128 through 135 current: chain 'W' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 24 through 25 current: chain 'W' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 56 through 65 current: chain 'W' and resid 105 through 122 removed outlier: 6.001A pdb=" N GLU W 132 " --> pdb=" O ASN W 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE W 117 " --> pdb=" O GLU W 130 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU W 130 " --> pdb=" O PHE W 117 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU W 119 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU W 128 " --> pdb=" O LEU W 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 128 through 135 current: chain 'c' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 24 through 25 current: chain 'c' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 56 through 65 current: chain 'c' and resid 105 through 122 removed outlier: 6.021A pdb=" N GLU c 132 " --> pdb=" O ASN c 115 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE c 117 " --> pdb=" O GLU c 130 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU c 130 " --> pdb=" O PHE c 117 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU c 119 " --> pdb=" O GLU c 128 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU c 128 " --> pdb=" O LEU c 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 128 through 135 current: chain 'i' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 24 through 25 current: chain 'i' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 56 through 65 current: chain 'i' and resid 105 through 122 removed outlier: 5.827A pdb=" N HIS i 114 " --> pdb=" O GLY i 134 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY i 134 " --> pdb=" O HIS i 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 128 through 135 current: chain 'o' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 24 through 25 current: chain 'o' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 56 through 65 current: chain 'o' and resid 105 through 122 removed outlier: 6.030A pdb=" N GLU o 132 " --> pdb=" O ASN o 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE o 117 " --> pdb=" O GLU o 130 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU o 130 " --> pdb=" O PHE o 117 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU o 119 " --> pdb=" O GLU o 128 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU o 128 " --> pdb=" O LEU o 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 41 through 43 removed outlier: 3.577A pdb=" N ASP E 41 " --> pdb=" O THR E 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 27 through 30 removed outlier: 5.412A pdb=" N ILE I 82 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS I 63 " --> pdb=" O PRO I 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 44 through 48 Processing sheet with id=AA9, first strand: chain 'K' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'O' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE M 6 " --> pdb=" O SER P 74 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 5 through 13 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 27 through 30 current: chain 'U' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 57 through 63 current: chain 'U' and resid 78 through 87 removed outlier: 5.390A pdb=" N ILE U 82 " --> pdb=" O GLU U 97 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU U 97 " --> pdb=" O ILE U 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 44 through 48 Processing sheet with id=AB4, first strand: chain 'W' and resid 41 through 43 removed outlier: 3.555A pdb=" N ASP W 41 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 27 through 30 removed outlier: 5.405A pdb=" N ILE a 82 " --> pdb=" O GLU a 97 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU a 97 " --> pdb=" O ILE a 82 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS a 63 " --> pdb=" O PRO a 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 44 through 48 Processing sheet with id=AB7, first strand: chain 'c' and resid 41 through 43 removed outlier: 3.512A pdb=" N ASP c 41 " --> pdb=" O THR c 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 27 through 30 removed outlier: 5.394A pdb=" N ILE g 82 " --> pdb=" O GLU g 97 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU g 97 " --> pdb=" O ILE g 82 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS g 63 " --> pdb=" O PRO g 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 44 through 48 Processing sheet with id=AC1, first strand: chain 'i' and resid 41 through 43 removed outlier: 3.525A pdb=" N ASP i 41 " --> pdb=" O THR i 52 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 27 through 30 removed outlier: 5.381A pdb=" N ILE m 82 " --> pdb=" O GLU m 97 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU m 97 " --> pdb=" O ILE m 82 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS m 63 " --> pdb=" O PRO m 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'm' and resid 44 through 48 Processing sheet with id=AC4, first strand: chain 'o' and resid 41 through 43 removed outlier: 3.562A pdb=" N ASP o 41 " --> pdb=" O THR o 52 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3192 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: 5.03 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9154 1.33 - 1.45: 5092 1.45 - 1.57: 17483 1.57 - 1.69: 62 1.69 - 1.81: 218 Bond restraints: 32009 Sorted by residual: bond pdb=" N MET N 1 " pdb=" CA MET N 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.56e+00 bond pdb=" N MET M 1 " pdb=" CA MET M 1 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N MET O 1 " pdb=" CA MET O 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.38e+00 bond pdb=" N ALA E 2 " pdb=" CA ALA E 2 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.36e+00 bond pdb=" N TYR F 159 " pdb=" CA TYR F 159 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.31e+00 ... (remaining 32004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 41691 2.17 - 4.35: 1465 4.35 - 6.52: 107 6.52 - 8.70: 0 8.70 - 10.87: 1 Bond angle restraints: 43264 Sorted by residual: angle pdb=" OP1 DA Q 1 " pdb=" P DA Q 1 " pdb=" OP2 DA Q 1 " ideal model delta sigma weight residual 120.00 109.13 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CA TYR D 8 " pdb=" CB TYR D 8 " pdb=" CG TYR D 8 " ideal model delta sigma weight residual 113.90 120.05 -6.15 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA ARG H 10 " pdb=" CB ARG H 10 " pdb=" CG ARG H 10 " ideal model delta sigma weight residual 114.10 107.59 6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA ARG T 10 " pdb=" CB ARG T 10 " pdb=" CG ARG T 10 " ideal model delta sigma weight residual 114.10 107.66 6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA ARG O 19 " pdb=" CB ARG O 19 " pdb=" CG ARG O 19 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 ... (remaining 43259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 17559 17.29 - 34.58: 1446 34.58 - 51.87: 270 51.87 - 69.15: 94 69.15 - 86.44: 53 Dihedral angle restraints: 19422 sinusoidal: 8269 harmonic: 11153 Sorted by residual: dihedral pdb=" CA ILE b 62 " pdb=" C ILE b 62 " pdb=" N ASP b 63 " pdb=" CA ASP b 63 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+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 -151.39 -28.61 0 5.00e+00 4.00e-02 3.28e+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 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 19419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4192 0.092 - 0.184: 507 0.184 - 0.276: 2 0.276 - 0.368: 0 0.368 - 0.461: 1 Chirality restraints: 4702 Sorted by residual: chirality pdb=" P DA Q 1 " pdb=" OP1 DA Q 1 " pdb=" OP2 DA Q 1 " pdb=" O5' DA Q 1 " both_signs ideal model delta sigma weight residual True 2.35 2.81 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA PHE O 31 " pdb=" N PHE O 31 " pdb=" C PHE O 31 " pdb=" CB PHE O 31 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE l 85 " pdb=" N PHE l 85 " pdb=" C PHE l 85 " pdb=" CB PHE l 85 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 4699 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP h 65 " -0.001 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP h 65 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP h 65 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP h 65 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP h 65 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP h 65 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP h 65 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP h 65 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP h 65 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP h 65 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 44 " -0.325 9.50e-02 1.11e+02 1.46e-01 1.32e+01 pdb=" NE ARG P 44 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG P 44 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG P 44 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG P 44 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 30 " -0.320 9.50e-02 1.11e+02 1.44e-01 1.26e+01 pdb=" NE ARG O 30 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG O 30 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG O 30 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG O 30 " -0.011 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1737 2.72 - 3.26: 31220 3.26 - 3.81: 48503 3.81 - 4.35: 64342 4.35 - 4.90: 109304 Nonbonded interactions: 255106 Sorted by model distance: nonbonded pdb=" OD1 ASP W 74 " pdb=" NH2 ARG c 141 " model vdw 2.175 3.120 nonbonded pdb=" OD1 ASP c 74 " pdb=" NH2 ARG i 141 " model vdw 2.198 3.120 nonbonded pdb=" OH TYR J 18 " pdb=" OD2 ASP J 84 " model vdw 2.253 3.040 nonbonded pdb=" O ASP c 127 " pdb=" OD1 ASP c 127 " model vdw 2.277 3.040 nonbonded pdb=" O ASP i 127 " pdb=" OD1 ASP i 127 " model vdw 2.292 3.040 ... (remaining 255101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'U' selection = chain 'a' selection = chain 'g' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'V' selection = chain 'b' selection = chain 'h' selection = chain 'n' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'W' selection = chain 'c' selection = chain 'i' selection = chain 'o' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'X' selection = chain 'd' selection = chain 'j' selection = chain 'p' } ncs_group { reference = (chain 'M' and resid 1 through 37) selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.990 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.007 0.055 32009 Z= 0.317 Angle : 0.893 10.872 43264 Z= 0.531 Chirality : 0.056 0.461 4702 Planarity : 0.011 0.146 5530 Dihedral : 14.351 86.443 12234 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 0.15 % Allowed : 1.95 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.13), residues: 3699 helix: -1.37 (0.13), residues: 1057 sheet: 0.14 (0.15), residues: 1212 loop : -0.25 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG o 10 TYR 0.039 0.005 TYR P 51 PHE 0.031 0.003 PHE O 31 TRP 0.056 0.007 TRP h 65 HIS 0.009 0.002 HIS b 74 Details of bonding type rmsd covalent geometry : bond 0.00701 (32009) covalent geometry : angle 0.89349 (43264) hydrogen bonds : bond 0.13781 ( 1146) hydrogen bonds : angle 7.56671 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1555 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ILE cc_start: 0.9487 (pt) cc_final: 0.9213 (mt) REVERT: B 19 ASP cc_start: 0.7873 (m-30) cc_final: 0.7611 (m-30) REVERT: B 25 ILE cc_start: 0.9091 (mt) cc_final: 0.8794 (mt) REVERT: B 29 CYS cc_start: 0.8621 (m) cc_final: 0.8171 (m) REVERT: B 68 MET cc_start: 0.8993 (mtp) cc_final: 0.8787 (mtm) REVERT: B 85 PHE cc_start: 0.8657 (m-80) cc_final: 0.8372 (m-80) REVERT: C 52 ASP cc_start: 0.8761 (m-30) cc_final: 0.8384 (m-30) REVERT: C 56 ASP cc_start: 0.8558 (t0) cc_final: 0.8049 (t0) REVERT: C 58 SER cc_start: 0.9042 (t) cc_final: 0.8667 (m) REVERT: C 86 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7171 (mtp-110) REVERT: C 98 GLU cc_start: 0.8577 (tt0) cc_final: 0.8131 (tt0) REVERT: D 119 SER cc_start: 0.9170 (t) cc_final: 0.8822 (p) REVERT: E 27 LEU cc_start: 0.8843 (mt) cc_final: 0.8641 (tp) REVERT: E 46 MET cc_start: 0.2855 (ttt) cc_final: 0.2457 (tpp) REVERT: E 56 VAL cc_start: 0.9333 (t) cc_final: 0.9073 (p) REVERT: E 93 SER cc_start: 0.8898 (t) cc_final: 0.8625 (p) REVERT: G 4 LEU cc_start: 0.8751 (tp) cc_final: 0.8172 (tp) REVERT: G 94 ASN cc_start: 0.9179 (t0) cc_final: 0.8968 (t0) REVERT: H 15 ASP cc_start: 0.7451 (p0) cc_final: 0.7100 (p0) REVERT: H 19 ASP cc_start: 0.8207 (m-30) cc_final: 0.7702 (m-30) REVERT: H 63 ILE cc_start: 0.8587 (tt) cc_final: 0.8256 (tt) REVERT: H 69 THR cc_start: 0.9196 (m) cc_final: 0.8913 (t) REVERT: H 95 TYR cc_start: 0.8241 (t80) cc_final: 0.7643 (t80) REVERT: J 15 LEU cc_start: 0.9414 (mt) cc_final: 0.9074 (mt) REVERT: J 92 ASN cc_start: 0.8428 (m110) cc_final: 0.8063 (t0) REVERT: J 109 ASP cc_start: 0.8003 (p0) cc_final: 0.7791 (p0) REVERT: K 50 TYR cc_start: 0.5205 (p90) cc_final: 0.4915 (p90) REVERT: K 90 GLU cc_start: 0.7730 (tt0) cc_final: 0.7443 (tt0) REVERT: K 91 VAL cc_start: 0.9157 (t) cc_final: 0.8954 (m) REVERT: K 126 ILE cc_start: 0.8830 (mt) cc_final: 0.8182 (mp) REVERT: O 32 LYS cc_start: 0.6974 (tttt) cc_final: 0.6749 (tttt) REVERT: P 12 GLN cc_start: 0.6472 (tt0) cc_final: 0.6034 (tp40) REVERT: P 16 MET cc_start: 0.8616 (mtp) cc_final: 0.8347 (mtp) REVERT: P 68 LEU cc_start: 0.8273 (mt) cc_final: 0.8056 (mp) REVERT: P 75 HIS cc_start: 0.7543 (m-70) cc_final: 0.7072 (m-70) REVERT: P 99 TYR cc_start: 0.7869 (t80) cc_final: 0.7382 (t80) REVERT: P 102 ILE cc_start: 0.9021 (mm) cc_final: 0.8790 (tp) REVERT: S 21 GLN cc_start: 0.7827 (mt0) cc_final: 0.7499 (mt0) REVERT: S 77 SER cc_start: 0.9104 (m) cc_final: 0.8820 (p) REVERT: S 94 ASN cc_start: 0.9471 (t0) cc_final: 0.9192 (t0) REVERT: T 19 ASP cc_start: 0.8160 (m-30) cc_final: 0.7895 (m-30) REVERT: T 23 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7730 (mt-10) REVERT: T 63 ILE cc_start: 0.8612 (tt) cc_final: 0.8377 (tp) REVERT: T 77 SER cc_start: 0.8999 (m) cc_final: 0.8599 (t) REVERT: U 8 ILE cc_start: 0.8911 (mt) cc_final: 0.8423 (tt) REVERT: U 57 VAL cc_start: 0.9269 (t) cc_final: 0.8985 (m) REVERT: V 49 TYR cc_start: 0.9056 (t80) cc_final: 0.8826 (t80) REVERT: V 79 LYS cc_start: 0.8635 (tptp) cc_final: 0.8197 (tttm) REVERT: W 46 MET cc_start: 0.0903 (ttt) cc_final: 0.0671 (tpp) REVERT: W 151 THR cc_start: 0.5541 (p) cc_final: 0.5213 (m) REVERT: Y 19 ASP cc_start: 0.8557 (m-30) cc_final: 0.8115 (m-30) REVERT: Y 20 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8024 (tp30) REVERT: Z 94 ASN cc_start: 0.8667 (t0) cc_final: 0.8346 (t0) REVERT: a 56 ASP cc_start: 0.8917 (t0) cc_final: 0.8496 (t0) REVERT: a 94 TYR cc_start: 0.8892 (m-80) cc_final: 0.8530 (m-10) REVERT: a 98 GLU cc_start: 0.8767 (tt0) cc_final: 0.8192 (tt0) REVERT: b 57 ASP cc_start: 0.8413 (t70) cc_final: 0.7932 (t0) REVERT: b 80 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7811 (ttt90) REVERT: b 94 TYR cc_start: 0.9200 (m-80) cc_final: 0.8991 (m-80) REVERT: b 125 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7961 (mtpt) REVERT: c 116 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8202 (ttmm) REVERT: c 129 TYR cc_start: 0.9224 (p90) cc_final: 0.8527 (p90) REVERT: e 19 ASP cc_start: 0.7964 (m-30) cc_final: 0.7732 (m-30) REVERT: e 20 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8510 (mm-30) REVERT: e 36 MET cc_start: 0.8777 (mtp) cc_final: 0.8478 (mtp) REVERT: e 51 MET cc_start: 0.9019 (mtt) cc_final: 0.8797 (ttm) REVERT: e 68 MET cc_start: 0.8429 (mtp) cc_final: 0.7939 (mtm) REVERT: f 23 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8313 (tp30) REVERT: g 49 GLU cc_start: 0.7843 (tt0) cc_final: 0.7179 (tt0) REVERT: h 32 ILE cc_start: 0.9241 (mm) cc_final: 0.8965 (mm) REVERT: h 40 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8658 (mtpp) REVERT: h 45 ASN cc_start: 0.8588 (m110) cc_final: 0.8264 (m-40) REVERT: h 69 ASP cc_start: 0.8246 (t0) cc_final: 0.7726 (t0) REVERT: h 99 ASP cc_start: 0.8012 (t0) cc_final: 0.7633 (t0) REVERT: h 116 LEU cc_start: 0.9236 (mt) cc_final: 0.8827 (mt) REVERT: i 74 ASP cc_start: 0.7360 (t0) cc_final: 0.7140 (t0) REVERT: i 102 SER cc_start: 0.9132 (m) cc_final: 0.8857 (p) REVERT: j 168 ASP cc_start: 0.8018 (t0) cc_final: 0.7813 (t70) REVERT: l 33 LEU cc_start: 0.9276 (tp) cc_final: 0.9020 (tp) REVERT: l 68 MET cc_start: 0.9007 (mtp) cc_final: 0.8316 (mtm) REVERT: l 69 THR cc_start: 0.9391 (m) cc_final: 0.9139 (p) REVERT: l 70 SER cc_start: 0.9488 (t) cc_final: 0.9255 (t) REVERT: l 74 ASP cc_start: 0.8697 (m-30) cc_final: 0.8485 (m-30) REVERT: l 78 ASN cc_start: 0.8401 (m-40) cc_final: 0.8023 (m-40) REVERT: m 8 ILE cc_start: 0.9172 (mt) cc_final: 0.8848 (tt) REVERT: n 41 MET cc_start: 0.8169 (tpt) cc_final: 0.7945 (tpp) REVERT: n 85 LEU cc_start: 0.9257 (mt) cc_final: 0.9026 (mt) REVERT: n 99 ASP cc_start: 0.8196 (t0) cc_final: 0.7994 (t0) REVERT: n 116 LEU cc_start: 0.9324 (mt) cc_final: 0.9029 (mm) REVERT: n 119 SER cc_start: 0.9419 (t) cc_final: 0.9025 (p) REVERT: o 39 ASP cc_start: 0.8202 (t0) cc_final: 0.7909 (p0) REVERT: o 40 THR cc_start: 0.8216 (p) cc_final: 0.7937 (t) REVERT: o 71 ASP cc_start: 0.7843 (p0) cc_final: 0.7544 (m-30) outliers start: 5 outliers final: 0 residues processed: 1557 average time/residue: 0.1923 time to fit residues: 456.8255 Evaluate side-chains 958 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 958 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN D 30 GLN D 45 ASN D 74 HIS E 136 ASN G 32 GLN J 74 HIS J 113 GLN P 14 HIS P 29 GLN V 74 HIS V 113 GLN W 124 ASN Z 21 GLN a 13 GLN a 76 ASN b 74 HIS c 51 ASN c 136 ASN h 74 HIS h 113 GLN i 136 ASN k 32 GLN l 43 GLN m 76 ASN n 74 HIS n 105 GLN n 113 GLN o 136 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.099144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.081852 restraints weight = 59867.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084496 restraints weight = 28461.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086224 restraints weight = 16841.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087366 restraints weight = 11584.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088139 restraints weight = 8898.526| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32009 Z= 0.138 Angle : 0.610 9.230 43264 Z= 0.336 Chirality : 0.043 0.155 4702 Planarity : 0.004 0.046 5530 Dihedral : 10.466 84.598 4537 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.40 % Allowed : 15.33 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3699 helix: 0.84 (0.16), residues: 1053 sheet: 0.26 (0.15), residues: 1104 loop : 0.12 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 10 TYR 0.023 0.001 TYR i 32 PHE 0.015 0.001 PHE O 17 TRP 0.022 0.002 TRP P 96 HIS 0.009 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00307 (32009) covalent geometry : angle 0.60978 (43264) hydrogen bonds : bond 0.04230 ( 1146) hydrogen bonds : angle 4.89596 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1167 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8231 (m-30) cc_final: 0.7972 (m-30) REVERT: A 24 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7581 (tp30) REVERT: B 14 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8659 (ttpt) REVERT: B 25 ILE cc_start: 0.9023 (mt) cc_final: 0.8680 (mt) REVERT: C 52 ASP cc_start: 0.8644 (m-30) cc_final: 0.8355 (m-30) REVERT: C 58 SER cc_start: 0.9027 (t) cc_final: 0.8776 (m) REVERT: C 86 ARG cc_start: 0.8064 (ttm170) cc_final: 0.7466 (mtp-110) REVERT: D 12 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: D 62 ILE cc_start: 0.9184 (pt) cc_final: 0.8612 (pt) REVERT: D 64 ILE cc_start: 0.9347 (mt) cc_final: 0.9069 (mt) REVERT: D 85 LEU cc_start: 0.9166 (mp) cc_final: 0.8958 (mp) REVERT: D 88 SER cc_start: 0.9050 (t) cc_final: 0.8731 (t) REVERT: D 97 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7205 (mm-30) REVERT: D 109 ASP cc_start: 0.7479 (p0) cc_final: 0.7258 (t0) REVERT: D 119 SER cc_start: 0.9058 (t) cc_final: 0.8669 (p) REVERT: E 116 LYS cc_start: 0.8498 (tttt) cc_final: 0.8245 (ttpt) REVERT: G 94 ASN cc_start: 0.8939 (t0) cc_final: 0.8482 (t0) REVERT: H 15 ASP cc_start: 0.7705 (p0) cc_final: 0.7363 (p0) REVERT: H 16 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7539 (tm-30) REVERT: H 19 ASP cc_start: 0.8200 (m-30) cc_final: 0.7442 (m-30) REVERT: H 95 TYR cc_start: 0.7995 (t80) cc_final: 0.7369 (t80) REVERT: J 45 ASN cc_start: 0.9127 (m-40) cc_final: 0.8510 (m-40) REVERT: K 94 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8629 (mtt-85) REVERT: L 168 ASP cc_start: 0.8641 (t0) cc_final: 0.8245 (t0) REVERT: M 5 LYS cc_start: 0.9013 (mttt) cc_final: 0.8394 (mttp) REVERT: M 11 GLU cc_start: 0.7453 (pm20) cc_final: 0.7033 (pm20) REVERT: M 16 LYS cc_start: 0.7840 (tttt) cc_final: 0.7242 (tttt) REVERT: M 17 PHE cc_start: 0.8841 (t80) cc_final: 0.8601 (t80) REVERT: M 18 LYS cc_start: 0.8819 (tptt) cc_final: 0.8250 (mmtt) REVERT: M 21 ILE cc_start: 0.9135 (mm) cc_final: 0.8922 (mm) REVERT: M 29 GLN cc_start: 0.8608 (mt0) cc_final: 0.8335 (mp10) REVERT: N 7 LYS cc_start: 0.8187 (tptp) cc_final: 0.7921 (tptt) REVERT: N 16 LYS cc_start: 0.8296 (tppt) cc_final: 0.7359 (tppt) REVERT: N 20 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8090 (mm-40) REVERT: O 20 GLN cc_start: 0.8770 (pt0) cc_final: 0.8559 (pt0) REVERT: P 38 ARG cc_start: 0.8741 (mmm-85) cc_final: 0.8157 (mmm-85) REVERT: P 44 ARG cc_start: 0.8397 (ttt90) cc_final: 0.7989 (ttt90) REVERT: P 45 GLU cc_start: 0.8184 (tt0) cc_final: 0.7678 (tt0) REVERT: P 61 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: P 81 PHE cc_start: 0.7681 (m-10) cc_final: 0.7236 (m-10) REVERT: P 99 TYR cc_start: 0.7863 (t80) cc_final: 0.7562 (t80) REVERT: S 46 GLU cc_start: 0.7352 (tp30) cc_final: 0.7068 (tp30) REVERT: S 77 SER cc_start: 0.9244 (m) cc_final: 0.8924 (p) REVERT: S 86 LYS cc_start: 0.9186 (mmtp) cc_final: 0.8928 (mmmt) REVERT: S 94 ASN cc_start: 0.9336 (t0) cc_final: 0.9081 (t0) REVERT: T 63 ILE cc_start: 0.8525 (tt) cc_final: 0.8236 (tp) REVERT: T 77 SER cc_start: 0.8993 (m) cc_final: 0.8557 (t) REVERT: T 94 ASN cc_start: 0.8815 (t0) cc_final: 0.8372 (t0) REVERT: U 8 ILE cc_start: 0.9104 (mt) cc_final: 0.8747 (tt) REVERT: V 79 LYS cc_start: 0.8842 (tptp) cc_final: 0.8288 (tttm) REVERT: W 66 MET cc_start: 0.8744 (mtp) cc_final: 0.8534 (mtm) REVERT: X 168 ASP cc_start: 0.7950 (t0) cc_final: 0.7669 (t0) REVERT: Y 41 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (m) REVERT: Z 86 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8669 (mmmm) REVERT: a 56 ASP cc_start: 0.8811 (t0) cc_final: 0.8337 (t0) REVERT: a 86 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: b 57 ASP cc_start: 0.8000 (t70) cc_final: 0.7747 (t0) REVERT: b 62 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9105 (mt) REVERT: c 129 TYR cc_start: 0.9054 (p90) cc_final: 0.8296 (p90) REVERT: e 51 MET cc_start: 0.8718 (mtt) cc_final: 0.8387 (ttm) REVERT: e 68 MET cc_start: 0.8104 (mtp) cc_final: 0.7599 (mtm) REVERT: f 43 GLN cc_start: 0.7293 (mp10) cc_final: 0.7078 (mp10) REVERT: f 50 TYR cc_start: 0.9093 (p90) cc_final: 0.8834 (p90) REVERT: g 2 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8718 (ttt180) REVERT: g 20 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8430 (tmmt) REVERT: g 25 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7319 (mm-30) REVERT: g 49 GLU cc_start: 0.7396 (tt0) cc_final: 0.6976 (tt0) REVERT: h 40 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8695 (mttp) REVERT: h 41 MET cc_start: 0.7564 (mtm) cc_final: 0.7309 (mtm) REVERT: h 69 ASP cc_start: 0.8069 (t0) cc_final: 0.7671 (t0) REVERT: h 90 LYS cc_start: 0.9130 (tppt) cc_final: 0.8889 (tppt) REVERT: h 99 ASP cc_start: 0.7960 (t0) cc_final: 0.7666 (t0) REVERT: j 168 ASP cc_start: 0.8631 (t0) cc_final: 0.8429 (t70) REVERT: k 43 GLN cc_start: 0.8311 (tp40) cc_final: 0.7860 (tp-100) REVERT: k 44 ILE cc_start: 0.9202 (mt) cc_final: 0.8694 (mt) REVERT: l 11 ILE cc_start: 0.8641 (pt) cc_final: 0.8347 (pt) REVERT: l 27 LYS cc_start: 0.8631 (tttm) cc_final: 0.8394 (ttpt) REVERT: l 78 ASN cc_start: 0.8479 (m-40) cc_final: 0.8256 (m-40) REVERT: l 86 LYS cc_start: 0.9067 (tppt) cc_final: 0.8570 (tttp) REVERT: n 13 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7223 (mt-10) REVERT: n 68 SER cc_start: 0.9030 (p) cc_final: 0.8641 (t) REVERT: n 119 SER cc_start: 0.9362 (t) cc_final: 0.9094 (p) REVERT: o 10 ARG cc_start: 0.8824 (mtt-85) cc_final: 0.8565 (mtt90) outliers start: 81 outliers final: 42 residues processed: 1204 average time/residue: 0.1706 time to fit residues: 325.7330 Evaluate side-chains 1011 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 965 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 62 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 133 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 339 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 156 optimal weight: 0.0020 chunk 141 optimal weight: 1.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN E 51 ASN I 76 ASN K 6 ASN O 20 GLN P 29 GLN W 124 ASN Z 97 ASN a 76 ASN c 6 ASN c 114 HIS e 21 GLN ** e 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 GLN g 55 ASN ** h 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 18 GLN k 43 GLN l 21 GLN m 37 ASN m 76 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.078339 restraints weight = 60773.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080825 restraints weight = 29493.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082479 restraints weight = 17700.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083585 restraints weight = 12256.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084336 restraints weight = 9467.962| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32009 Z= 0.193 Angle : 0.593 6.980 43264 Z= 0.325 Chirality : 0.043 0.168 4702 Planarity : 0.004 0.044 5530 Dihedral : 10.309 87.210 4537 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.38 % Allowed : 17.52 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.14), residues: 3699 helix: 1.26 (0.16), residues: 1059 sheet: 0.22 (0.16), residues: 1080 loop : -0.04 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 47 TYR 0.020 0.002 TYR i 50 PHE 0.020 0.002 PHE i 72 TRP 0.017 0.002 TRP P 52 HIS 0.024 0.001 HIS P 14 Details of bonding type rmsd covalent geometry : bond 0.00449 (32009) covalent geometry : angle 0.59314 (43264) hydrogen bonds : bond 0.04130 ( 1146) hydrogen bonds : angle 4.66774 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 995 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ILE cc_start: 0.9201 (mt) cc_final: 0.8785 (mp) REVERT: B 50 TYR cc_start: 0.8909 (p90) cc_final: 0.8508 (p90) REVERT: B 86 LYS cc_start: 0.9080 (tppt) cc_final: 0.8879 (tppt) REVERT: C 56 ASP cc_start: 0.7979 (t0) cc_final: 0.7773 (t0) REVERT: C 78 ILE cc_start: 0.9083 (mm) cc_final: 0.8829 (mt) REVERT: C 86 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7351 (mtp-110) REVERT: D 5 LEU cc_start: 0.9293 (tp) cc_final: 0.9007 (tt) REVERT: D 12 TYR cc_start: 0.9110 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: D 97 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7197 (mm-30) REVERT: G 63 ILE cc_start: 0.9394 (mt) cc_final: 0.9174 (mp) REVERT: G 94 ASN cc_start: 0.8928 (t0) cc_final: 0.8446 (t0) REVERT: H 19 ASP cc_start: 0.7995 (m-30) cc_final: 0.7771 (m-30) REVERT: H 86 LYS cc_start: 0.9107 (tppt) cc_final: 0.8901 (tppt) REVERT: H 95 TYR cc_start: 0.8068 (t80) cc_final: 0.7427 (t80) REVERT: J 12 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: J 24 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8357 (m) REVERT: M 18 LYS cc_start: 0.8741 (tptt) cc_final: 0.8221 (tptt) REVERT: M 21 ILE cc_start: 0.9179 (mm) cc_final: 0.8952 (mm) REVERT: M 29 GLN cc_start: 0.8816 (mt0) cc_final: 0.8331 (mp10) REVERT: N 16 LYS cc_start: 0.8298 (tppt) cc_final: 0.7878 (mmtm) REVERT: N 20 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8117 (mm-40) REVERT: O 6 ILE cc_start: 0.8373 (mp) cc_final: 0.8120 (mt) REVERT: P 17 LYS cc_start: 0.8983 (tppp) cc_final: 0.8722 (tppt) REVERT: P 35 TYR cc_start: 0.8733 (t80) cc_final: 0.8356 (t80) REVERT: P 45 GLU cc_start: 0.8273 (tt0) cc_final: 0.7852 (tt0) REVERT: P 81 PHE cc_start: 0.7742 (m-10) cc_final: 0.7226 (m-10) REVERT: P 96 TRP cc_start: 0.8117 (t-100) cc_final: 0.7862 (t-100) REVERT: P 99 TYR cc_start: 0.8032 (t80) cc_final: 0.7491 (t80) REVERT: P 102 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8542 (tp) REVERT: S 77 SER cc_start: 0.9144 (m) cc_final: 0.8934 (p) REVERT: S 94 ASN cc_start: 0.9245 (t0) cc_final: 0.9003 (t0) REVERT: T 9 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8268 (ttpp) REVERT: T 77 SER cc_start: 0.8925 (m) cc_final: 0.8376 (t) REVERT: T 86 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9024 (mmmt) REVERT: T 94 ASN cc_start: 0.8735 (t0) cc_final: 0.8293 (t0) REVERT: U 8 ILE cc_start: 0.9118 (mt) cc_final: 0.8835 (tt) REVERT: U 34 ILE cc_start: 0.8954 (mm) cc_final: 0.8537 (tt) REVERT: V 79 LYS cc_start: 0.8882 (tptp) cc_final: 0.8345 (ttpp) REVERT: X 168 ASP cc_start: 0.8109 (t0) cc_final: 0.7882 (t70) REVERT: Z 86 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8697 (mmmm) REVERT: a 56 ASP cc_start: 0.8870 (t0) cc_final: 0.8503 (t0) REVERT: b 12 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.8418 (m-10) REVERT: b 57 ASP cc_start: 0.7828 (t70) cc_final: 0.7379 (t0) REVERT: b 124 TYR cc_start: 0.9000 (m-80) cc_final: 0.8626 (m-80) REVERT: c 116 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8843 (ttpt) REVERT: c 129 TYR cc_start: 0.9114 (p90) cc_final: 0.8499 (p90) REVERT: e 68 MET cc_start: 0.7947 (mtp) cc_final: 0.7433 (mtm) REVERT: f 50 TYR cc_start: 0.9103 (p90) cc_final: 0.8786 (p90) REVERT: g 2 ARG cc_start: 0.9191 (ttm-80) cc_final: 0.8906 (ttt180) REVERT: g 25 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7236 (mm-30) REVERT: h 69 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7328 (t0) REVERT: k 43 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7752 (tp-100) REVERT: k 44 ILE cc_start: 0.9227 (mt) cc_final: 0.8631 (mt) REVERT: k 51 MET cc_start: 0.8950 (mtt) cc_final: 0.8512 (mtt) REVERT: l 78 ASN cc_start: 0.8554 (m-40) cc_final: 0.8258 (m-40) REVERT: l 86 LYS cc_start: 0.9019 (tppt) cc_final: 0.8658 (tttp) REVERT: m 91 GLU cc_start: 0.7684 (mp0) cc_final: 0.7129 (mp0) REVERT: n 13 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7377 (mt-10) REVERT: n 41 MET cc_start: 0.7966 (tpp) cc_final: 0.7573 (mmm) REVERT: o 10 ARG cc_start: 0.8848 (mtt-85) cc_final: 0.8626 (mtt90) REVERT: o 94 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7821 (ttm110) outliers start: 148 outliers final: 94 residues processed: 1060 average time/residue: 0.1730 time to fit residues: 292.1770 Evaluate side-chains 1011 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 909 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 116 LYS Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 61 VAL Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 21 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 45 ASN D 59 ASN I 90 HIS P 29 GLN S 21 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN a 76 ASN e 78 ASN h 30 GLN h 105 GLN m 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.077320 restraints weight = 60715.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079780 restraints weight = 29700.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081409 restraints weight = 17878.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082495 restraints weight = 12438.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083239 restraints weight = 9637.347| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32009 Z= 0.200 Angle : 0.580 7.510 43264 Z= 0.317 Chirality : 0.043 0.158 4702 Planarity : 0.003 0.038 5530 Dihedral : 10.296 88.523 4537 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.88 % Allowed : 19.15 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.14), residues: 3699 helix: 1.39 (0.16), residues: 1060 sheet: 0.05 (0.15), residues: 1104 loop : -0.19 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG k 10 TYR 0.019 0.002 TYR i 32 PHE 0.019 0.002 PHE i 72 TRP 0.013 0.002 TRP P 96 HIS 0.004 0.001 HIS W 36 Details of bonding type rmsd covalent geometry : bond 0.00466 (32009) covalent geometry : angle 0.57961 (43264) hydrogen bonds : bond 0.04017 ( 1146) hydrogen bonds : angle 4.63479 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 950 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9462 (mt) cc_final: 0.9187 (tt) REVERT: B 21 GLN cc_start: 0.8249 (mt0) cc_final: 0.7890 (tt0) REVERT: B 25 ILE cc_start: 0.9180 (mt) cc_final: 0.8866 (mp) REVERT: B 50 TYR cc_start: 0.8792 (p90) cc_final: 0.8430 (p90) REVERT: B 86 LYS cc_start: 0.9061 (tppt) cc_final: 0.8779 (tppt) REVERT: D 12 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: D 92 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8107 (p0) REVERT: D 97 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7238 (mm-30) REVERT: G 63 ILE cc_start: 0.9400 (mt) cc_final: 0.9175 (mp) REVERT: G 94 ASN cc_start: 0.8959 (t0) cc_final: 0.8473 (t0) REVERT: H 19 ASP cc_start: 0.7943 (m-30) cc_final: 0.7709 (m-30) REVERT: H 95 TYR cc_start: 0.8050 (t80) cc_final: 0.7444 (t80) REVERT: J 4 ASN cc_start: 0.8677 (m110) cc_final: 0.8455 (m110) REVERT: J 12 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: J 24 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8564 (m) REVERT: J 40 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8682 (mttt) REVERT: M 18 LYS cc_start: 0.8741 (tptt) cc_final: 0.8175 (tptt) REVERT: M 21 ILE cc_start: 0.9187 (mm) cc_final: 0.8983 (mm) REVERT: M 29 GLN cc_start: 0.8872 (mt0) cc_final: 0.8367 (mp10) REVERT: N 11 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: P 17 LYS cc_start: 0.9049 (tppp) cc_final: 0.8698 (tppt) REVERT: P 34 GLU cc_start: 0.8392 (tp30) cc_final: 0.8148 (tp30) REVERT: P 45 GLU cc_start: 0.8283 (tt0) cc_final: 0.7650 (tt0) REVERT: P 81 PHE cc_start: 0.7784 (m-10) cc_final: 0.7209 (m-10) REVERT: P 109 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7635 (mt-10) REVERT: S 77 SER cc_start: 0.9177 (m) cc_final: 0.8916 (p) REVERT: S 94 ASN cc_start: 0.9244 (t0) cc_final: 0.8980 (t0) REVERT: T 77 SER cc_start: 0.8893 (m) cc_final: 0.8311 (t) REVERT: T 94 ASN cc_start: 0.8703 (t0) cc_final: 0.8253 (t0) REVERT: U 8 ILE cc_start: 0.9120 (mt) cc_final: 0.8882 (tt) REVERT: U 34 ILE cc_start: 0.8849 (mm) cc_final: 0.8490 (tt) REVERT: V 79 LYS cc_start: 0.9017 (tptp) cc_final: 0.8416 (ttpp) REVERT: W 26 MET cc_start: 0.8994 (tpp) cc_final: 0.8195 (ttt) REVERT: X 168 ASP cc_start: 0.8057 (t0) cc_final: 0.7771 (t70) REVERT: Z 10 ARG cc_start: 0.7985 (ttt180) cc_final: 0.7658 (ttt180) REVERT: Z 86 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8768 (mmmm) REVERT: a 56 ASP cc_start: 0.8847 (t0) cc_final: 0.8503 (t0) REVERT: b 12 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: b 106 LEU cc_start: 0.8912 (mm) cc_final: 0.8671 (mm) REVERT: b 124 TYR cc_start: 0.8943 (m-80) cc_final: 0.8730 (m-10) REVERT: c 129 TYR cc_start: 0.9065 (p90) cc_final: 0.8509 (p90) REVERT: e 68 MET cc_start: 0.7931 (mtp) cc_final: 0.7490 (mtm) REVERT: e 78 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: f 50 TYR cc_start: 0.9110 (p90) cc_final: 0.8786 (p90) REVERT: g 25 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7452 (mm-30) REVERT: g 100 ASN cc_start: 0.7654 (m-40) cc_final: 0.7395 (m-40) REVERT: h 34 TYR cc_start: 0.7836 (m-80) cc_final: 0.7625 (m-80) REVERT: h 69 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7370 (t0) REVERT: h 90 LYS cc_start: 0.9186 (tppt) cc_final: 0.8942 (tppt) REVERT: k 51 MET cc_start: 0.9004 (mtt) cc_final: 0.8603 (mtt) REVERT: l 78 ASN cc_start: 0.8544 (m-40) cc_final: 0.8255 (m-40) REVERT: m 91 GLU cc_start: 0.7804 (mp0) cc_final: 0.7245 (mp0) REVERT: n 12 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7339 (t80) REVERT: n 13 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7281 (mt-10) REVERT: n 24 SER cc_start: 0.8676 (m) cc_final: 0.8461 (m) outliers start: 165 outliers final: 116 residues processed: 1026 average time/residue: 0.1747 time to fit residues: 285.0010 Evaluate side-chains 1018 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 893 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 59 THR Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 99 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 244 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 310 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 313 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN C 90 HIS D 45 ASN D 59 ASN P 29 GLN S 21 GLN W 111 GLN W 114 HIS W 124 ASN Z 97 ASN e 78 ASN f 21 GLN l 21 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077398 restraints weight = 60708.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079846 restraints weight = 29697.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.081472 restraints weight = 17911.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082558 restraints weight = 12457.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083186 restraints weight = 9635.961| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32009 Z= 0.181 Angle : 0.569 6.890 43264 Z= 0.311 Chirality : 0.043 0.157 4702 Planarity : 0.003 0.039 5530 Dihedral : 10.199 89.618 4537 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.18 % Allowed : 20.12 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.14), residues: 3699 helix: 1.56 (0.16), residues: 1047 sheet: 0.09 (0.16), residues: 1090 loop : -0.33 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 86 TYR 0.019 0.002 TYR i 32 PHE 0.019 0.001 PHE i 72 TRP 0.011 0.002 TRP K 89 HIS 0.003 0.001 HIS m 72 Details of bonding type rmsd covalent geometry : bond 0.00421 (32009) covalent geometry : angle 0.56911 (43264) hydrogen bonds : bond 0.03833 ( 1146) hydrogen bonds : angle 4.59801 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 948 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9400 (mt) cc_final: 0.9139 (tt) REVERT: B 25 ILE cc_start: 0.9178 (mt) cc_final: 0.8874 (mp) REVERT: B 50 TYR cc_start: 0.8751 (p90) cc_final: 0.8451 (p90) REVERT: B 86 LYS cc_start: 0.9050 (tppt) cc_final: 0.8801 (tppt) REVERT: C 86 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7811 (mtp-110) REVERT: D 97 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7230 (mm-30) REVERT: H 86 LYS cc_start: 0.9084 (tppt) cc_final: 0.8821 (tppt) REVERT: H 95 TYR cc_start: 0.8013 (t80) cc_final: 0.7365 (t80) REVERT: J 12 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: J 24 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8552 (m) REVERT: K 59 THR cc_start: 0.9414 (t) cc_final: 0.9062 (m) REVERT: M 18 LYS cc_start: 0.8741 (tptt) cc_final: 0.8093 (tptt) REVERT: M 19 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7961 (mtp85) REVERT: M 21 ILE cc_start: 0.9259 (mm) cc_final: 0.9056 (mm) REVERT: M 29 GLN cc_start: 0.8844 (mt0) cc_final: 0.8349 (mp10) REVERT: N 11 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: N 16 LYS cc_start: 0.9003 (mmtm) cc_final: 0.8640 (tppt) REVERT: N 30 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7453 (tpt90) REVERT: O 6 ILE cc_start: 0.8294 (mp) cc_final: 0.7094 (mt) REVERT: P 17 LYS cc_start: 0.9023 (tppp) cc_final: 0.8427 (tppt) REVERT: P 38 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: P 44 ARG cc_start: 0.8707 (ttt90) cc_final: 0.8499 (ttt90) REVERT: P 45 GLU cc_start: 0.8362 (tt0) cc_final: 0.7672 (tt0) REVERT: P 61 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7447 (mtm-85) REVERT: P 81 PHE cc_start: 0.7794 (m-10) cc_final: 0.7331 (m-10) REVERT: P 108 GLU cc_start: 0.7833 (pp20) cc_final: 0.7610 (pp20) REVERT: P 109 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7818 (mt-10) REVERT: S 77 SER cc_start: 0.9201 (m) cc_final: 0.8940 (p) REVERT: S 94 ASN cc_start: 0.9247 (t0) cc_final: 0.8978 (t0) REVERT: T 94 ASN cc_start: 0.8755 (t0) cc_final: 0.8284 (t0) REVERT: U 8 ILE cc_start: 0.9121 (mt) cc_final: 0.8903 (tt) REVERT: U 34 ILE cc_start: 0.8867 (mm) cc_final: 0.8524 (tt) REVERT: V 12 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7678 (t80) REVERT: V 79 LYS cc_start: 0.9004 (tptp) cc_final: 0.8420 (ttpp) REVERT: W 26 MET cc_start: 0.8977 (tpp) cc_final: 0.8334 (ttt) REVERT: X 168 ASP cc_start: 0.8132 (t0) cc_final: 0.7899 (t70) REVERT: Y 34 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8725 (tt) REVERT: Z 10 ARG cc_start: 0.8250 (ttt180) cc_final: 0.7888 (tpt-90) REVERT: Z 36 MET cc_start: 0.9014 (mtm) cc_final: 0.8751 (mtt) REVERT: Z 86 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: a 56 ASP cc_start: 0.8830 (t0) cc_final: 0.8517 (t0) REVERT: b 12 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: b 106 LEU cc_start: 0.8932 (mm) cc_final: 0.8664 (mm) REVERT: c 66 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8406 (mtp) REVERT: c 90 GLU cc_start: 0.7658 (tt0) cc_final: 0.7439 (tt0) REVERT: c 129 TYR cc_start: 0.9172 (p90) cc_final: 0.8386 (p90) REVERT: e 68 MET cc_start: 0.7899 (mtp) cc_final: 0.7445 (mtm) REVERT: f 50 TYR cc_start: 0.9067 (p90) cc_final: 0.8763 (p90) REVERT: g 25 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7403 (mm-30) REVERT: g 100 ASN cc_start: 0.7680 (m-40) cc_final: 0.7318 (m-40) REVERT: h 34 TYR cc_start: 0.7896 (m-80) cc_final: 0.7650 (m-80) REVERT: h 69 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7384 (t0) REVERT: h 90 LYS cc_start: 0.9164 (tppt) cc_final: 0.8908 (tppt) REVERT: k 51 MET cc_start: 0.8994 (mtt) cc_final: 0.8546 (mtt) REVERT: l 78 ASN cc_start: 0.8562 (m-40) cc_final: 0.8271 (m-40) REVERT: m 91 GLU cc_start: 0.7905 (mp0) cc_final: 0.7377 (mp0) REVERT: n 12 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7278 (t80) REVERT: n 13 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7264 (mt-10) REVERT: n 24 SER cc_start: 0.8704 (m) cc_final: 0.8450 (m) REVERT: n 41 MET cc_start: 0.7910 (tpp) cc_final: 0.7427 (mmm) REVERT: o 66 MET cc_start: 0.8617 (mtm) cc_final: 0.8198 (mtp) REVERT: o 94 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7969 (ttm110) outliers start: 175 outliers final: 125 residues processed: 1031 average time/residue: 0.1700 time to fit residues: 279.5153 Evaluate side-chains 1020 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 885 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 66 MET Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 61 VAL Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 21 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 21 GLN Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 281 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 313 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN D 45 ASN D 59 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN S 21 GLN W 124 ASN ** e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 78 ASN ** g 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.076536 restraints weight = 60712.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078957 restraints weight = 29784.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080569 restraints weight = 17990.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081645 restraints weight = 12531.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082374 restraints weight = 9725.508| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32009 Z= 0.210 Angle : 0.592 8.291 43264 Z= 0.323 Chirality : 0.043 0.158 4702 Planarity : 0.004 0.043 5530 Dihedral : 10.198 89.344 4537 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.30 % Allowed : 20.89 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.14), residues: 3699 helix: 1.55 (0.16), residues: 1047 sheet: -0.04 (0.16), residues: 1078 loop : -0.47 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 94 TYR 0.018 0.002 TYR D 8 PHE 0.021 0.002 PHE i 72 TRP 0.012 0.002 TRP P 52 HIS 0.004 0.001 HIS m 72 Details of bonding type rmsd covalent geometry : bond 0.00491 (32009) covalent geometry : angle 0.59202 (43264) hydrogen bonds : bond 0.03954 ( 1146) hydrogen bonds : angle 4.66055 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 920 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9438 (mt) cc_final: 0.9149 (tt) REVERT: B 25 ILE cc_start: 0.9175 (mt) cc_final: 0.8902 (mp) REVERT: B 50 TYR cc_start: 0.8739 (p90) cc_final: 0.8400 (p90) REVERT: D 97 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7278 (mm-30) REVERT: H 88 TYR cc_start: 0.8876 (m-80) cc_final: 0.8599 (m-80) REVERT: H 95 TYR cc_start: 0.7980 (t80) cc_final: 0.7364 (t80) REVERT: J 12 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: J 24 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8614 (m) REVERT: K 59 THR cc_start: 0.9413 (t) cc_final: 0.9100 (p) REVERT: M 19 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7694 (mtp85) REVERT: M 29 GLN cc_start: 0.8843 (mt0) cc_final: 0.8339 (mp10) REVERT: N 11 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: N 16 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8433 (mmmt) REVERT: N 30 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7867 (tpt90) REVERT: P 34 GLU cc_start: 0.8446 (tp30) cc_final: 0.7972 (tm-30) REVERT: P 38 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8278 (mmm-85) REVERT: P 45 GLU cc_start: 0.8344 (tt0) cc_final: 0.7676 (tt0) REVERT: P 61 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: P 81 PHE cc_start: 0.7905 (m-10) cc_final: 0.6888 (m-10) REVERT: P 108 GLU cc_start: 0.7874 (pp20) cc_final: 0.7664 (pp20) REVERT: P 109 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7750 (mt-10) REVERT: S 77 SER cc_start: 0.9181 (m) cc_final: 0.8942 (p) REVERT: T 86 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8851 (mmmt) REVERT: T 94 ASN cc_start: 0.8752 (t0) cc_final: 0.8289 (t0) REVERT: U 8 ILE cc_start: 0.9130 (mt) cc_final: 0.8907 (tt) REVERT: U 34 ILE cc_start: 0.8892 (mm) cc_final: 0.8560 (tt) REVERT: V 12 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7646 (t80) REVERT: W 26 MET cc_start: 0.9020 (tpp) cc_final: 0.8480 (ttt) REVERT: Y 10 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7487 (ttt90) REVERT: Y 34 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8753 (tt) REVERT: Z 86 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8776 (mmmm) REVERT: a 56 ASP cc_start: 0.8817 (t0) cc_final: 0.8504 (t0) REVERT: b 12 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: b 98 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7817 (tm-30) REVERT: b 106 LEU cc_start: 0.8907 (mm) cc_final: 0.8653 (mm) REVERT: c 66 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (mtp) REVERT: c 129 TYR cc_start: 0.9206 (p90) cc_final: 0.8573 (p90) REVERT: e 68 MET cc_start: 0.7915 (mtp) cc_final: 0.7465 (mtm) REVERT: e 78 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: f 43 GLN cc_start: 0.7415 (mp10) cc_final: 0.7023 (mp10) REVERT: f 50 TYR cc_start: 0.8989 (p90) cc_final: 0.8668 (p90) REVERT: g 25 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7372 (mm-30) REVERT: g 100 ASN cc_start: 0.7755 (m-40) cc_final: 0.7395 (m-40) REVERT: h 34 TYR cc_start: 0.7949 (m-80) cc_final: 0.7685 (m-80) REVERT: h 69 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7472 (t0) REVERT: h 90 LYS cc_start: 0.9165 (tppt) cc_final: 0.8894 (tppt) REVERT: k 29 CYS cc_start: 0.8606 (m) cc_final: 0.8323 (m) REVERT: k 43 GLN cc_start: 0.8030 (tp40) cc_final: 0.7500 (tp-100) REVERT: k 44 ILE cc_start: 0.9008 (mt) cc_final: 0.8761 (tt) REVERT: k 51 MET cc_start: 0.8997 (mtt) cc_final: 0.8616 (mtt) REVERT: l 78 ASN cc_start: 0.8552 (m-40) cc_final: 0.8285 (m-40) REVERT: l 86 LYS cc_start: 0.8959 (tppt) cc_final: 0.8668 (tttp) REVERT: n 12 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.7262 (t80) REVERT: n 13 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7261 (mt-10) REVERT: n 24 SER cc_start: 0.8698 (m) cc_final: 0.8394 (m) REVERT: o 94 ARG cc_start: 0.8216 (ttm110) cc_final: 0.7999 (ttm110) outliers start: 179 outliers final: 136 residues processed: 1008 average time/residue: 0.1681 time to fit residues: 269.9034 Evaluate side-chains 1028 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 880 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 66 MET Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain d residue 166 LYS Chi-restraints excluded: chain e residue 6 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 41 VAL Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 61 VAL Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 21 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 253 optimal weight: 0.0030 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN C 100 ASN D 45 ASN D 59 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN e 18 GLN e 78 ASN g 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.078757 restraints weight = 60450.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081231 restraints weight = 29400.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082884 restraints weight = 17657.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083976 restraints weight = 12240.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.084702 restraints weight = 9456.044| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32009 Z= 0.135 Angle : 0.562 9.444 43264 Z= 0.304 Chirality : 0.041 0.158 4702 Planarity : 0.003 0.041 5530 Dihedral : 10.032 88.730 4537 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.32 % Allowed : 22.94 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3699 helix: 1.67 (0.16), residues: 1045 sheet: -0.01 (0.16), residues: 1098 loop : -0.39 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 86 TYR 0.026 0.001 TYR W 129 PHE 0.015 0.001 PHE i 72 TRP 0.013 0.002 TRP P 52 HIS 0.003 0.001 HIS h 74 Details of bonding type rmsd covalent geometry : bond 0.00313 (32009) covalent geometry : angle 0.56212 (43264) hydrogen bonds : bond 0.03491 ( 1146) hydrogen bonds : angle 4.52783 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 950 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9436 (mt) cc_final: 0.9186 (tt) REVERT: B 25 ILE cc_start: 0.9149 (mt) cc_final: 0.8878 (mp) REVERT: B 50 TYR cc_start: 0.8625 (p90) cc_final: 0.8318 (p90) REVERT: D 97 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7343 (mm-30) REVERT: H 53 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8406 (ttmm) REVERT: H 88 TYR cc_start: 0.8808 (m-80) cc_final: 0.8366 (m-80) REVERT: H 95 TYR cc_start: 0.7853 (t80) cc_final: 0.7383 (t80) REVERT: J 12 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: J 24 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8514 (m) REVERT: M 18 LYS cc_start: 0.8814 (tptt) cc_final: 0.8113 (mmtt) REVERT: N 16 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8497 (mmmt) REVERT: N 30 ARG cc_start: 0.8276 (mmm160) cc_final: 0.7935 (tpt90) REVERT: P 34 GLU cc_start: 0.8365 (tp30) cc_final: 0.8030 (tp30) REVERT: P 38 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8117 (mmm-85) REVERT: P 45 GLU cc_start: 0.8405 (tt0) cc_final: 0.7660 (tt0) REVERT: P 61 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7483 (mtm-85) REVERT: P 81 PHE cc_start: 0.7860 (m-10) cc_final: 0.7199 (m-10) REVERT: P 109 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7728 (mt-10) REVERT: S 77 SER cc_start: 0.9125 (m) cc_final: 0.8886 (p) REVERT: T 86 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8926 (mmmt) REVERT: T 94 ASN cc_start: 0.8770 (t0) cc_final: 0.8271 (t0) REVERT: U 8 ILE cc_start: 0.9120 (mt) cc_final: 0.8913 (tt) REVERT: U 34 ILE cc_start: 0.8868 (mm) cc_final: 0.8551 (tt) REVERT: U 91 GLU cc_start: 0.7606 (mp0) cc_final: 0.7137 (mp0) REVERT: V 12 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7664 (t80) REVERT: W 26 MET cc_start: 0.9005 (tpp) cc_final: 0.8434 (ttt) REVERT: Y 34 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8699 (tt) REVERT: Z 86 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8761 (mmmm) REVERT: a 56 ASP cc_start: 0.8773 (t0) cc_final: 0.8429 (t0) REVERT: b 12 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: b 98 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7839 (tm-30) REVERT: c 128 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: c 129 TYR cc_start: 0.9067 (p90) cc_final: 0.8402 (p90) REVERT: e 68 MET cc_start: 0.7866 (mtp) cc_final: 0.7444 (mtm) REVERT: f 8 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8689 (mttt) REVERT: f 43 GLN cc_start: 0.7334 (mp10) cc_final: 0.7099 (mp10) REVERT: f 50 TYR cc_start: 0.9027 (p90) cc_final: 0.8623 (p90) REVERT: g 25 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7260 (mm-30) REVERT: g 49 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7226 (mt-10) REVERT: g 100 ASN cc_start: 0.7889 (m-40) cc_final: 0.7490 (m-40) REVERT: h 69 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7398 (t0) REVERT: h 90 LYS cc_start: 0.9179 (tppt) cc_final: 0.8932 (tppt) REVERT: i 32 TYR cc_start: 0.8646 (t80) cc_final: 0.8179 (t80) REVERT: k 29 CYS cc_start: 0.8580 (m) cc_final: 0.8311 (m) REVERT: k 43 GLN cc_start: 0.8119 (tp40) cc_final: 0.7514 (tp-100) REVERT: k 44 ILE cc_start: 0.8853 (mt) cc_final: 0.8583 (tt) REVERT: k 51 MET cc_start: 0.9007 (mtt) cc_final: 0.8601 (mtt) REVERT: l 78 ASN cc_start: 0.8512 (m-40) cc_final: 0.8212 (m-40) REVERT: l 86 LYS cc_start: 0.8922 (tppt) cc_final: 0.8642 (tttp) REVERT: m 47 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (mt0) REVERT: n 12 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7300 (t80) REVERT: n 13 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7175 (mt-10) REVERT: n 24 SER cc_start: 0.8685 (m) cc_final: 0.8432 (m) REVERT: n 110 THR cc_start: 0.8779 (p) cc_final: 0.8562 (p) REVERT: o 10 ARG cc_start: 0.8804 (mtt-85) cc_final: 0.8391 (mtt90) outliers start: 146 outliers final: 99 residues processed: 1019 average time/residue: 0.1668 time to fit residues: 272.0101 Evaluate side-chains 1004 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 893 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 4 TYR Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 86 LYS Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 28 LEU Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 28 SER Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 254 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 271 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 ASN N 20 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN e 18 GLN e 78 ASN k 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079131 restraints weight = 60281.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081611 restraints weight = 29350.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083257 restraints weight = 17643.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084350 restraints weight = 12236.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.085082 restraints weight = 9449.333| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32009 Z= 0.138 Angle : 0.577 13.168 43264 Z= 0.310 Chirality : 0.041 0.159 4702 Planarity : 0.003 0.062 5530 Dihedral : 9.951 88.130 4537 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.91 % Allowed : 23.65 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.14), residues: 3699 helix: 1.67 (0.16), residues: 1045 sheet: -0.05 (0.16), residues: 1104 loop : -0.36 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 94 TYR 0.022 0.001 TYR W 129 PHE 0.016 0.001 PHE i 72 TRP 0.012 0.001 TRP P 52 HIS 0.003 0.001 HIS h 74 Details of bonding type rmsd covalent geometry : bond 0.00323 (32009) covalent geometry : angle 0.57688 (43264) hydrogen bonds : bond 0.03467 ( 1146) hydrogen bonds : angle 4.53214 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 928 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9427 (mt) cc_final: 0.9199 (tt) REVERT: B 6 ASP cc_start: 0.8581 (m-30) cc_final: 0.8188 (m-30) REVERT: B 21 GLN cc_start: 0.7900 (tt0) cc_final: 0.7626 (tt0) REVERT: B 25 ILE cc_start: 0.9105 (mt) cc_final: 0.8827 (mp) REVERT: B 50 TYR cc_start: 0.8613 (p90) cc_final: 0.8303 (p90) REVERT: C 12 GLU cc_start: 0.8154 (tt0) cc_final: 0.7762 (tt0) REVERT: D 97 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7336 (mm-30) REVERT: H 95 TYR cc_start: 0.7851 (t80) cc_final: 0.7373 (t80) REVERT: I 91 GLU cc_start: 0.7922 (mp0) cc_final: 0.7688 (mp0) REVERT: J 12 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: N 16 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8475 (mmmt) REVERT: N 26 LYS cc_start: 0.8811 (mttp) cc_final: 0.8586 (mttp) REVERT: N 30 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7852 (tpt90) REVERT: P 16 MET cc_start: 0.6190 (tpt) cc_final: 0.5832 (tpt) REVERT: P 17 LYS cc_start: 0.9088 (tppp) cc_final: 0.8745 (tppt) REVERT: P 34 GLU cc_start: 0.8368 (tp30) cc_final: 0.8018 (tm-30) REVERT: P 44 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8574 (tpp80) REVERT: P 45 GLU cc_start: 0.8358 (tt0) cc_final: 0.7652 (tt0) REVERT: P 61 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: P 81 PHE cc_start: 0.7814 (m-10) cc_final: 0.7120 (m-10) REVERT: S 77 SER cc_start: 0.9054 (m) cc_final: 0.8809 (p) REVERT: T 94 ASN cc_start: 0.8781 (t0) cc_final: 0.8317 (t0) REVERT: U 34 ILE cc_start: 0.8880 (mm) cc_final: 0.8570 (tt) REVERT: U 82 ILE cc_start: 0.9280 (mt) cc_final: 0.9072 (mt) REVERT: U 91 GLU cc_start: 0.7759 (mp0) cc_final: 0.7302 (mp0) REVERT: V 12 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7651 (t80) REVERT: W 26 MET cc_start: 0.8923 (tpp) cc_final: 0.8343 (ttt) REVERT: Y 34 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8693 (tt) REVERT: a 56 ASP cc_start: 0.8697 (t0) cc_final: 0.8396 (t0) REVERT: b 12 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8483 (m-10) REVERT: b 98 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7950 (tm-30) REVERT: c 128 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7871 (pt0) REVERT: c 129 TYR cc_start: 0.9063 (p90) cc_final: 0.8288 (p90) REVERT: e 68 MET cc_start: 0.7881 (mtp) cc_final: 0.7544 (mtm) REVERT: e 86 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8414 (tppt) REVERT: f 50 TYR cc_start: 0.9034 (p90) cc_final: 0.8610 (p90) REVERT: g 25 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7267 (mm-30) REVERT: g 74 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8733 (mp) REVERT: h 69 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7378 (t0) REVERT: h 90 LYS cc_start: 0.9157 (tppt) cc_final: 0.8922 (tppt) REVERT: i 32 TYR cc_start: 0.8621 (t80) cc_final: 0.8223 (t80) REVERT: k 29 CYS cc_start: 0.8652 (m) cc_final: 0.8399 (m) REVERT: k 43 GLN cc_start: 0.7913 (tp40) cc_final: 0.7374 (tp-100) REVERT: k 44 ILE cc_start: 0.8790 (mt) cc_final: 0.8473 (tt) REVERT: k 51 MET cc_start: 0.8989 (mtt) cc_final: 0.8595 (mtt) REVERT: l 78 ASN cc_start: 0.8486 (m-40) cc_final: 0.8212 (m-40) REVERT: l 86 LYS cc_start: 0.8844 (tppt) cc_final: 0.8597 (tttp) REVERT: m 47 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: n 12 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7408 (t80) REVERT: n 13 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6981 (mt-10) REVERT: n 24 SER cc_start: 0.8664 (m) cc_final: 0.8415 (m) REVERT: n 110 THR cc_start: 0.8778 (p) cc_final: 0.8533 (p) REVERT: o 10 ARG cc_start: 0.8790 (mtt-85) cc_final: 0.8466 (mtt90) outliers start: 132 outliers final: 105 residues processed: 991 average time/residue: 0.1669 time to fit residues: 265.9822 Evaluate side-chains 994 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 880 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 82 LEU Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 28 SER Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 94 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 196 optimal weight: 0.0870 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 321 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 GLN D 6 GLN D 45 ASN I 26 ASN K 114 HIS ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN b 105 GLN e 18 GLN m 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.092872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.076034 restraints weight = 61190.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.078483 restraints weight = 29875.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.080099 restraints weight = 18003.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081192 restraints weight = 12552.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.081926 restraints weight = 9727.748| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32009 Z= 0.232 Angle : 0.644 20.581 43264 Z= 0.345 Chirality : 0.044 0.159 4702 Planarity : 0.004 0.052 5530 Dihedral : 10.142 89.816 4537 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.00 % Allowed : 24.27 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3699 helix: 1.62 (0.16), residues: 1047 sheet: -0.13 (0.16), residues: 1062 loop : -0.52 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 10 TYR 0.022 0.002 TYR l 50 PHE 0.022 0.002 PHE i 72 TRP 0.015 0.002 TRP P 52 HIS 0.004 0.001 HIS m 90 Details of bonding type rmsd covalent geometry : bond 0.00545 (32009) covalent geometry : angle 0.64372 (43264) hydrogen bonds : bond 0.04098 ( 1146) hydrogen bonds : angle 4.68931 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 886 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8512 (mtm) cc_final: 0.8305 (mtm) REVERT: A 91 ILE cc_start: 0.9461 (mt) cc_final: 0.9212 (tt) REVERT: B 6 ASP cc_start: 0.8645 (m-30) cc_final: 0.8209 (m-30) REVERT: B 25 ILE cc_start: 0.9214 (mt) cc_final: 0.8986 (mp) REVERT: B 50 TYR cc_start: 0.8632 (p90) cc_final: 0.8344 (p90) REVERT: B 93 ASP cc_start: 0.7766 (p0) cc_final: 0.7530 (p0) REVERT: C 12 GLU cc_start: 0.8165 (tt0) cc_final: 0.7781 (tt0) REVERT: D 97 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7364 (mm-30) REVERT: E 128 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: H 86 LYS cc_start: 0.9059 (tppt) cc_final: 0.8774 (tppt) REVERT: H 95 TYR cc_start: 0.7926 (t80) cc_final: 0.7453 (t80) REVERT: J 12 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: M 29 GLN cc_start: 0.8896 (mt0) cc_final: 0.8434 (mp10) REVERT: N 16 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8508 (mmmt) REVERT: N 26 LYS cc_start: 0.8583 (mttp) cc_final: 0.8381 (mttp) REVERT: N 30 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7836 (tpt90) REVERT: P 34 GLU cc_start: 0.8411 (tp30) cc_final: 0.8001 (tp30) REVERT: P 38 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7761 (mmm-85) REVERT: P 45 GLU cc_start: 0.8390 (tt0) cc_final: 0.7787 (tt0) REVERT: P 61 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: P 81 PHE cc_start: 0.7930 (m-10) cc_final: 0.7168 (m-10) REVERT: T 94 ASN cc_start: 0.8764 (t0) cc_final: 0.8248 (t0) REVERT: U 91 GLU cc_start: 0.8042 (mp0) cc_final: 0.7587 (mp0) REVERT: V 12 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7720 (t80) REVERT: W 26 MET cc_start: 0.8885 (tpp) cc_final: 0.8449 (ttt) REVERT: Y 18 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6834 (mm-40) REVERT: Y 34 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8724 (tt) REVERT: Z 36 MET cc_start: 0.8920 (mtm) cc_final: 0.8593 (mtt) REVERT: a 56 ASP cc_start: 0.8751 (t0) cc_final: 0.8525 (t0) REVERT: b 12 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: b 98 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7899 (tm-30) REVERT: c 128 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: c 129 TYR cc_start: 0.9183 (p90) cc_final: 0.8319 (p90) REVERT: e 68 MET cc_start: 0.8044 (mtp) cc_final: 0.7595 (mtm) REVERT: e 86 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8463 (tppt) REVERT: f 41 VAL cc_start: 0.8961 (t) cc_final: 0.8681 (p) REVERT: f 43 GLN cc_start: 0.7359 (mp10) cc_final: 0.7130 (mp10) REVERT: f 50 TYR cc_start: 0.9037 (p90) cc_final: 0.8625 (p90) REVERT: g 25 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7331 (mm-30) REVERT: g 74 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8516 (mp) REVERT: g 98 GLU cc_start: 0.8218 (tt0) cc_final: 0.7898 (tt0) REVERT: h 69 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7915 (t0) REVERT: i 35 SER cc_start: 0.8670 (t) cc_final: 0.8360 (p) REVERT: j 163 ASP cc_start: 0.8415 (t0) cc_final: 0.8071 (t0) REVERT: k 29 CYS cc_start: 0.8691 (m) cc_final: 0.8451 (m) REVERT: k 43 GLN cc_start: 0.8200 (tp40) cc_final: 0.7671 (tp-100) REVERT: k 44 ILE cc_start: 0.8947 (mt) cc_final: 0.8529 (tt) REVERT: k 51 MET cc_start: 0.9024 (mtt) cc_final: 0.8565 (mtt) REVERT: l 19 ASP cc_start: 0.8691 (m-30) cc_final: 0.8322 (m-30) REVERT: l 78 ASN cc_start: 0.8622 (m-40) cc_final: 0.8274 (m-40) REVERT: l 86 LYS cc_start: 0.8853 (tppt) cc_final: 0.8570 (tttp) REVERT: n 12 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7295 (t80) REVERT: n 13 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7236 (mt-10) REVERT: n 24 SER cc_start: 0.8675 (m) cc_final: 0.8399 (m) REVERT: n 92 ASN cc_start: 0.8581 (t0) cc_final: 0.8321 (t0) REVERT: n 126 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9112 (t) REVERT: o 10 ARG cc_start: 0.8873 (mtt-85) cc_final: 0.8602 (mtt90) outliers start: 135 outliers final: 108 residues processed: 950 average time/residue: 0.1697 time to fit residues: 258.3900 Evaluate side-chains 976 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 858 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 13 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 21 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 70 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 126 THR Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 86 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 GLN I 26 ASN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN W 124 ASN f 21 GLN ** h 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.077364 restraints weight = 60751.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.079849 restraints weight = 29606.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081482 restraints weight = 17822.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082581 restraints weight = 12409.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083332 restraints weight = 9614.663| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32009 Z= 0.171 Angle : 0.617 19.881 43264 Z= 0.329 Chirality : 0.042 0.166 4702 Planarity : 0.004 0.054 5530 Dihedral : 10.017 88.648 4537 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.70 % Allowed : 24.56 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.14), residues: 3699 helix: 1.63 (0.16), residues: 1049 sheet: -0.21 (0.16), residues: 1080 loop : -0.46 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 94 TYR 0.024 0.001 TYR H 50 PHE 0.018 0.001 PHE i 72 TRP 0.018 0.002 TRP P 52 HIS 0.003 0.001 HIS m 90 Details of bonding type rmsd covalent geometry : bond 0.00402 (32009) covalent geometry : angle 0.61737 (43264) hydrogen bonds : bond 0.03745 ( 1146) hydrogen bonds : angle 4.61504 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 888 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8464 (mtm) cc_final: 0.8255 (mtm) REVERT: A 91 ILE cc_start: 0.9441 (mt) cc_final: 0.9204 (tt) REVERT: B 6 ASP cc_start: 0.8617 (m-30) cc_final: 0.8254 (m-30) REVERT: B 21 GLN cc_start: 0.8635 (tt0) cc_final: 0.8423 (tt0) REVERT: B 25 ILE cc_start: 0.9137 (mt) cc_final: 0.8907 (mp) REVERT: B 50 TYR cc_start: 0.8538 (p90) cc_final: 0.8219 (p90) REVERT: C 12 GLU cc_start: 0.8190 (tt0) cc_final: 0.7772 (tt0) REVERT: D 12 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8871 (m-80) REVERT: D 97 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7333 (mm-30) REVERT: E 128 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7544 (pt0) REVERT: J 12 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: M 19 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8478 (mtp85) REVERT: N 16 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8518 (mmmt) REVERT: N 30 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7932 (tpt90) REVERT: P 17 LYS cc_start: 0.8892 (tppt) cc_final: 0.8573 (tppt) REVERT: P 34 GLU cc_start: 0.8331 (tp30) cc_final: 0.7853 (tp30) REVERT: P 38 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7654 (mmm-85) REVERT: P 45 GLU cc_start: 0.8430 (tt0) cc_final: 0.7820 (tt0) REVERT: P 61 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7426 (mtm-85) REVERT: P 81 PHE cc_start: 0.7904 (m-10) cc_final: 0.7213 (m-10) REVERT: T 94 ASN cc_start: 0.8775 (t0) cc_final: 0.8290 (t0) REVERT: U 91 GLU cc_start: 0.7985 (mp0) cc_final: 0.7523 (mp0) REVERT: V 12 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7690 (t80) REVERT: W 26 MET cc_start: 0.8830 (tpp) cc_final: 0.8359 (ttt) REVERT: Y 34 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8688 (tt) REVERT: Z 36 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8522 (mtt) REVERT: a 56 ASP cc_start: 0.8706 (t0) cc_final: 0.8419 (t0) REVERT: b 12 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: b 98 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7847 (tm-30) REVERT: c 128 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: c 129 TYR cc_start: 0.9130 (p90) cc_final: 0.8243 (p90) REVERT: e 68 MET cc_start: 0.7973 (mtp) cc_final: 0.7628 (mtm) REVERT: e 86 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8441 (tppt) REVERT: f 41 VAL cc_start: 0.8980 (t) cc_final: 0.8719 (p) REVERT: f 43 GLN cc_start: 0.7294 (mp10) cc_final: 0.7050 (mp10) REVERT: f 50 TYR cc_start: 0.8996 (p90) cc_final: 0.8589 (p90) REVERT: g 25 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7177 (mm-30) REVERT: g 74 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8464 (mp) REVERT: h 69 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7601 (t0) REVERT: h 90 LYS cc_start: 0.9175 (tppt) cc_final: 0.8948 (tppt) REVERT: i 44 ASP cc_start: 0.7841 (p0) cc_final: 0.7523 (t0) REVERT: j 163 ASP cc_start: 0.8454 (t0) cc_final: 0.8078 (t0) REVERT: k 29 CYS cc_start: 0.8681 (m) cc_final: 0.8430 (m) REVERT: k 43 GLN cc_start: 0.8208 (tp40) cc_final: 0.7634 (tp-100) REVERT: k 44 ILE cc_start: 0.8876 (mt) cc_final: 0.8476 (tt) REVERT: k 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8597 (mtt) REVERT: l 78 ASN cc_start: 0.8588 (m-40) cc_final: 0.8273 (m-40) REVERT: l 86 LYS cc_start: 0.8853 (tppt) cc_final: 0.8592 (tttp) REVERT: n 12 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7327 (t80) REVERT: n 13 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6963 (mt-10) REVERT: n 24 SER cc_start: 0.8652 (m) cc_final: 0.8386 (m) REVERT: n 92 ASN cc_start: 0.8625 (t0) cc_final: 0.8365 (t0) REVERT: n 126 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9065 (t) REVERT: o 10 ARG cc_start: 0.8899 (mtt-85) cc_final: 0.8615 (mtt90) outliers start: 125 outliers final: 107 residues processed: 945 average time/residue: 0.1680 time to fit residues: 255.3032 Evaluate side-chains 986 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 867 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 114 GLU Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain N residue 11 GLU Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain X residue 167 GLU Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 36 MET Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 17 LYS Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain g residue 14 VAL Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 74 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 61 VAL Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 21 GLN Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 126 THR Chi-restraints excluded: chain o residue 7 SER Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 283 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 358 optimal weight: 0.2980 chunk 35 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 145 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 282 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN G 43 GLN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN W 124 ASN e 18 GLN f 21 GLN ** h 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078224 restraints weight = 60691.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080721 restraints weight = 29406.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082377 restraints weight = 17600.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083464 restraints weight = 12184.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084209 restraints weight = 9444.773| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32009 Z= 0.151 Angle : 0.613 20.040 43264 Z= 0.325 Chirality : 0.042 0.160 4702 Planarity : 0.004 0.050 5530 Dihedral : 9.932 87.415 4537 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.91 % Allowed : 24.59 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.14), residues: 3699 helix: 1.64 (0.16), residues: 1049 sheet: -0.21 (0.16), residues: 1080 loop : -0.41 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 94 TYR 0.022 0.001 TYR l 50 PHE 0.017 0.001 PHE i 72 TRP 0.020 0.002 TRP P 52 HIS 0.003 0.001 HIS V 74 Details of bonding type rmsd covalent geometry : bond 0.00355 (32009) covalent geometry : angle 0.61330 (43264) hydrogen bonds : bond 0.03564 ( 1146) hydrogen bonds : angle 4.56669 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5640.34 seconds wall clock time: 98 minutes 1.29 seconds (5881.29 seconds total)