Starting phenix.real_space_refine on Sun Jul 5 22:38:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu2_48617/07_2026/9mu2_48617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu2_48617/07_2026/9mu2_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_48617/07_2026/9mu2_48617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu2_48617/07_2026/9mu2_48617.map" model { file = "/net/cci-nas-00/data/ceres_data/9mu2_48617/07_2026/9mu2_48617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu2_48617/07_2026/9mu2_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-dev-6108/lib/python3.11/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: 6.25, 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 5.20 Time building geometry restraints manager: 3.49 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=" C1' DT R 20 " pdb=" N1 DT R 20 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C3' DG R 17 " pdb=" C2' DG R 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 bond pdb=" C3' DA Q 1 " pdb=" C2' DA Q 1 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.78e+00 bond pdb=" C3' DT Q 16 " pdb=" C2' DT Q 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.40e+00 bond pdb=" C3' DT Q 2 " pdb=" O3' DT Q 2 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.09e+00 ... (remaining 32004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 41641 2.17 - 4.35: 1510 4.35 - 6.52: 112 6.52 - 8.70: 0 8.70 - 10.87: 1 Bond angle restraints: 43264 Sorted by residual: angle pdb=" O4' DA R 7 " pdb=" C1' DA R 7 " pdb=" N9 DA R 7 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" C4' DG Q 3 " pdb=" O4' DG Q 3 " pdb=" C1' DG Q 3 " ideal model delta sigma weight residual 110.10 105.69 4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" N3 DT Q 8 " pdb=" C4 DT Q 8 " pdb=" O4 DT Q 8 " ideal model delta sigma weight residual 119.90 122.23 -2.33 6.00e-01 2.78e+00 1.51e+01 angle pdb=" N3 DT R 10 " pdb=" C4 DT R 10 " pdb=" O4 DT R 10 " ideal model delta sigma weight residual 119.90 122.23 -2.33 6.00e-01 2.78e+00 1.51e+01 angle pdb=" N3 DT Q 15 " pdb=" C4 DT Q 15 " pdb=" O4 DT Q 15 " ideal model delta sigma weight residual 119.90 122.22 -2.32 6.00e-01 2.78e+00 1.49e+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 - 0.094: 4203 0.094 - 0.188: 496 0.188 - 0.283: 2 0.283 - 0.377: 0 0.377 - 0.471: 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 2.34 2.81 -0.47 2.00e-01 2.50e+01 5.54e+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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.150 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.120 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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= 0.336 Angle : 0.901 10.872 43264 Z= 0.549 Chirality : 0.057 0.471 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 are 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/Z covalent geometry : bond 0.00708 / 0.34 (32009) covalent geometry : angle 0.90059 / 0.55 (43264) hydrogen bonds : bond 0.13781 / 8.92 ( 1146) hydrogen bonds : angle 7.56671 / 5.29 ( 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 : 1.204 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: 0.8624 (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: 0.9470 (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: 0.0904 (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: 0.2254 time to fit residues: 538.2504 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 : 1.152 ------------------------------------------------------------------------------- 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... B 61 ASN D 30 GLN D 45 ASN D 74 HIS E 136 ASN G 32 GLN H 21 GLN J 74 HIS J 113 GLN O 20 GLN P 14 HIS P 29 GLN V 74 HIS V 113 GLN W 124 ASN a 13 GLN a 55 ASN a 76 ASN b 74 HIS c 136 ASN f 21 GLN h 74 HIS h 113 GLN i 136 ASN k 18 GLN k 32 GLN l 21 GLN l 43 GLN m 37 ASN m 76 ASN n 74 HIS n 105 GLN n 113 GLN o 136 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.081007 restraints weight = 59825.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083635 restraints weight = 28512.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085345 restraints weight = 16852.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086475 restraints weight = 11578.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.087251 restraints weight = 8905.049| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32009 Z= 0.162 Angle : 0.698 8.944 43264 Z= 0.387 Chirality : 0.045 0.188 4702 Planarity : 0.004 0.049 5530 Dihedral : 11.012 80.503 4537 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.60 % Allowed : 14.89 % Favored : 82.51 % 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 are not related in a simple way. whole: 0.26 (0.14), residues: 3699 helix: 0.52 (0.16), residues: 1054 sheet: 0.24 (0.15), residues: 1146 loop : 0.06 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 10 TYR 0.028 0.002 TYR i 32 PHE 0.021 0.002 PHE O 17 TRP 0.020 0.002 TRP P 96 HIS 0.011 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (32009) covalent geometry : angle 0.69835 / 0.39 (43264) hydrogen bonds : bond 0.05419 / 3.49 ( 1146) hydrogen bonds : angle 5.29577 / 3.71 ( 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 1187 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1099 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8385 (m-30) cc_final: 0.8131 (m-30) REVERT: B 25 ILE cc_start: 0.9175 (mt) cc_final: 0.8893 (mt) REVERT: B 85 PHE cc_start: 0.8598 (m-80) cc_final: 0.8266 (m-80) REVERT: C 58 SER cc_start: 0.9044 (t) cc_final: 0.8702 (m) REVERT: C 86 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7490 (mtp-110) REVERT: D 62 ILE cc_start: 0.9157 (pt) cc_final: 0.8578 (pt) REVERT: D 97 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7238 (mm-30) REVERT: D 119 SER cc_start: 0.9073 (t) cc_final: 0.8720 (p) REVERT: E 46 MET cc_start: 0.2469 (ttt) cc_final: 0.2142 (tpp) REVERT: E 84 VAL cc_start: 0.8808 (t) cc_final: 0.8591 (p) REVERT: F 168 ASP cc_start: 0.9062 (t0) cc_final: 0.8833 (t70) REVERT: G 94 ASN cc_start: 0.8998 (t0) cc_final: 0.8647 (t0) REVERT: H 19 ASP cc_start: 0.8081 (m-30) cc_final: 0.7423 (m-30) REVERT: H 77 SER cc_start: 0.9268 (t) cc_final: 0.8743 (m) REVERT: H 95 TYR cc_start: 0.7969 (t80) cc_final: 0.7439 (t80) REVERT: I 13 GLN cc_start: 0.7873 (tt0) cc_final: 0.7465 (mt0) REVERT: J 1 MET cc_start: 0.7623 (mtm) cc_final: 0.7376 (mtt) REVERT: K 50 TYR cc_start: 0.5466 (p90) cc_final: 0.5220 (p90) REVERT: M 5 LYS cc_start: 0.9064 (mttt) cc_final: 0.8617 (mttp) REVERT: M 11 GLU cc_start: 0.7508 (pm20) cc_final: 0.7253 (pm20) REVERT: M 21 ILE cc_start: 0.9161 (mm) cc_final: 0.8921 (mm) REVERT: M 26 LYS cc_start: 0.8453 (mppt) cc_final: 0.8163 (mmtm) REVERT: N 7 LYS cc_start: 0.8243 (tptp) cc_final: 0.7882 (tptt) REVERT: N 11 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6489 (tm-30) REVERT: N 16 LYS cc_start: 0.8337 (tppt) cc_final: 0.7546 (tppt) REVERT: N 18 LYS cc_start: 0.9258 (mtpp) cc_final: 0.9054 (mtpp) REVERT: N 20 GLN cc_start: 0.8695 (mm-40) cc_final: 0.7907 (mm-40) REVERT: P 17 LYS cc_start: 0.8993 (tppp) cc_final: 0.8643 (tppt) REVERT: P 45 GLU cc_start: 0.7930 (tt0) cc_final: 0.7271 (tt0) REVERT: P 81 PHE cc_start: 0.7783 (m-80) cc_final: 0.7388 (m-10) REVERT: P 87 ARG cc_start: 0.7741 (mtp85) cc_final: 0.6854 (mpt180) REVERT: S 21 GLN cc_start: 0.7627 (mt0) cc_final: 0.7414 (mt0) REVERT: S 49 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8516 (m) REVERT: S 77 SER cc_start: 0.9188 (m) cc_final: 0.8877 (p) REVERT: S 86 LYS cc_start: 0.9173 (mmtp) cc_final: 0.8881 (mmmt) REVERT: T 63 ILE cc_start: 0.8504 (tt) cc_final: 0.8239 (tp) REVERT: T 77 SER cc_start: 0.8994 (m) cc_final: 0.8531 (t) REVERT: U 8 ILE cc_start: 0.9090 (mt) cc_final: 0.8578 (tt) REVERT: V 79 LYS cc_start: 0.8780 (tptp) cc_final: 0.8300 (tttm) REVERT: W 66 MET cc_start: 0.8689 (mtp) cc_final: 0.8486 (mtp) REVERT: W 71 ASP cc_start: 0.7616 (p0) cc_final: 0.7390 (p0) REVERT: W 151 THR cc_start: 0.5499 (p) cc_final: 0.5040 (m) REVERT: X 168 ASP cc_start: 0.7906 (t0) cc_final: 0.7672 (t0) REVERT: Y 41 VAL cc_start: 0.8312 (t) cc_final: 0.8054 (m) REVERT: Z 10 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7612 (ttt180) REVERT: Z 11 ILE cc_start: 0.8106 (pt) cc_final: 0.7872 (mt) REVERT: Z 86 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8698 (mmmm) REVERT: Z 94 ASN cc_start: 0.8396 (t0) cc_final: 0.8108 (t0) REVERT: a 13 GLN cc_start: 0.6983 (tt0) cc_final: 0.6744 (mt0) REVERT: a 56 ASP cc_start: 0.8682 (t0) cc_final: 0.8320 (t0) REVERT: a 94 TYR cc_start: 0.8963 (m-80) cc_final: 0.8681 (m-10) REVERT: b 62 ILE cc_start: 0.9442 (mp) cc_final: 0.9176 (mt) REVERT: c 116 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8590 (ttpp) REVERT: c 129 TYR cc_start: 0.9131 (p90) cc_final: 0.8460 (p90) REVERT: e 51 MET cc_start: 0.8738 (mtt) cc_final: 0.8486 (ttm) REVERT: e 68 MET cc_start: 0.8116 (mtp) cc_final: 0.7709 (mtm) REVERT: f 74 ASP cc_start: 0.9154 (m-30) cc_final: 0.8874 (m-30) REVERT: g 24 LYS cc_start: 0.8988 (ptmt) cc_final: 0.8579 (ptmt) REVERT: g 49 GLU cc_start: 0.7448 (tt0) cc_final: 0.7016 (tt0) REVERT: h 34 TYR cc_start: 0.8280 (m-80) cc_final: 0.8018 (m-80) REVERT: h 40 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8621 (mtpp) REVERT: h 69 ASP cc_start: 0.7831 (t0) cc_final: 0.7507 (t0) REVERT: h 99 ASP cc_start: 0.7888 (t0) cc_final: 0.7559 (t0) REVERT: h 116 LEU cc_start: 0.9216 (mt) cc_final: 0.9001 (mt) REVERT: i 102 SER cc_start: 0.9108 (m) cc_final: 0.8746 (p) REVERT: i 126 ILE cc_start: 0.8824 (mm) cc_final: 0.8612 (mm) REVERT: k 10 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7392 (ttt180) REVERT: l 68 MET cc_start: 0.8721 (mtp) cc_final: 0.8509 (mtm) REVERT: l 86 LYS cc_start: 0.9024 (tppt) cc_final: 0.8616 (tppt) REVERT: l 89 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7767 (mt-10) REVERT: n 68 SER cc_start: 0.8950 (p) cc_final: 0.8535 (t) REVERT: n 85 LEU cc_start: 0.9205 (mt) cc_final: 0.8921 (mt) REVERT: n 99 ASP cc_start: 0.7965 (t0) cc_final: 0.7755 (t0) REVERT: n 119 SER cc_start: 0.9400 (t) cc_final: 0.9058 (p) REVERT: o 10 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8403 (mtt90) outliers start: 88 outliers final: 53 residues processed: 1139 average time/residue: 0.2062 time to fit residues: 372.5853 Evaluate side-chains 1003 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 949 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 63 ILE 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 21 GLN Chi-restraints excluded: chain H residue 49 SER 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 M residue 22 ASP Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 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 71 LEU Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 80 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 a residue 99 VAL Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 35 SER 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 87 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain m residue 37 ASN Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 133 optimal weight: 40.0000 chunk 265 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 317 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN G 61 ASN I 76 ASN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN P 14 HIS P 29 GLN V 92 ASN W 124 ASN Z 21 GLN Z 97 ASN a 55 ASN a 76 ASN c 114 HIS e 21 GLN e 83 ASN m 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078771 restraints weight = 60658.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081321 restraints weight = 29485.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082981 restraints weight = 17713.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084091 restraints weight = 12341.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.084850 restraints weight = 9565.702| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32009 Z= 0.203 Angle : 0.634 7.586 43264 Z= 0.352 Chirality : 0.045 0.204 4702 Planarity : 0.004 0.058 5530 Dihedral : 10.711 80.442 4537 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.85 % Allowed : 17.49 % Favored : 78.66 % 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 are not related in a simple way. whole: 0.28 (0.14), residues: 3699 helix: 0.92 (0.16), residues: 1059 sheet: 0.15 (0.15), residues: 1086 loop : -0.15 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 47 TYR 0.027 0.002 TYR i 32 PHE 0.024 0.002 PHE K 14 TRP 0.014 0.002 TRP P 96 HIS 0.016 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (32009) covalent geometry : angle 0.63441 / 0.35 (43264) hydrogen bonds : bond 0.04804 / 3.09 ( 1146) hydrogen bonds : angle 4.93471 / 3.44 ( 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 1109 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 979 time to evaluate : 1.319 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 21 GLN cc_start: 0.7987 (mt0) cc_final: 0.7666 (mt0) REVERT: B 25 ILE cc_start: 0.9187 (mt) cc_final: 0.8767 (mp) REVERT: C 56 ASP cc_start: 0.8015 (t0) cc_final: 0.7736 (t0) REVERT: C 58 SER cc_start: 0.9094 (t) cc_final: 0.8805 (m) REVERT: C 86 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7757 (ttm110) REVERT: D 5 LEU cc_start: 0.9177 (tp) cc_final: 0.8857 (tt) REVERT: D 12 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: D 97 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7067 (mm-30) REVERT: E 116 LYS cc_start: 0.8450 (tttt) cc_final: 0.8237 (ttpt) REVERT: F 168 ASP cc_start: 0.9047 (t0) cc_final: 0.8844 (t70) REVERT: H 77 SER cc_start: 0.9243 (t) cc_final: 0.8765 (m) REVERT: H 95 TYR cc_start: 0.7999 (t80) cc_final: 0.7446 (t80) REVERT: I 13 GLN cc_start: 0.8028 (tt0) cc_final: 0.7754 (mt0) REVERT: J 12 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: K 50 TYR cc_start: 0.5622 (p90) cc_final: 0.5378 (p90) REVERT: M 5 LYS cc_start: 0.9043 (mttt) cc_final: 0.8619 (mttp) REVERT: M 19 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8510 (mtp85) REVERT: M 21 ILE cc_start: 0.9159 (mm) cc_final: 0.8914 (mm) REVERT: N 16 LYS cc_start: 0.8304 (tppt) cc_final: 0.7661 (tppt) REVERT: N 20 GLN cc_start: 0.8590 (mm-40) cc_final: 0.7840 (mm-40) REVERT: P 17 LYS cc_start: 0.9071 (tppp) cc_final: 0.8853 (tppt) REVERT: P 45 GLU cc_start: 0.8084 (tt0) cc_final: 0.7415 (tt0) REVERT: P 81 PHE cc_start: 0.7703 (m-80) cc_final: 0.7354 (m-10) REVERT: P 87 ARG cc_start: 0.7788 (mtp85) cc_final: 0.6843 (mpt180) REVERT: S 77 SER cc_start: 0.9145 (m) cc_final: 0.8889 (p) REVERT: S 86 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8977 (mmmm) REVERT: T 9 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8197 (ttpp) REVERT: T 77 SER cc_start: 0.8984 (m) cc_final: 0.8492 (t) REVERT: T 94 ASN cc_start: 0.8716 (t0) cc_final: 0.8236 (t0) REVERT: U 8 ILE cc_start: 0.9172 (mt) cc_final: 0.8732 (tt) REVERT: U 55 ASN cc_start: 0.8997 (t0) cc_final: 0.8767 (t0) REVERT: V 79 LYS cc_start: 0.8836 (tptp) cc_final: 0.8330 (ttpp) REVERT: X 168 ASP cc_start: 0.7856 (t0) cc_final: 0.7600 (t0) REVERT: Y 41 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7922 (m) REVERT: Z 51 MET cc_start: 0.8563 (mtm) cc_final: 0.8345 (mtm) REVERT: Z 94 ASN cc_start: 0.8304 (t0) cc_final: 0.8030 (t0) REVERT: a 56 ASP cc_start: 0.8701 (t0) cc_final: 0.8312 (t0) REVERT: b 12 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.8224 (m-10) REVERT: c 26 MET cc_start: 0.8157 (tpp) cc_final: 0.7850 (tpp) REVERT: c 116 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8580 (ttpp) REVERT: c 129 TYR cc_start: 0.9108 (p90) cc_final: 0.8458 (p90) REVERT: e 51 MET cc_start: 0.8657 (mtt) cc_final: 0.8410 (ttm) REVERT: f 50 TYR cc_start: 0.9052 (p90) cc_final: 0.8758 (p90) REVERT: f 74 ASP cc_start: 0.9100 (m-30) cc_final: 0.8865 (m-30) REVERT: g 49 GLU cc_start: 0.7314 (tt0) cc_final: 0.7012 (tt0) REVERT: h 40 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8671 (mtpp) REVERT: h 69 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7525 (t0) REVERT: h 90 LYS cc_start: 0.9176 (tppt) cc_final: 0.8966 (tppt) REVERT: h 99 ASP cc_start: 0.7855 (t0) cc_final: 0.7606 (t0) REVERT: i 126 ILE cc_start: 0.8885 (mm) cc_final: 0.8621 (mm) REVERT: k 43 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7658 (tp-100) REVERT: k 44 ILE cc_start: 0.9230 (mt) cc_final: 0.8651 (mt) REVERT: k 51 MET cc_start: 0.8971 (mtt) cc_final: 0.8641 (mtt) REVERT: l 78 ASN cc_start: 0.8672 (m-40) cc_final: 0.8118 (m110) REVERT: l 86 LYS cc_start: 0.9053 (tppt) cc_final: 0.8787 (tppt) REVERT: n 69 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7586 (t0) REVERT: n 85 LEU cc_start: 0.9200 (mt) cc_final: 0.8907 (mt) REVERT: n 119 SER cc_start: 0.9383 (t) cc_final: 0.9168 (p) REVERT: o 10 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8484 (mtt90) outliers start: 130 outliers final: 85 residues processed: 1036 average time/residue: 0.2096 time to fit residues: 344.8652 Evaluate side-chains 986 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 895 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 GLU 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 24 SER Chi-restraints excluded: chain J residue 71 LEU 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 22 ASP Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain S residue 11 ILE 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 63 ILE Chi-restraints excluded: chain S residue 73 VAL 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 12 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 49 SER 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 77 SER Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 83 ASN Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU 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 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 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 55 SER 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: 7.9990 chunk 116 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 45 ASN E 51 ASN I 76 ASN P 14 HIS P 29 GLN W 114 HIS W 124 ASN Z 97 ASN a 76 ASN e 78 ASN l 21 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077629 restraints weight = 60800.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080130 restraints weight = 29690.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081767 restraints weight = 17946.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082879 restraints weight = 12552.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083635 restraints weight = 9767.767| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 32009 Z= 0.213 Angle : 0.617 7.360 43264 Z= 0.341 Chirality : 0.044 0.153 4702 Planarity : 0.004 0.037 5530 Dihedral : 10.612 80.793 4537 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.17 % Allowed : 19.44 % Favored : 76.38 % 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 are not related in a simple way. whole: 0.17 (0.14), residues: 3699 helix: 0.99 (0.16), residues: 1059 sheet: -0.02 (0.15), residues: 1080 loop : -0.27 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 33 TYR 0.031 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 m 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (32009) covalent geometry : angle 0.61652 / 0.34 (43264) hydrogen bonds : bond 0.04523 / 2.94 ( 1146) hydrogen bonds : angle 4.83208 / 3.38 ( 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 1102 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 961 time to evaluate : 1.299 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 2 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7573 (p) REVERT: B 25 ILE cc_start: 0.9118 (mt) cc_final: 0.8767 (mp) REVERT: C 56 ASP cc_start: 0.8213 (t0) cc_final: 0.7993 (t0) REVERT: C 58 SER cc_start: 0.9125 (t) cc_final: 0.8835 (m) REVERT: D 12 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: D 63 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: D 97 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7146 (mm-30) REVERT: E 116 LYS cc_start: 0.8458 (tttt) cc_final: 0.8232 (ttpt) REVERT: F 168 ASP cc_start: 0.8985 (t0) cc_final: 0.8783 (t70) REVERT: H 77 SER cc_start: 0.9236 (t) cc_final: 0.8771 (m) REVERT: H 95 TYR cc_start: 0.8039 (t80) cc_final: 0.7448 (t80) REVERT: J 1 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7445 (mtm) REVERT: J 12 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: J 24 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8503 (m) REVERT: L 168 ASP cc_start: 0.8568 (t0) cc_final: 0.8285 (t0) REVERT: M 21 ILE cc_start: 0.9199 (mm) cc_final: 0.8977 (mm) REVERT: N 16 LYS cc_start: 0.8328 (tppt) cc_final: 0.7633 (tppt) REVERT: N 20 GLN cc_start: 0.8625 (mm-40) cc_final: 0.7793 (mm-40) REVERT: N 30 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8111 (tpt90) REVERT: P 16 MET cc_start: 0.6051 (mmt) cc_final: 0.5584 (mmt) REVERT: P 34 GLU cc_start: 0.8314 (tp30) cc_final: 0.8056 (tp30) REVERT: P 38 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8297 (mmm-85) REVERT: P 45 GLU cc_start: 0.8255 (tt0) cc_final: 0.7361 (tt0) REVERT: P 81 PHE cc_start: 0.7734 (m-80) cc_final: 0.7265 (m-10) REVERT: P 103 ARG cc_start: 0.7962 (ptm160) cc_final: 0.7746 (ptm160) REVERT: S 77 SER cc_start: 0.9152 (m) cc_final: 0.8914 (p) REVERT: S 86 LYS cc_start: 0.9193 (mmtp) cc_final: 0.8956 (mmmm) REVERT: T 9 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8227 (ttpp) REVERT: T 77 SER cc_start: 0.8961 (m) cc_final: 0.8424 (t) REVERT: T 94 ASN cc_start: 0.8758 (t0) cc_final: 0.8313 (t0) REVERT: U 8 ILE cc_start: 0.9204 (mt) cc_final: 0.8804 (tt) REVERT: U 34 ILE cc_start: 0.8877 (mm) cc_final: 0.8477 (tt) REVERT: U 55 ASN cc_start: 0.9080 (t0) cc_final: 0.8872 (t0) REVERT: V 79 LYS cc_start: 0.9014 (tptp) cc_final: 0.8426 (ttpp) REVERT: X 168 ASP cc_start: 0.8027 (t0) cc_final: 0.7725 (t0) REVERT: Y 41 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7964 (m) REVERT: Z 94 ASN cc_start: 0.8321 (t0) cc_final: 0.8030 (t0) REVERT: a 56 ASP cc_start: 0.8762 (t0) cc_final: 0.8364 (t0) REVERT: b 12 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.8280 (m-10) REVERT: c 129 TYR cc_start: 0.9081 (p90) cc_final: 0.8546 (p90) REVERT: e 51 MET cc_start: 0.8628 (mtt) cc_final: 0.8325 (ttm) REVERT: f 17 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8743 (mmtt) REVERT: f 50 TYR cc_start: 0.9078 (p90) cc_final: 0.8815 (p90) REVERT: f 74 ASP cc_start: 0.9127 (m-30) cc_final: 0.8908 (m-30) REVERT: g 25 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7254 (mm-30) REVERT: g 49 GLU cc_start: 0.7283 (tt0) cc_final: 0.7068 (tt0) REVERT: h 69 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7507 (t0) REVERT: i 126 ILE cc_start: 0.8942 (mm) cc_final: 0.8647 (mm) REVERT: k 43 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7831 (tp-100) REVERT: k 44 ILE cc_start: 0.9202 (mt) cc_final: 0.8636 (mt) REVERT: k 51 MET cc_start: 0.9022 (mtt) cc_final: 0.8675 (mtt) REVERT: l 78 ASN cc_start: 0.8656 (m-40) cc_final: 0.8448 (m110) REVERT: l 86 LYS cc_start: 0.9059 (tppt) cc_final: 0.8775 (tppt) REVERT: n 13 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7387 (mt-10) REVERT: n 85 LEU cc_start: 0.9207 (mt) cc_final: 0.8849 (mt) REVERT: n 119 SER cc_start: 0.9385 (t) cc_final: 0.9181 (p) REVERT: o 66 MET cc_start: 0.8689 (mtm) cc_final: 0.8469 (mtp) REVERT: o 94 ARG cc_start: 0.8367 (ttm110) cc_final: 0.8006 (ttm110) outliers start: 141 outliers final: 90 residues processed: 1020 average time/residue: 0.1994 time to fit residues: 325.3908 Evaluate side-chains 1010 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 911 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU 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 43 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU 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 43 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 87 GLU 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 J residue 1 MET 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 71 LEU 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 10 ILE Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain P residue 40 LYS Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 102 ILE 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 41 VAL 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 61 SER Chi-restraints excluded: chain W residue 146 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 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 61 VAL Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain d residue 166 LYS Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 77 SER 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 44 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU 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 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL 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 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 244 optimal weight: 0.7980 chunk 332 optimal weight: 0.0050 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 310 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 313 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 307 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 GLN E 51 ASN I 76 ASN K 124 ASN P 29 GLN W 124 ASN Z 97 ASN a 76 ASN c 124 ASN g 37 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.080199 restraints weight = 59957.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.082821 restraints weight = 28786.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084519 restraints weight = 17113.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085645 restraints weight = 11825.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086417 restraints weight = 9141.783| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 32009 Z= 0.121 Angle : 0.565 6.689 43264 Z= 0.312 Chirality : 0.043 0.294 4702 Planarity : 0.003 0.045 5530 Dihedral : 10.458 84.972 4537 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.82 % Allowed : 20.60 % Favored : 75.58 % 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 are not related in a simple way. whole: 0.21 (0.14), residues: 3699 helix: 1.14 (0.16), residues: 1059 sheet: -0.06 (0.15), residues: 1126 loop : -0.28 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 86 TYR 0.033 0.001 TYR i 32 PHE 0.013 0.001 PHE i 72 TRP 0.028 0.002 TRP P 52 HIS 0.003 0.001 HIS m 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (32009) covalent geometry : angle 0.56500 / 0.31 (43264) hydrogen bonds : bond 0.03924 / 2.55 ( 1146) hydrogen bonds : angle 4.70163 / 3.30 ( 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 1146 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1017 time to evaluate : 1.264 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: B 21 GLN cc_start: 0.8018 (mt0) cc_final: 0.7799 (tt0) REVERT: B 25 ILE cc_start: 0.9116 (mt) cc_final: 0.8768 (mp) REVERT: C 58 SER cc_start: 0.9114 (t) cc_final: 0.8884 (m) REVERT: C 86 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7983 (mtp-110) REVERT: D 5 LEU cc_start: 0.8963 (tp) cc_final: 0.8749 (tt) REVERT: D 12 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: D 97 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7336 (mm-30) REVERT: F 168 ASP cc_start: 0.9013 (t0) cc_final: 0.8722 (t70) REVERT: G 63 ILE cc_start: 0.9397 (mt) cc_final: 0.9158 (mp) REVERT: H 44 ILE cc_start: 0.9246 (mp) cc_final: 0.8958 (mt) REVERT: H 95 TYR cc_start: 0.7995 (t80) cc_final: 0.7392 (t80) REVERT: I 98 GLU cc_start: 0.8430 (tt0) cc_final: 0.8229 (tt0) REVERT: J 1 MET cc_start: 0.7596 (mtm) cc_final: 0.7226 (mtp) REVERT: J 12 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: J 24 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8355 (m) REVERT: K 128 GLU cc_start: 0.7382 (mp0) cc_final: 0.7062 (mp0) REVERT: M 18 LYS cc_start: 0.8823 (tptt) cc_final: 0.8595 (mmtt) REVERT: M 21 ILE cc_start: 0.9155 (mm) cc_final: 0.8922 (mm) REVERT: M 28 VAL cc_start: 0.9369 (t) cc_final: 0.9159 (p) REVERT: N 16 LYS cc_start: 0.8303 (tppt) cc_final: 0.8043 (mmtp) REVERT: N 20 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8074 (mm-40) REVERT: N 30 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8114 (tpt90) REVERT: P 16 MET cc_start: 0.5861 (mmt) cc_final: 0.5642 (mmt) REVERT: P 34 GLU cc_start: 0.8314 (tp30) cc_final: 0.8111 (tp30) REVERT: P 38 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8335 (mmm-85) REVERT: P 45 GLU cc_start: 0.8119 (tt0) cc_final: 0.7861 (tt0) REVERT: P 81 PHE cc_start: 0.7673 (m-80) cc_final: 0.7233 (m-10) REVERT: P 96 TRP cc_start: 0.8144 (t-100) cc_final: 0.7812 (t-100) REVERT: S 33 LEU cc_start: 0.9281 (tp) cc_final: 0.9010 (tp) REVERT: S 77 SER cc_start: 0.9216 (m) cc_final: 0.8955 (p) REVERT: T 77 SER cc_start: 0.8978 (m) cc_final: 0.8527 (t) REVERT: T 94 ASN cc_start: 0.8770 (t0) cc_final: 0.8327 (t0) REVERT: U 8 ILE cc_start: 0.9190 (mt) cc_final: 0.8837 (tt) REVERT: U 34 ILE cc_start: 0.8945 (mm) cc_final: 0.8528 (tt) REVERT: U 49 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7515 (tm-30) REVERT: U 55 ASN cc_start: 0.9031 (t0) cc_final: 0.8817 (t0) REVERT: V 79 LYS cc_start: 0.8986 (tptp) cc_final: 0.8389 (ttpp) REVERT: X 168 ASP cc_start: 0.8011 (t0) cc_final: 0.7648 (t0) REVERT: Y 10 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7318 (tpt90) REVERT: Y 34 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8777 (tt) REVERT: Y 41 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7954 (m) REVERT: a 46 LYS cc_start: 0.8729 (tttt) cc_final: 0.8433 (tttm) REVERT: a 56 ASP cc_start: 0.8833 (t0) cc_final: 0.8482 (t0) REVERT: a 85 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8615 (t) REVERT: a 95 TYR cc_start: 0.8986 (m-80) cc_final: 0.8418 (m-10) REVERT: b 12 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: c 129 TYR cc_start: 0.9201 (p90) cc_final: 0.8542 (p90) REVERT: f 17 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8729 (mmtt) REVERT: f 50 TYR cc_start: 0.9065 (p90) cc_final: 0.8690 (p90) REVERT: g 25 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7438 (mm-30) REVERT: g 97 GLU cc_start: 0.7877 (mp0) cc_final: 0.7652 (mp0) REVERT: h 69 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7693 (t0) REVERT: i 126 ILE cc_start: 0.8942 (mm) cc_final: 0.8688 (mm) REVERT: k 43 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7894 (tp-100) REVERT: k 44 ILE cc_start: 0.9083 (mt) cc_final: 0.8543 (mt) REVERT: k 51 MET cc_start: 0.8999 (mtt) cc_final: 0.8702 (mtt) REVERT: l 78 ASN cc_start: 0.8671 (m-40) cc_final: 0.8369 (m110) REVERT: l 86 LYS cc_start: 0.9076 (tppt) cc_final: 0.8806 (tppt) REVERT: n 13 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7289 (mt-10) REVERT: n 119 SER cc_start: 0.9334 (t) cc_final: 0.9133 (p) REVERT: o 94 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8027 (ttm110) outliers start: 129 outliers final: 81 residues processed: 1069 average time/residue: 0.2048 time to fit residues: 350.3199 Evaluate side-chains 1024 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 934 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE 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 D residue 12 TYR Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 114 GLU 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 73 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 87 GLU 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 K residue 56 VAL Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 34 LEU 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 82 LEU Chi-restraints excluded: chain U residue 14 VAL 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 12 ILE Chi-restraints excluded: chain W residue 56 VAL 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 49 SER 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 43 GLN Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 124 ASN Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain f residue 31 SER Chi-restraints excluded: chain f residue 77 SER 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 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 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain o residue 34 LEU Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 99 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 281 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 299 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 21 GLN I 76 ASN K 114 HIS K 124 ASN P 19 ASN P 29 GLN W 124 ASN Z 97 ASN a 76 ASN b 105 GLN g 10 GLN g 55 ASN h 30 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.078089 restraints weight = 60617.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.080614 restraints weight = 29366.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082269 restraints weight = 17604.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083366 restraints weight = 12257.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.084079 restraints weight = 9518.331| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32009 Z= 0.197 Angle : 0.597 9.243 43264 Z= 0.327 Chirality : 0.043 0.279 4702 Planarity : 0.004 0.067 5530 Dihedral : 10.428 84.582 4537 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.85 % Allowed : 21.28 % Favored : 74.87 % 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 are not related in a simple way. whole: 0.18 (0.14), residues: 3699 helix: 1.23 (0.16), residues: 1058 sheet: -0.16 (0.15), residues: 1114 loop : -0.31 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 94 TYR 0.035 0.002 TYR i 32 PHE 0.019 0.002 PHE i 72 TRP 0.010 0.001 TRP i 89 HIS 0.004 0.001 HIS h 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (32009) covalent geometry : angle 0.59709 / 0.33 (43264) hydrogen bonds : bond 0.04003 / 2.61 ( 1146) hydrogen bonds : angle 4.72985 / 3.33 ( 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 1066 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 936 time to evaluate : 2.074 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: 0.9360 (mt) cc_final: 0.9079 (tt) REVERT: B 21 GLN cc_start: 0.8069 (mt0) cc_final: 0.7853 (tt0) REVERT: B 25 ILE cc_start: 0.9119 (mt) cc_final: 0.8844 (mp) REVERT: B 50 TYR cc_start: 0.8927 (p90) cc_final: 0.8471 (p90) REVERT: C 58 SER cc_start: 0.9170 (t) cc_final: 0.8907 (m) REVERT: C 86 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7674 (mtp-110) REVERT: D 5 LEU cc_start: 0.9142 (tp) cc_final: 0.8897 (tt) REVERT: D 12 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: D 97 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7338 (mm-30) REVERT: F 168 ASP cc_start: 0.9021 (t0) cc_final: 0.8756 (t70) REVERT: G 63 ILE cc_start: 0.9386 (mt) cc_final: 0.9154 (mp) REVERT: H 95 TYR cc_start: 0.8056 (t80) cc_final: 0.7413 (t80) REVERT: J 12 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: J 24 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8344 (m) REVERT: K 128 GLU cc_start: 0.7502 (mp0) cc_final: 0.7256 (mp0) REVERT: M 4 TYR cc_start: 0.7666 (t80) cc_final: 0.7326 (t80) REVERT: N 30 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7999 (tpt90) REVERT: P 16 MET cc_start: 0.6008 (mmt) cc_final: 0.5487 (mmt) REVERT: P 38 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8469 (mmm-85) REVERT: P 45 GLU cc_start: 0.8276 (tt0) cc_final: 0.7882 (tt0) REVERT: P 81 PHE cc_start: 0.7553 (m-80) cc_final: 0.7048 (m-10) REVERT: P 96 TRP cc_start: 0.8214 (t-100) cc_final: 0.7833 (t-100) REVERT: S 21 GLN cc_start: 0.7708 (mt0) cc_final: 0.7300 (tt0) REVERT: S 77 SER cc_start: 0.9208 (m) cc_final: 0.8984 (p) REVERT: T 9 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8343 (ttpt) REVERT: T 77 SER cc_start: 0.8903 (m) cc_final: 0.8350 (t) REVERT: T 94 ASN cc_start: 0.8791 (t0) cc_final: 0.8334 (t0) REVERT: U 8 ILE cc_start: 0.9152 (mt) cc_final: 0.8915 (tt) REVERT: U 34 ILE cc_start: 0.8868 (mm) cc_final: 0.8510 (tt) REVERT: U 55 ASN cc_start: 0.9033 (t0) cc_final: 0.8827 (t0) REVERT: V 79 LYS cc_start: 0.9014 (tptp) cc_final: 0.8412 (ttpp) REVERT: X 168 ASP cc_start: 0.8062 (t0) cc_final: 0.7802 (t70) REVERT: Y 34 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8777 (tt) REVERT: a 56 ASP cc_start: 0.8880 (t0) cc_final: 0.8496 (t0) REVERT: a 85 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8683 (t) REVERT: b 12 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8418 (m-10) REVERT: c 129 TYR cc_start: 0.9202 (p90) cc_final: 0.8460 (p90) REVERT: f 17 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8707 (mmtt) REVERT: f 50 TYR cc_start: 0.9041 (p90) cc_final: 0.8737 (p90) REVERT: g 25 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7440 (mm-30) REVERT: h 69 ASP cc_start: 0.7838 (t0) cc_final: 0.7536 (t0) REVERT: i 126 ILE cc_start: 0.8983 (mm) cc_final: 0.8722 (mm) REVERT: k 43 GLN cc_start: 0.8348 (tp-100) cc_final: 0.7776 (tp-100) REVERT: k 44 ILE cc_start: 0.9096 (mt) cc_final: 0.8484 (mt) REVERT: k 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8694 (mtt) REVERT: l 50 TYR cc_start: 0.8946 (p90) cc_final: 0.8694 (p90) REVERT: l 78 ASN cc_start: 0.8628 (m-40) cc_final: 0.8306 (m-40) REVERT: l 86 LYS cc_start: 0.9105 (tppt) cc_final: 0.8862 (tppt) REVERT: n 13 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7331 (mt-10) outliers start: 130 outliers final: 93 residues processed: 995 average time/residue: 0.2059 time to fit residues: 329.6740 Evaluate side-chains 1004 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 905 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE 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 B residue 53 LYS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU 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 73 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS 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 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 L residue 170 LEU Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 34 LEU 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 35 SER 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 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 146 LEU Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 83 ASN Chi-restraints excluded: chain f residue 26 ILE Chi-restraints excluded: chain f residue 33 LEU 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 55 SER Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU 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 43 GLN Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 67 VAL 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 70 ASP 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: 9.9990 chunk 207 optimal weight: 8.9990 chunk 274 optimal weight: 0.6980 chunk 253 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 279 optimal weight: 0.0370 chunk 270 optimal weight: 7.9990 overall best weight: 3.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 29 GLN Z 97 ASN f 21 GLN ** g 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 GLN m 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077259 restraints weight = 60764.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079718 restraints weight = 29639.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081339 restraints weight = 17811.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082424 restraints weight = 12400.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.083164 restraints weight = 9601.047| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32009 Z= 0.220 Angle : 0.622 12.379 43264 Z= 0.338 Chirality : 0.044 0.367 4702 Planarity : 0.004 0.057 5530 Dihedral : 10.443 85.834 4537 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.50 % Allowed : 21.72 % Favored : 73.78 % 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 are not related in a simple way. whole: 0.10 (0.14), residues: 3699 helix: 1.26 (0.16), residues: 1054 sheet: -0.27 (0.15), residues: 1116 loop : -0.39 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 19 TYR 0.037 0.002 TYR i 32 PHE 0.020 0.002 PHE i 72 TRP 0.010 0.001 TRP P 96 HIS 0.004 0.001 HIS h 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (32009) covalent geometry : angle 0.62226 / 0.34 (43264) hydrogen bonds : bond 0.04099 / 2.68 ( 1146) hydrogen bonds : angle 4.77982 / 3.37 ( 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 1074 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 922 time to evaluate : 1.303 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: 0.9382 (mt) cc_final: 0.9093 (tt) REVERT: B 25 ILE cc_start: 0.9137 (mt) cc_final: 0.8858 (mp) REVERT: B 50 TYR cc_start: 0.8809 (p90) cc_final: 0.8457 (p90) REVERT: C 58 SER cc_start: 0.9141 (t) cc_final: 0.8845 (m) REVERT: C 86 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7618 (mtp-110) REVERT: D 12 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: D 97 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7353 (mm-30) REVERT: F 168 ASP cc_start: 0.8993 (t0) cc_final: 0.8756 (t70) REVERT: G 63 ILE cc_start: 0.9385 (mt) cc_final: 0.9161 (mp) REVERT: H 95 TYR cc_start: 0.8058 (t80) cc_final: 0.7401 (t80) REVERT: J 12 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: K 90 GLU cc_start: 0.7745 (tt0) cc_final: 0.7265 (tt0) REVERT: K 128 GLU cc_start: 0.7576 (mp0) cc_final: 0.7262 (mp0) REVERT: M 4 TYR cc_start: 0.7673 (t80) cc_final: 0.7316 (t80) REVERT: N 16 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8040 (mmmt) REVERT: N 21 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8844 (tt) REVERT: P 16 MET cc_start: 0.5928 (mmt) cc_final: 0.5520 (mmt) REVERT: P 34 GLU cc_start: 0.8421 (tp30) cc_final: 0.7988 (tp30) REVERT: P 38 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8265 (mmm-85) REVERT: P 45 GLU cc_start: 0.8267 (tt0) cc_final: 0.7874 (tt0) REVERT: P 61 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7410 (mtm-85) REVERT: P 81 PHE cc_start: 0.7788 (m-80) cc_final: 0.7161 (m-10) REVERT: S 33 LEU cc_start: 0.9281 (tp) cc_final: 0.9054 (tp) REVERT: T 77 SER cc_start: 0.8873 (m) cc_final: 0.8321 (t) REVERT: T 94 ASN cc_start: 0.8780 (t0) cc_final: 0.8332 (t0) REVERT: U 8 ILE cc_start: 0.9156 (mt) cc_final: 0.8951 (tt) REVERT: U 34 ILE cc_start: 0.8880 (mm) cc_final: 0.8547 (tt) REVERT: U 55 ASN cc_start: 0.9013 (t0) cc_final: 0.8801 (t0) REVERT: V 79 LYS cc_start: 0.9049 (tptp) cc_final: 0.8457 (ttpp) REVERT: W 26 MET cc_start: 0.9033 (tpp) cc_final: 0.8368 (ttt) REVERT: X 164 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8493 (p) REVERT: X 168 ASP cc_start: 0.8099 (t0) cc_final: 0.7852 (t70) REVERT: Y 10 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7618 (tpt90) REVERT: Y 34 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8705 (tt) REVERT: a 56 ASP cc_start: 0.8857 (t0) cc_final: 0.8560 (t0) REVERT: a 85 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8605 (t) REVERT: b 12 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: c 129 TYR cc_start: 0.9240 (p90) cc_final: 0.8549 (p90) REVERT: f 17 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8684 (mmtt) REVERT: f 50 TYR cc_start: 0.9088 (p90) cc_final: 0.8767 (p90) REVERT: g 25 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7372 (mm-30) REVERT: h 69 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7549 (t0) REVERT: i 126 ILE cc_start: 0.8960 (mm) cc_final: 0.8740 (mm) REVERT: k 43 GLN cc_start: 0.8356 (tp-100) cc_final: 0.7785 (tp-100) REVERT: k 44 ILE cc_start: 0.9071 (mt) cc_final: 0.8468 (mt) REVERT: k 51 MET cc_start: 0.9003 (mtt) cc_final: 0.8653 (mtt) REVERT: l 50 TYR cc_start: 0.8940 (p90) cc_final: 0.8668 (p90) REVERT: l 78 ASN cc_start: 0.8644 (m-40) cc_final: 0.8289 (m-40) REVERT: l 86 LYS cc_start: 0.9093 (tppt) cc_final: 0.8885 (tppt) REVERT: n 12 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7401 (t80) REVERT: n 13 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7292 (mt-10) REVERT: o 94 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8002 (ttm110) outliers start: 152 outliers final: 115 residues processed: 988 average time/residue: 0.2077 time to fit residues: 328.8023 Evaluate side-chains 1015 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 890 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE 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 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 12 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 80 VAL 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 39 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 63 ILE 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 62 ILE Chi-restraints excluded: chain I residue 66 ILE 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 K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 34 LEU 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 35 SER Chi-restraints excluded: chain U residue 14 VAL 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 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 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 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 43 GLN 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 a residue 48 LEU Chi-restraints excluded: chain a residue 85 THR 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 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 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE 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 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 h residue 71 LEU Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU 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 43 GLN 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 61 VAL Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 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 70 ASP 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: 2.9990 chunk 34 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 329 optimal weight: 3.9990 chunk 90 optimal weight: 0.0020 chunk 216 optimal weight: 0.9990 chunk 271 optimal weight: 0.0000 chunk 122 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN I 90 HIS M 37 GLN P 29 GLN W 124 ASN c 124 ASN l 21 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079221 restraints weight = 59905.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081750 restraints weight = 29342.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083405 restraints weight = 17655.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084528 restraints weight = 12285.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085284 restraints weight = 9509.493| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32009 Z= 0.134 Angle : 0.590 9.552 43264 Z= 0.322 Chirality : 0.043 0.310 4702 Planarity : 0.004 0.053 5530 Dihedral : 10.368 89.215 4537 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.94 % Allowed : 22.34 % Favored : 73.72 % 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 are not related in a simple way. whole: 0.09 (0.14), residues: 3699 helix: 1.26 (0.16), residues: 1059 sheet: -0.24 (0.15), residues: 1134 loop : -0.43 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 94 TYR 0.034 0.001 TYR i 32 PHE 0.014 0.001 PHE c 72 TRP 0.012 0.002 TRP i 89 HIS 0.005 0.001 HIS m 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (32009) covalent geometry : angle 0.59026 / 0.32 (43264) hydrogen bonds : bond 0.03799 / 2.48 ( 1146) hydrogen bonds : angle 4.70689 / 3.32 ( 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 1105 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 972 time to evaluate : 1.334 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: A 51 MET cc_start: 0.8479 (mtt) cc_final: 0.8120 (mtt) REVERT: A 91 ILE cc_start: 0.9356 (mt) cc_final: 0.9121 (tt) REVERT: B 21 GLN cc_start: 0.8335 (tt0) cc_final: 0.8060 (tt0) REVERT: B 25 ILE cc_start: 0.9128 (mt) cc_final: 0.8798 (mp) REVERT: B 50 TYR cc_start: 0.8927 (p90) cc_final: 0.8484 (p90) REVERT: C 58 SER cc_start: 0.9153 (t) cc_final: 0.8817 (m) REVERT: C 86 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7490 (mtp-110) REVERT: C 100 ASN cc_start: 0.7591 (t0) cc_final: 0.7386 (m-40) REVERT: D 12 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: F 168 ASP cc_start: 0.8969 (t0) cc_final: 0.8756 (t70) REVERT: G 63 ILE cc_start: 0.9383 (mt) cc_final: 0.9165 (mp) REVERT: H 95 TYR cc_start: 0.7982 (t80) cc_final: 0.7331 (t80) REVERT: J 12 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: J 108 ASP cc_start: 0.8707 (t0) cc_final: 0.8503 (t0) REVERT: K 90 GLU cc_start: 0.7717 (tt0) cc_final: 0.7484 (tm-30) REVERT: K 128 GLU cc_start: 0.7516 (mp0) cc_final: 0.7287 (mp0) REVERT: M 4 TYR cc_start: 0.7583 (t80) cc_final: 0.7284 (t80) REVERT: N 16 LYS cc_start: 0.8393 (mmtp) cc_final: 0.7442 (mmmt) REVERT: N 18 LYS cc_start: 0.9451 (mtpt) cc_final: 0.8357 (mtpp) REVERT: N 20 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8142 (mm-40) REVERT: N 21 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8830 (tt) REVERT: P 16 MET cc_start: 0.6545 (mmt) cc_final: 0.6054 (mmt) REVERT: P 34 GLU cc_start: 0.8411 (tp30) cc_final: 0.8000 (tp30) REVERT: P 38 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8184 (mmm-85) REVERT: P 45 GLU cc_start: 0.8064 (tt0) cc_final: 0.7574 (tt0) REVERT: P 61 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7459 (mtm-85) REVERT: P 81 PHE cc_start: 0.7814 (m-80) cc_final: 0.7031 (m-10) REVERT: P 99 TYR cc_start: 0.8080 (t80) cc_final: 0.7377 (t80) REVERT: S 33 LEU cc_start: 0.9225 (tp) cc_final: 0.8977 (tp) REVERT: T 77 SER cc_start: 0.8924 (m) cc_final: 0.8366 (t) REVERT: T 94 ASN cc_start: 0.8717 (t0) cc_final: 0.8251 (t0) REVERT: U 34 ILE cc_start: 0.8854 (mm) cc_final: 0.8540 (tt) REVERT: V 79 LYS cc_start: 0.9029 (tptp) cc_final: 0.8452 (ttpp) REVERT: W 26 MET cc_start: 0.9043 (tpp) cc_final: 0.8326 (ttt) REVERT: X 164 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8487 (p) REVERT: X 168 ASP cc_start: 0.7985 (t0) cc_final: 0.7753 (t70) REVERT: Y 10 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7661 (tpt90) REVERT: Y 34 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8658 (tt) REVERT: a 46 LYS cc_start: 0.8776 (tttt) cc_final: 0.8496 (tttm) REVERT: a 56 ASP cc_start: 0.8825 (t0) cc_final: 0.8498 (t0) REVERT: a 85 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8590 (t) REVERT: a 95 TYR cc_start: 0.9058 (m-80) cc_final: 0.8485 (m-10) REVERT: b 12 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8596 (m-80) REVERT: c 129 TYR cc_start: 0.9176 (p90) cc_final: 0.8554 (p90) REVERT: f 17 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8638 (mmtt) REVERT: f 50 TYR cc_start: 0.9103 (p90) cc_final: 0.8709 (p90) REVERT: g 24 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8626 (ptmt) REVERT: g 25 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7210 (mm-30) REVERT: g 74 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8685 (mp) REVERT: h 69 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7356 (t0) REVERT: i 118 GLU cc_start: 0.7942 (tt0) cc_final: 0.7484 (tm-30) REVERT: k 43 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8008 (tp-100) REVERT: k 44 ILE cc_start: 0.9054 (mt) cc_final: 0.8493 (mt) REVERT: k 51 MET cc_start: 0.8961 (mtt) cc_final: 0.8624 (mtt) REVERT: l 50 TYR cc_start: 0.8958 (p90) cc_final: 0.8685 (p90) REVERT: l 78 ASN cc_start: 0.8613 (m-40) cc_final: 0.8236 (m-40) REVERT: n 12 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7300 (t80) REVERT: n 13 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7191 (mt-10) REVERT: n 24 SER cc_start: 0.8633 (m) cc_final: 0.8420 (m) REVERT: o 94 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8076 (ttm110) outliers start: 133 outliers final: 99 residues processed: 1023 average time/residue: 0.2072 time to fit residues: 339.2477 Evaluate side-chains 1021 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 911 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE 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 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 114 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 39 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 53 LYS 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 44 SER Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 79 SER Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain S residue 34 LEU 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 U residue 14 VAL Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 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 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 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 124 ASN Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 51 MET 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 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 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU 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 43 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 o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1246 > 50: distance: 112 - 192: 25.108 distance: 115 - 189: 4.153 distance: 130 - 171: 7.716 distance: 151 - 156: 7.062 distance: 156 - 157: 13.395 distance: 157 - 158: 4.073 distance: 157 - 160: 6.327 distance: 158 - 159: 5.350 distance: 158 - 168: 3.062 distance: 160 - 161: 8.474 distance: 161 - 163: 12.459 distance: 162 - 164: 7.989 distance: 163 - 165: 5.710 distance: 164 - 166: 5.962 distance: 165 - 166: 9.162 distance: 166 - 167: 5.198 distance: 168 - 169: 4.387 distance: 169 - 170: 5.997 distance: 169 - 172: 4.583 distance: 170 - 171: 3.366 distance: 170 - 177: 3.941 distance: 172 - 173: 8.033 distance: 174 - 175: 3.733 distance: 174 - 176: 5.123 distance: 177 - 178: 5.879 distance: 178 - 179: 9.115 distance: 178 - 181: 7.015 distance: 179 - 180: 16.248 distance: 181 - 182: 11.208 distance: 182 - 183: 5.908 distance: 182 - 184: 9.346 distance: 183 - 185: 4.466 distance: 185 - 187: 6.493 distance: 186 - 187: 7.795 distance: 187 - 188: 3.926 distance: 189 - 190: 20.692 distance: 190 - 191: 8.553 distance: 191 - 192: 17.623 distance: 191 - 193: 7.863 distance: 193 - 194: 9.162 distance: 194 - 195: 8.996 distance: 194 - 197: 10.817 distance: 195 - 196: 6.603 distance: 195 - 200: 21.059 distance: 197 - 198: 9.378 distance: 197 - 199: 13.137 distance: 200 - 201: 17.253 distance: 201 - 202: 10.461 distance: 201 - 204: 3.122 distance: 202 - 203: 31.698 distance: 202 - 208: 28.181 distance: 204 - 205: 5.655 distance: 205 - 206: 4.915 distance: 205 - 207: 18.862 distance: 208 - 209: 22.229 distance: 209 - 210: 16.075 distance: 210 - 211: 19.195 distance: 210 - 212: 15.161 distance: 212 - 213: 10.283 distance: 213 - 214: 10.203 distance: 213 - 216: 16.241 distance: 214 - 215: 9.407 distance: 214 - 223: 8.041 distance: 216 - 217: 15.431 distance: 217 - 218: 4.953 distance: 218 - 219: 8.590 distance: 219 - 220: 8.553 distance: 220 - 221: 4.396 distance: 220 - 222: 6.540 distance: 223 - 224: 7.263 distance: 224 - 225: 4.329 distance: 224 - 227: 12.054 distance: 225 - 226: 9.509 distance: 225 - 234: 11.653 distance: 227 - 228: 3.317 distance: 228 - 229: 6.642 distance: 228 - 230: 5.100 distance: 229 - 231: 5.235 distance: 230 - 232: 4.031 distance: 231 - 233: 4.178 distance: 232 - 233: 4.904 distance: 234 - 235: 7.561 distance: 236 - 237: 13.351 distance: 236 - 243: 8.704 distance: 238 - 239: 4.510 distance: 240 - 241: 8.445 distance: 240 - 242: 11.855