Starting phenix.real_space_refine on Wed Aug 27 02:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw9_48698/08_2025/9mw9_48698.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw9_48698/08_2025/9mw9_48698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw9_48698/08_2025/9mw9_48698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw9_48698/08_2025/9mw9_48698.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw9_48698/08_2025/9mw9_48698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw9_48698/08_2025/9mw9_48698.cif" } resolution = 3.0 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= 0.005 sd= 0.033 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 44 5.49 5 S 110 5.16 5 C 29392 2.51 5 N 7700 2.21 5 O 8206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45452 Number of models: 1 Model: "" Number of chains: 33 Chain: "e" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "f" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "g" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "h" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "i" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "j" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "k" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "c" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "d" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "a" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "b" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "G" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "H" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "E" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "F" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "A" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "B" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "C" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "I" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "J" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "K" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "L" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "M" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "N" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "O" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "P" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "Q" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "R" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "U" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "V" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "S" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "T" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Time building chain proxies: 10.89, per 1000 atoms: 0.24 Number of scatterers: 45452 At special positions: 0 Unit cell: (200.75, 195.64, 203.67, 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 110 16.00 P 44 15.00 O 8206 8.00 N 7700 7.00 C 29392 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: 2.93 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10516 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 56 sheets defined 40.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'G' and resid 12 through 26 removed outlier: 4.392A pdb=" N GLU G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 48 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 68 through 83 removed outlier: 3.912A pdb=" N ASP G 73 " --> pdb=" O ASP G 69 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU G 74 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU G 75 " --> pdb=" O CYS G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 120 Processing helix chain 'G' and resid 129 through 143 Processing helix chain 'G' and resid 177 through 182 removed outlier: 4.049A pdb=" N HIS G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 removed outlier: 3.956A pdb=" N ASP G 188 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 190 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 222 Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 26 removed outlier: 4.174A pdb=" N LEU H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 removed outlier: 4.201A pdb=" N ILE H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 67 Processing helix chain 'H' and resid 68 through 83 removed outlier: 3.676A pdb=" N GLU H 74 " --> pdb=" O TRP H 70 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 75 " --> pdb=" O CYS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 100 removed outlier: 4.040A pdb=" N LEU H 100 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 119 Processing helix chain 'H' and resid 129 through 144 removed outlier: 4.520A pdb=" N ASN H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 182 removed outlier: 3.507A pdb=" N TRP H 182 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 removed outlier: 3.554A pdb=" N ASP H 188 " --> pdb=" O LYS H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 222 Processing helix chain 'H' and resid 223 through 225 No H-bonds generated for 'chain 'H' and resid 223 through 225' Processing helix chain 'E' and resid 9 through 11 No H-bonds generated for 'chain 'E' and resid 9 through 11' Processing helix chain 'E' and resid 12 through 26 removed outlier: 4.016A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 removed outlier: 4.091A pdb=" N ILE E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 67 Processing helix chain 'E' and resid 68 through 83 removed outlier: 3.570A pdb=" N GLU E 74 " --> pdb=" O TRP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'E' and resid 106 through 119 removed outlier: 3.504A pdb=" N ARG E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 144 removed outlier: 4.560A pdb=" N ASN E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.030A pdb=" N HIS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.896A pdb=" N ASP E 188 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 222 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 26 removed outlier: 3.983A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 removed outlier: 4.261A pdb=" N ILE F 48 " --> pdb=" O ILE F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 67 Processing helix chain 'F' and resid 68 through 83 Processing helix chain 'F' and resid 96 through 100 Processing helix chain 'F' and resid 106 through 120 Processing helix chain 'F' and resid 129 through 143 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 213 through 222 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 26 removed outlier: 4.111A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.092A pdb=" N ILE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 84 removed outlier: 3.974A pdb=" N LYS A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.558A pdb=" N ARG A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 144 removed outlier: 4.639A pdb=" N ASN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.177A pdb=" N HIS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.791A pdb=" N ILE A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 26 removed outlier: 4.154A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 129 through 144 removed outlier: 4.586A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.578A pdb=" N TRP B 182 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 12 through 26 removed outlier: 3.545A pdb=" N VAL C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 removed outlier: 4.127A pdb=" N ILE C 48 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 83 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 106 through 120 Processing helix chain 'C' and resid 129 through 144 removed outlier: 4.653A pdb=" N ASN C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.945A pdb=" N HIS C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.676A pdb=" N ILE C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'D' and resid 12 through 26 removed outlier: 3.990A pdb=" N GLU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 68 through 83 removed outlier: 3.513A pdb=" N ASP D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 74 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 Processing helix chain 'D' and resid 129 through 143 Processing helix chain 'D' and resid 169 through 173 removed outlier: 4.311A pdb=" N ASN D 173 " --> pdb=" O PRO D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 removed outlier: 4.163A pdb=" N HIS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'I' and resid 9 through 11 No H-bonds generated for 'chain 'I' and resid 9 through 11' Processing helix chain 'I' and resid 12 through 26 removed outlier: 4.035A pdb=" N GLU I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 48 removed outlier: 4.267A pdb=" N ILE I 48 " --> pdb=" O ILE I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 67 Processing helix chain 'I' and resid 68 through 84 removed outlier: 3.587A pdb=" N GLU I 74 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 100 Processing helix chain 'I' and resid 106 through 120 removed outlier: 3.511A pdb=" N LEU I 120 " --> pdb=" O ILE I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 143 Processing helix chain 'I' and resid 177 through 182 removed outlier: 4.153A pdb=" N HIS I 181 " --> pdb=" O ASP I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 190 removed outlier: 4.148A pdb=" N ASP I 188 " --> pdb=" O LYS I 185 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE I 190 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 222 Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'J' and resid 9 through 11 No H-bonds generated for 'chain 'J' and resid 9 through 11' Processing helix chain 'J' and resid 12 through 26 removed outlier: 4.081A pdb=" N GLU J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 48 removed outlier: 4.200A pdb=" N ILE J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 106 through 120 Processing helix chain 'J' and resid 129 through 144 removed outlier: 4.756A pdb=" N ASN J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 removed outlier: 3.570A pdb=" N TRP J 182 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 190 removed outlier: 3.508A pdb=" N ASP J 188 " --> pdb=" O LYS J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 222 Processing helix chain 'J' and resid 223 through 225 No H-bonds generated for 'chain 'J' and resid 223 through 225' Processing helix chain 'K' and resid 9 through 11 No H-bonds generated for 'chain 'K' and resid 9 through 11' Processing helix chain 'K' and resid 12 through 26 removed outlier: 3.508A pdb=" N VAL K 16 " --> pdb=" O ASP K 12 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL K 19 " --> pdb=" O ILE K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 48 removed outlier: 4.085A pdb=" N ILE K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 68 through 83 removed outlier: 3.606A pdb=" N GLU K 74 " --> pdb=" O TRP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'K' and resid 129 through 144 removed outlier: 4.561A pdb=" N ASN K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 182 removed outlier: 3.976A pdb=" N HIS K 181 " --> pdb=" O ASP K 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 190 removed outlier: 3.778A pdb=" N ILE K 190 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 222 Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'L' and resid 9 through 11 No H-bonds generated for 'chain 'L' and resid 9 through 11' Processing helix chain 'L' and resid 12 through 26 removed outlier: 3.505A pdb=" N LEU L 17 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 67 Processing helix chain 'L' and resid 68 through 83 removed outlier: 3.564A pdb=" N GLU L 74 " --> pdb=" O TRP L 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 75 " --> pdb=" O CYS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 100 removed outlier: 3.532A pdb=" N LEU L 100 " --> pdb=" O ARG L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 120 Processing helix chain 'L' and resid 129 through 144 removed outlier: 4.736A pdb=" N ASN L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 182 removed outlier: 4.126A pdb=" N HIS L 181 " --> pdb=" O ASP L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 removed outlier: 3.646A pdb=" N ILE L 190 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 222 Processing helix chain 'L' and resid 223 through 225 No H-bonds generated for 'chain 'L' and resid 223 through 225' Processing helix chain 'M' and resid 9 through 11 No H-bonds generated for 'chain 'M' and resid 9 through 11' Processing helix chain 'M' and resid 12 through 26 removed outlier: 3.829A pdb=" N LEU M 17 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL M 19 " --> pdb=" O ILE M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 68 through 83 removed outlier: 3.782A pdb=" N GLU M 74 " --> pdb=" O TRP M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 100 Processing helix chain 'M' and resid 106 through 120 removed outlier: 3.541A pdb=" N LEU M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 143 Processing helix chain 'M' and resid 177 through 182 removed outlier: 4.085A pdb=" N HIS M 181 " --> pdb=" O ASP M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 190 removed outlier: 3.736A pdb=" N ASP M 188 " --> pdb=" O LYS M 185 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE M 190 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 222 Processing helix chain 'M' and resid 223 through 225 No H-bonds generated for 'chain 'M' and resid 223 through 225' Processing helix chain 'N' and resid 9 through 11 No H-bonds generated for 'chain 'N' and resid 9 through 11' Processing helix chain 'N' and resid 12 through 26 removed outlier: 3.592A pdb=" N LEU N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL N 19 " --> pdb=" O ILE N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 48 Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 84 removed outlier: 4.107A pdb=" N LYS N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 120 Processing helix chain 'N' and resid 129 through 144 removed outlier: 3.519A pdb=" N GLY N 135 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN N 144 " --> pdb=" O ALA N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 181 Processing helix chain 'N' and resid 185 through 190 removed outlier: 3.592A pdb=" N ASP N 188 " --> pdb=" O LYS N 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE N 190 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 222 Processing helix chain 'N' and resid 223 through 225 No H-bonds generated for 'chain 'N' and resid 223 through 225' Processing helix chain 'O' and resid 9 through 11 No H-bonds generated for 'chain 'O' and resid 9 through 11' Processing helix chain 'O' and resid 12 through 26 removed outlier: 4.037A pdb=" N GLU O 18 " --> pdb=" O LYS O 14 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 48 removed outlier: 4.043A pdb=" N ILE O 48 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 67 Processing helix chain 'O' and resid 68 through 81 removed outlier: 3.801A pdb=" N GLN O 77 " --> pdb=" O ASP O 73 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA O 78 " --> pdb=" O GLU O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 120 Processing helix chain 'O' and resid 129 through 144 removed outlier: 4.728A pdb=" N ASN O 144 " --> pdb=" O ALA O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 182 removed outlier: 3.965A pdb=" N HIS O 181 " --> pdb=" O ASP O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 190 removed outlier: 3.856A pdb=" N ILE O 190 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 222 Processing helix chain 'O' and resid 223 through 225 No H-bonds generated for 'chain 'O' and resid 223 through 225' Processing helix chain 'P' and resid 9 through 11 No H-bonds generated for 'chain 'P' and resid 9 through 11' Processing helix chain 'P' and resid 12 through 26 removed outlier: 4.428A pdb=" N GLU P 18 " --> pdb=" O LYS P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 removed outlier: 4.416A pdb=" N ILE P 48 " --> pdb=" O ILE P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 67 Processing helix chain 'P' and resid 68 through 83 Processing helix chain 'P' and resid 96 through 100 Processing helix chain 'P' and resid 106 through 120 Processing helix chain 'P' and resid 129 through 144 removed outlier: 4.632A pdb=" N ASN P 144 " --> pdb=" O ALA P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 181 Processing helix chain 'P' and resid 185 through 190 removed outlier: 3.504A pdb=" N ASP P 188 " --> pdb=" O LYS P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 222 Processing helix chain 'P' and resid 223 through 225 No H-bonds generated for 'chain 'P' and resid 223 through 225' Processing helix chain 'Q' and resid 9 through 11 No H-bonds generated for 'chain 'Q' and resid 9 through 11' Processing helix chain 'Q' and resid 12 through 26 removed outlier: 3.584A pdb=" N GLU Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 48 removed outlier: 4.019A pdb=" N ILE Q 48 " --> pdb=" O ILE Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 67 Processing helix chain 'Q' and resid 68 through 81 Processing helix chain 'Q' and resid 96 through 100 Processing helix chain 'Q' and resid 106 through 119 Processing helix chain 'Q' and resid 129 through 143 Processing helix chain 'Q' and resid 177 through 182 removed outlier: 4.286A pdb=" N HIS Q 181 " --> pdb=" O ASP Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 190 removed outlier: 4.126A pdb=" N ASP Q 188 " --> pdb=" O LYS Q 185 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE Q 190 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 222 Processing helix chain 'Q' and resid 223 through 225 No H-bonds generated for 'chain 'Q' and resid 223 through 225' Processing helix chain 'R' and resid 12 through 26 removed outlier: 4.103A pdb=" N GLU R 18 " --> pdb=" O LYS R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 48 removed outlier: 3.562A pdb=" N ILE R 48 " --> pdb=" O GLN R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 67 Processing helix chain 'R' and resid 68 through 83 Processing helix chain 'R' and resid 106 through 120 removed outlier: 3.544A pdb=" N THR R 118 " --> pdb=" O GLU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 144 removed outlier: 3.779A pdb=" N GLY R 135 " --> pdb=" O THR R 131 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASN R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 182 removed outlier: 3.891A pdb=" N HIS R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 190 Processing helix chain 'R' and resid 213 through 222 Processing helix chain 'R' and resid 223 through 225 No H-bonds generated for 'chain 'R' and resid 223 through 225' Processing helix chain 'U' and resid 9 through 11 No H-bonds generated for 'chain 'U' and resid 9 through 11' Processing helix chain 'U' and resid 12 through 26 removed outlier: 3.563A pdb=" N VAL U 16 " --> pdb=" O ASP U 12 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU U 18 " --> pdb=" O LYS U 14 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL U 19 " --> pdb=" O ILE U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 67 Processing helix chain 'U' and resid 68 through 83 Processing helix chain 'U' and resid 106 through 120 Processing helix chain 'U' and resid 129 through 144 removed outlier: 4.325A pdb=" N ASN U 144 " --> pdb=" O ALA U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 182 removed outlier: 3.992A pdb=" N HIS U 181 " --> pdb=" O ASP U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 213 through 222 Processing helix chain 'U' and resid 223 through 225 No H-bonds generated for 'chain 'U' and resid 223 through 225' Processing helix chain 'V' and resid 9 through 11 No H-bonds generated for 'chain 'V' and resid 9 through 11' Processing helix chain 'V' and resid 12 through 26 removed outlier: 4.069A pdb=" N GLU V 18 " --> pdb=" O LYS V 14 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 48 removed outlier: 3.698A pdb=" N ILE V 48 " --> pdb=" O GLN V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 67 Processing helix chain 'V' and resid 68 through 83 Processing helix chain 'V' and resid 106 through 120 Processing helix chain 'V' and resid 129 through 144 removed outlier: 4.678A pdb=" N ASN V 144 " --> pdb=" O ALA V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 177 through 182 removed outlier: 4.335A pdb=" N HIS V 181 " --> pdb=" O ASP V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 190 Processing helix chain 'V' and resid 213 through 222 Processing helix chain 'V' and resid 223 through 225 No H-bonds generated for 'chain 'V' and resid 223 through 225' Processing helix chain 'S' and resid 9 through 11 No H-bonds generated for 'chain 'S' and resid 9 through 11' Processing helix chain 'S' and resid 12 through 26 removed outlier: 4.251A pdb=" N GLU S 18 " --> pdb=" O LYS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 48 removed outlier: 4.162A pdb=" N ILE S 48 " --> pdb=" O ILE S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 67 Processing helix chain 'S' and resid 68 through 83 removed outlier: 3.636A pdb=" N LEU S 75 " --> pdb=" O CYS S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 100 Processing helix chain 'S' and resid 106 through 120 Processing helix chain 'S' and resid 129 through 144 removed outlier: 4.700A pdb=" N ASN S 144 " --> pdb=" O ALA S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 182 removed outlier: 3.600A pdb=" N TRP S 182 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 190 removed outlier: 3.857A pdb=" N ASP S 188 " --> pdb=" O LYS S 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE S 190 " --> pdb=" O GLU S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 222 Processing helix chain 'S' and resid 223 through 225 No H-bonds generated for 'chain 'S' and resid 223 through 225' Processing helix chain 'T' and resid 9 through 11 No H-bonds generated for 'chain 'T' and resid 9 through 11' Processing helix chain 'T' and resid 12 through 26 removed outlier: 3.513A pdb=" N LEU T 17 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU T 18 " --> pdb=" O LYS T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 48 Processing helix chain 'T' and resid 64 through 67 Processing helix chain 'T' and resid 68 through 81 Processing helix chain 'T' and resid 96 through 100 Processing helix chain 'T' and resid 106 through 120 Processing helix chain 'T' and resid 129 through 143 Processing helix chain 'T' and resid 177 through 181 Processing helix chain 'T' and resid 185 through 190 Processing helix chain 'T' and resid 213 through 222 Processing helix chain 'T' and resid 223 through 225 No H-bonds generated for 'chain 'T' and resid 223 through 225' Processing sheet with id=AA1, first strand: chain 'G' and resid 29 through 31 removed outlier: 6.404A pdb=" N ALA G 4 " --> pdb=" O TRP G 31 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE G 5 " --> pdb=" O TYR G 56 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN G 55 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE G 90 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE G 57 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE G 92 " --> pdb=" O PHE G 57 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA G 59 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 153 through 157 removed outlier: 8.002A pdb=" N ALA G 207 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN G 163 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR G 209 " --> pdb=" O GLN G 163 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL G 165 " --> pdb=" O TYR G 209 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL G 206 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE G 233 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU G 208 " --> pdb=" O PHE G 233 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU G 239 " --> pdb=" O ASN G 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 7.456A pdb=" N GLN H 3 " --> pdb=" O TYR H 56 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU H 58 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE H 5 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE H 60 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER H 7 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 88 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 7.456A pdb=" N GLN H 3 " --> pdb=" O TYR H 56 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU H 58 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE H 5 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE H 60 " --> pdb=" O PHE H 5 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER H 7 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE H 92 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA H 59 " --> pdb=" O ILE H 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'H' and resid 148 through 149 removed outlier: 6.338A pdb=" N VAL H 206 " --> pdb=" O PHE H 231 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE H 233 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU H 208 " --> pdb=" O PHE H 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 29 through 31 removed outlier: 6.620A pdb=" N ALA E 4 " --> pdb=" O TRP E 31 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN E 3 " --> pdb=" O TYR E 56 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU E 58 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE E 5 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE E 60 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER E 7 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN E 55 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE E 90 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N PHE E 57 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE E 92 " --> pdb=" O PHE E 57 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA E 59 " --> pdb=" O ILE E 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 153 through 157 removed outlier: 8.189A pdb=" N ALA E 207 " --> pdb=" O GLU E 161 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN E 163 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR E 209 " --> pdb=" O GLN E 163 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL E 165 " --> pdb=" O TYR E 209 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL E 206 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE E 233 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU E 208 " --> pdb=" O PHE E 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 29 through 31 removed outlier: 6.505A pdb=" N ALA F 4 " --> pdb=" O TRP F 31 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLN F 3 " --> pdb=" O TYR F 56 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU F 58 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE F 5 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE F 60 " --> pdb=" O PHE F 5 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER F 7 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN F 55 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ILE F 90 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE F 57 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE F 92 " --> pdb=" O PHE F 57 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA F 59 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.546A pdb=" N ARG F 153 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 149 removed outlier: 7.740A pdb=" N ALA F 207 " --> pdb=" O GLU F 161 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN F 163 " --> pdb=" O ALA F 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N TYR F 209 " --> pdb=" O GLN F 163 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL F 165 " --> pdb=" O TYR F 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN F 234 " --> pdb=" O GLU F 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU F 239 " --> pdb=" O ASN F 234 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.256A pdb=" N ALA A 4 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN A 3 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU A 58 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 5 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE A 60 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N SER A 7 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN A 55 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 90 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE A 57 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 92 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA A 59 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 153 through 157 removed outlier: 3.533A pdb=" N ARG A 153 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA A 207 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN A 163 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TYR A 209 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 165 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 206 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE A 233 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 208 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A 239 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 240 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 7 removed outlier: 7.203A pdb=" N SER B 7 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE B 57 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 92 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ALA B 59 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.528A pdb=" N ARG B 153 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 148 through 149 removed outlier: 6.363A pdb=" N VAL B 206 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N PHE B 233 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 208 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.189A pdb=" N ALA C 4 " --> pdb=" O TRP C 31 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLN C 3 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU C 58 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE C 5 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE C 60 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER C 7 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 88 " --> pdb=" O GLN C 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 153 through 157 removed outlier: 3.548A pdb=" N ARG C 153 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA C 207 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN C 163 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR C 209 " --> pdb=" O GLN C 163 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL C 165 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 206 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE C 233 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU C 208 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.246A pdb=" N ALA D 4 " --> pdb=" O TRP D 31 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLN D 3 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU D 58 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE D 5 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE D 60 " --> pdb=" O PHE D 5 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N SER D 7 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN D 55 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE D 90 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 57 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE D 92 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA D 59 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.723A pdb=" N ARG D 153 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 148 through 149 Processing sheet with id=AC4, first strand: chain 'I' and resid 29 through 31 removed outlier: 6.449A pdb=" N ALA I 4 " --> pdb=" O TRP I 31 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN I 55 " --> pdb=" O LYS I 88 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE I 90 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE I 57 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE I 92 " --> pdb=" O PHE I 57 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA I 59 " --> pdb=" O ILE I 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 153 through 157 removed outlier: 3.563A pdb=" N ARG I 153 " --> pdb=" O VAL I 164 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA I 207 " --> pdb=" O GLU I 161 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN I 163 " --> pdb=" O ALA I 207 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR I 209 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL I 165 " --> pdb=" O TYR I 209 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL I 206 " --> pdb=" O PHE I 231 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE I 233 " --> pdb=" O VAL I 206 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU I 208 " --> pdb=" O PHE I 233 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU I 239 " --> pdb=" O ASN I 234 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 6 through 7 removed outlier: 6.049A pdb=" N PHE J 57 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE J 92 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA J 59 " --> pdb=" O ILE J 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 148 through 149 Processing sheet with id=AC8, first strand: chain 'J' and resid 148 through 149 removed outlier: 6.446A pdb=" N VAL J 206 " --> pdb=" O PHE J 231 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N PHE J 233 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU J 208 " --> pdb=" O PHE J 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 29 through 31 removed outlier: 6.109A pdb=" N ALA K 4 " --> pdb=" O TRP K 31 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR K 56 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHE K 5 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL K 123 " --> pdb=" O ILE K 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 153 through 157 removed outlier: 3.543A pdb=" N ARG K 153 " --> pdb=" O VAL K 164 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA K 207 " --> pdb=" O GLU K 161 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN K 163 " --> pdb=" O ALA K 207 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N TYR K 209 " --> pdb=" O GLN K 163 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL K 165 " --> pdb=" O TYR K 209 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL K 206 " --> pdb=" O PHE K 231 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE K 233 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU K 208 " --> pdb=" O PHE K 233 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 29 through 31 removed outlier: 6.358A pdb=" N ALA L 4 " --> pdb=" O TRP L 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR L 56 " --> pdb=" O GLN L 3 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE L 5 " --> pdb=" O TYR L 56 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS L 88 " --> pdb=" O GLN L 55 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 148 through 149 Processing sheet with id=AD4, first strand: chain 'L' and resid 148 through 149 removed outlier: 3.529A pdb=" N PHE L 167 " --> pdb=" O TYR L 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN L 234 " --> pdb=" O GLU L 239 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU L 239 " --> pdb=" O ASN L 234 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.802A pdb=" N TRP M 31 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE M 6 " --> pdb=" O TRP M 31 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE M 57 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE M 92 " --> pdb=" O PHE M 57 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA M 59 " --> pdb=" O ILE M 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 153 through 157 removed outlier: 3.550A pdb=" N ARG M 153 " --> pdb=" O VAL M 164 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA M 207 " --> pdb=" O GLU M 161 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN M 163 " --> pdb=" O ALA M 207 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N TYR M 209 " --> pdb=" O GLN M 163 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL M 165 " --> pdb=" O TYR M 209 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL M 206 " --> pdb=" O PHE M 231 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE M 233 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU M 208 " --> pdb=" O PHE M 233 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU M 239 " --> pdb=" O ASN M 234 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.587A pdb=" N ALA N 4 " --> pdb=" O TRP N 31 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLN N 3 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU N 58 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE N 5 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE N 60 " --> pdb=" O PHE N 5 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER N 7 " --> pdb=" O PHE N 60 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL N 123 " --> pdb=" O PRO N 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.560A pdb=" N ARG N 153 " --> pdb=" O VAL N 164 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 148 through 149 Processing sheet with id=AE1, first strand: chain 'O' and resid 29 through 31 removed outlier: 6.293A pdb=" N ALA O 4 " --> pdb=" O TRP O 31 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN O 3 " --> pdb=" O TYR O 56 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU O 58 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE O 5 " --> pdb=" O LEU O 58 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE O 60 " --> pdb=" O PHE O 5 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER O 7 " --> pdb=" O PHE O 60 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN O 55 " --> pdb=" O LYS O 88 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE O 90 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N PHE O 57 " --> pdb=" O ILE O 90 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE O 92 " --> pdb=" O PHE O 57 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA O 59 " --> pdb=" O ILE O 92 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 153 through 157 removed outlier: 3.503A pdb=" N ARG O 153 " --> pdb=" O VAL O 164 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA O 207 " --> pdb=" O GLU O 161 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN O 163 " --> pdb=" O ALA O 207 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR O 209 " --> pdb=" O GLN O 163 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL O 165 " --> pdb=" O TYR O 209 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL O 206 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N PHE O 233 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU O 208 " --> pdb=" O PHE O 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 29 through 31 removed outlier: 6.261A pdb=" N ALA P 4 " --> pdb=" O TRP P 31 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLN P 3 " --> pdb=" O TYR P 56 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU P 58 " --> pdb=" O GLN P 3 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE P 5 " --> pdb=" O LEU P 58 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE P 60 " --> pdb=" O PHE P 5 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER P 7 " --> pdb=" O PHE P 60 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN P 55 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE P 90 " --> pdb=" O GLN P 55 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE P 57 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE P 92 " --> pdb=" O PHE P 57 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA P 59 " --> pdb=" O ILE P 92 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 148 through 149 Processing sheet with id=AE5, first strand: chain 'P' and resid 148 through 149 removed outlier: 7.771A pdb=" N ALA P 207 " --> pdb=" O GLU P 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN P 163 " --> pdb=" O ALA P 207 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR P 209 " --> pdb=" O GLN P 163 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL P 165 " --> pdb=" O TYR P 209 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU P 239 " --> pdb=" O ASN P 234 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 29 through 31 removed outlier: 6.554A pdb=" N ALA Q 4 " --> pdb=" O TRP Q 31 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN Q 55 " --> pdb=" O LYS Q 88 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE Q 90 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE Q 57 " --> pdb=" O ILE Q 90 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE Q 92 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA Q 59 " --> pdb=" O ILE Q 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 153 through 154 removed outlier: 3.508A pdb=" N TYR Q 209 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL Q 230 " --> pdb=" O VAL Q 243 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU Q 239 " --> pdb=" O ASN Q 234 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR Q 240 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 29 through 31 removed outlier: 6.462A pdb=" N ALA R 4 " --> pdb=" O TRP R 31 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN R 3 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU R 58 " --> pdb=" O GLN R 3 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE R 5 " --> pdb=" O LEU R 58 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE R 60 " --> pdb=" O PHE R 5 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER R 7 " --> pdb=" O PHE R 60 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN R 55 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE R 90 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE R 57 " --> pdb=" O ILE R 90 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE R 92 " --> pdb=" O PHE R 57 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA R 59 " --> pdb=" O ILE R 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 148 through 149 removed outlier: 3.563A pdb=" N ARG R 153 " --> pdb=" O VAL R 164 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 148 through 149 removed outlier: 6.387A pdb=" N VAL R 206 " --> pdb=" O PHE R 231 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE R 233 " --> pdb=" O VAL R 206 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU R 208 " --> pdb=" O PHE R 233 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 29 through 31 removed outlier: 3.639A pdb=" N PHE U 6 " --> pdb=" O TRP U 31 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN U 55 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE U 90 " --> pdb=" O GLN U 55 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE U 57 " --> pdb=" O ILE U 90 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE U 92 " --> pdb=" O PHE U 57 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA U 59 " --> pdb=" O ILE U 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 153 through 157 removed outlier: 7.963A pdb=" N ALA U 207 " --> pdb=" O GLU U 161 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN U 163 " --> pdb=" O ALA U 207 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR U 209 " --> pdb=" O GLN U 163 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL U 165 " --> pdb=" O TYR U 209 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL U 206 " --> pdb=" O PHE U 231 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N PHE U 233 " --> pdb=" O VAL U 206 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU U 208 " --> pdb=" O PHE U 233 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 29 through 31 removed outlier: 3.698A pdb=" N TRP V 31 " --> pdb=" O ALA V 4 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE V 6 " --> pdb=" O TRP V 31 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN V 3 " --> pdb=" O TYR V 56 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU V 58 " --> pdb=" O GLN V 3 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE V 5 " --> pdb=" O LEU V 58 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N PHE V 60 " --> pdb=" O PHE V 5 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER V 7 " --> pdb=" O PHE V 60 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE V 57 " --> pdb=" O ILE V 90 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE V 92 " --> pdb=" O PHE V 57 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA V 59 " --> pdb=" O ILE V 92 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 148 through 149 removed outlier: 3.710A pdb=" N ARG V 153 " --> pdb=" O VAL V 164 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 148 through 149 removed outlier: 3.565A pdb=" N TYR V 209 " --> pdb=" O VAL V 165 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN V 234 " --> pdb=" O GLU V 239 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU V 239 " --> pdb=" O ASN V 234 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 3 through 7 removed outlier: 7.235A pdb=" N GLN S 3 " --> pdb=" O TYR S 56 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU S 58 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE S 5 " --> pdb=" O LEU S 58 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE S 60 " --> pdb=" O PHE S 5 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER S 7 " --> pdb=" O PHE S 60 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN S 55 " --> pdb=" O LYS S 88 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE S 90 " --> pdb=" O GLN S 55 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE S 57 " --> pdb=" O ILE S 90 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE S 92 " --> pdb=" O PHE S 57 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA S 59 " --> pdb=" O ILE S 92 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL S 123 " --> pdb=" O ILE S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'S' and resid 153 through 157 removed outlier: 8.142A pdb=" N ALA S 207 " --> pdb=" O GLU S 161 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN S 163 " --> pdb=" O ALA S 207 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR S 209 " --> pdb=" O GLN S 163 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL S 165 " --> pdb=" O TYR S 209 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL S 206 " --> pdb=" O PHE S 231 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE S 233 " --> pdb=" O VAL S 206 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU S 208 " --> pdb=" O PHE S 233 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU S 239 " --> pdb=" O ASN S 234 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 29 through 31 removed outlier: 7.487A pdb=" N GLN T 3 " --> pdb=" O TYR T 56 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N LEU T 58 " --> pdb=" O GLN T 3 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE T 5 " --> pdb=" O LEU T 58 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE T 60 " --> pdb=" O PHE T 5 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER T 7 " --> pdb=" O PHE T 60 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N PHE T 57 " --> pdb=" O ILE T 90 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE T 92 " --> pdb=" O PHE T 57 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA T 59 " --> pdb=" O ILE T 92 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N VAL T 123 " --> pdb=" O ILE T 89 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'T' and resid 148 through 149 removed outlier: 3.610A pdb=" N ARG T 153 " --> pdb=" O VAL T 164 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 148 through 149 removed outlier: 6.342A pdb=" N VAL T 206 " --> pdb=" O PHE T 231 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE T 233 " --> pdb=" O VAL T 206 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU T 208 " --> pdb=" O PHE T 233 " (cutoff:3.500A) 1614 hydrogen bonds defined for protein. 4269 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: 11.22 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 7195 1.30 - 1.43: 12762 1.43 - 1.56: 26498 1.56 - 1.69: 85 1.69 - 1.82: 177 Bond restraints: 46717 Sorted by residual: bond pdb=" CG PRO R 127 " pdb=" CD PRO R 127 " ideal model delta sigma weight residual 1.503 1.169 0.334 3.40e-02 8.65e+02 9.64e+01 bond pdb=" N PRO R 127 " pdb=" CD PRO R 127 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CB PRO R 127 " pdb=" CG PRO R 127 " ideal model delta sigma weight residual 1.492 1.709 -0.217 5.00e-02 4.00e+02 1.89e+01 bond pdb=" N PRO R 127 " pdb=" CA PRO R 127 " ideal model delta sigma weight residual 1.466 1.423 0.044 1.13e-02 7.83e+03 1.50e+01 bond pdb=" CD GLN C 55 " pdb=" OE1 GLN C 55 " ideal model delta sigma weight residual 1.231 1.198 0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 46712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 63120 3.60 - 7.19: 420 7.19 - 10.79: 42 10.79 - 14.38: 13 14.38 - 17.98: 7 Bond angle restraints: 63602 Sorted by residual: angle pdb=" CA PRO R 127 " pdb=" N PRO R 127 " pdb=" CD PRO R 127 " ideal model delta sigma weight residual 112.00 94.75 17.25 1.40e+00 5.10e-01 1.52e+02 angle pdb=" N PRO R 127 " pdb=" CD PRO R 127 " pdb=" CG PRO R 127 " ideal model delta sigma weight residual 103.20 85.22 17.98 1.50e+00 4.44e-01 1.44e+02 angle pdb=" CA PRO R 127 " pdb=" CB PRO R 127 " pdb=" CG PRO R 127 " ideal model delta sigma weight residual 104.50 91.65 12.85 1.90e+00 2.77e-01 4.57e+01 angle pdb=" C PHE O 202 " pdb=" N ASP O 203 " pdb=" CA ASP O 203 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLN C 55 " pdb=" CA GLN C 55 " pdb=" CB GLN C 55 " ideal model delta sigma weight residual 109.99 117.90 -7.91 1.61e+00 3.86e-01 2.42e+01 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 23395 17.87 - 35.73: 3361 35.73 - 53.60: 762 53.60 - 71.47: 136 71.47 - 89.33: 55 Dihedral angle restraints: 27709 sinusoidal: 11583 harmonic: 16126 Sorted by residual: dihedral pdb=" CA SER C 54 " pdb=" C SER C 54 " pdb=" N GLN C 55 " pdb=" CA GLN C 55 " ideal model delta harmonic sigma weight residual -180.00 -151.34 -28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA SER K 54 " pdb=" C SER K 54 " pdb=" N GLN K 55 " pdb=" CA GLN K 55 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA SER G 238 " pdb=" C SER G 238 " pdb=" N GLU G 239 " pdb=" CA GLU G 239 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 27706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5749 0.052 - 0.105: 1116 0.105 - 0.157: 231 0.157 - 0.210: 9 0.210 - 0.262: 1 Chirality restraints: 7106 Sorted by residual: chirality pdb=" CA PRO R 127 " pdb=" N PRO R 127 " pdb=" C PRO R 127 " pdb=" CB PRO R 127 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE M 92 " pdb=" CA ILE M 92 " pdb=" CG1 ILE M 92 " pdb=" CG2 ILE M 92 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA ASP M 203 " pdb=" N ASP M 203 " pdb=" C ASP M 203 " pdb=" CB ASP M 203 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 7103 not shown) Planarity restraints: 7876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 126 " 0.094 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO G 127 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO G 127 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO G 127 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 126 " 0.083 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO R 127 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO R 127 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO R 127 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 126 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 127 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " 0.044 5.00e-02 4.00e+02 ... (remaining 7873 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 708 2.63 - 3.20: 42278 3.20 - 3.77: 73784 3.77 - 4.33: 100438 4.33 - 4.90: 160568 Nonbonded interactions: 377776 Sorted by model distance: nonbonded pdb=" OG SER Q 54 " pdb=" OE1 GLN Q 55 " model vdw 2.068 3.040 nonbonded pdb=" OH TYR J 56 " pdb=" OE1 GLU J 145 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR P 237 " pdb=" OE2 GLU P 239 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR K 56 " pdb=" OE1 GLU K 145 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR C 56 " pdb=" OE1 GLU C 145 " model vdw 2.135 3.040 ... (remaining 377771 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.420 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: 0.060 Extract box with map and model: 1.230 Check model and map are aligned: 0.150 Set scattering table: 0.130 Process input model: 40.410 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 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 : 0.004 0.334 46717 Z= 0.150 Angle : 0.760 17.976 63602 Z= 0.381 Chirality : 0.044 0.262 7106 Planarity : 0.005 0.140 7876 Dihedral : 17.370 89.332 17193 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.11 % Allowed : 35.30 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.12), residues: 5390 helix: 1.37 (0.15), residues: 1320 sheet: -0.60 (0.16), residues: 1188 loop : 0.61 (0.12), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG T 132 TYR 0.026 0.001 TYR K 56 PHE 0.020 0.001 PHE C 5 TRP 0.024 0.001 TRP D 70 HIS 0.003 0.000 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00365 (46717) covalent geometry : angle 0.75971 (63602) hydrogen bonds : bond 0.26951 ( 1592) hydrogen bonds : angle 8.26212 ( 4269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 502 time to evaluate : 2.511 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 183 ASP cc_start: 0.7914 (p0) cc_final: 0.7709 (p0) REVERT: F 12 ASP cc_start: 0.9167 (m-30) cc_final: 0.8917 (p0) REVERT: F 122 TYR cc_start: 0.8784 (p90) cc_final: 0.8502 (p90) REVERT: F 177 ASP cc_start: 0.9552 (p0) cc_final: 0.9242 (p0) REVERT: A 101 ASP cc_start: 0.9194 (t0) cc_final: 0.8897 (t0) REVERT: A 132 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8764 (ttp80) REVERT: A 203 ASP cc_start: 0.8963 (t0) cc_final: 0.8719 (m-30) REVERT: C 70 TRP cc_start: 0.9036 (m-90) cc_final: 0.8549 (t60) REVERT: D 26 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8374 (t) REVERT: I 55 GLN cc_start: 0.7047 (pm20) cc_final: 0.6559 (mp10) REVERT: K 132 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8297 (ttp80) REVERT: L 132 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8641 (tmm-80) REVERT: M 197 GLN cc_start: 0.9111 (pm20) cc_final: 0.8889 (pp30) REVERT: N 97 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8279 (tpm170) REVERT: N 185 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9207 (mmpt) REVERT: N 195 ASN cc_start: 0.9306 (m-40) cc_final: 0.9060 (p0) REVERT: O 101 ASP cc_start: 0.9274 (t0) cc_final: 0.9072 (t0) REVERT: Q 11 LYS cc_start: 0.9352 (tppp) cc_final: 0.8954 (tptp) REVERT: R 132 ARG cc_start: 0.9299 (tmm-80) cc_final: 0.9030 (pmt-80) REVERT: U 12 ASP cc_start: 0.8962 (m-30) cc_final: 0.8586 (p0) REVERT: U 130 MET cc_start: 0.9369 (tpt) cc_final: 0.8899 (tpp) REVERT: U 156 LYS cc_start: 0.9059 (tttt) cc_final: 0.8734 (tttm) REVERT: S 154 MET cc_start: 0.8737 (mmm) cc_final: 0.8284 (tmm) REVERT: S 160 THR cc_start: 0.9535 (m) cc_final: 0.9226 (t) REVERT: S 161 GLU cc_start: 0.8303 (tp30) cc_final: 0.7656 (tp30) outliers start: 103 outliers final: 83 residues processed: 600 average time/residue: 0.7811 time to fit residues: 581.3886 Evaluate side-chains 531 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 447 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 181 HIS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 101 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 188 ASP Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 247 SER Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain R residue 12 ASP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 58 LEU Chi-restraints excluded: chain V residue 95 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 181 HIS Chi-restraints excluded: chain V residue 188 ASP Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain T residue 12 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 22 HIS E 99 GLN E 158 ASN ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN C 22 HIS ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 GLN N 234 ASN P 234 ASN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 GLN ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044023 restraints weight = 175902.201| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.71 r_work: 0.2826 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 46717 Z= 0.177 Angle : 0.652 11.575 63602 Z= 0.327 Chirality : 0.046 0.276 7106 Planarity : 0.005 0.087 7876 Dihedral : 8.681 73.264 6446 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.98 % Allowed : 28.26 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.12), residues: 5390 helix: 1.39 (0.14), residues: 1562 sheet: -0.85 (0.15), residues: 1254 loop : 0.62 (0.13), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 132 TYR 0.022 0.002 TYR P 79 PHE 0.020 0.001 PHE K 112 TRP 0.019 0.001 TRP M 31 HIS 0.003 0.001 HIS K 8 Details of bonding type rmsd covalent geometry : bond 0.00410 (46717) covalent geometry : angle 0.65213 (63602) hydrogen bonds : bond 0.04298 ( 1592) hydrogen bonds : angle 5.30948 ( 4269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 505 time to evaluate : 1.945 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: G 15 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9179 (tp) REVERT: G 25 GLN cc_start: 0.9438 (tp40) cc_final: 0.8925 (mm-40) REVERT: G 132 ARG cc_start: 0.8966 (tmm-80) cc_final: 0.8749 (tmm-80) REVERT: G 148 ARG cc_start: 0.8487 (mpt-90) cc_final: 0.8148 (mpt-90) REVERT: H 122 TYR cc_start: 0.8209 (p90) cc_final: 0.7941 (p90) REVERT: H 132 ARG cc_start: 0.9191 (tmm160) cc_final: 0.8917 (tmm160) REVERT: H 183 ASP cc_start: 0.8182 (p0) cc_final: 0.7973 (p0) REVERT: E 77 GLN cc_start: 0.9616 (mt0) cc_final: 0.9311 (mt0) REVERT: E 119 ARG cc_start: 0.9204 (ptp90) cc_final: 0.8593 (ptp90) REVERT: E 132 ARG cc_start: 0.8797 (tmm-80) cc_final: 0.8563 (tmm-80) REVERT: E 143 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8728 (pm20) REVERT: E 184 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9192 (tm) REVERT: E 185 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9103 (ptpp) REVERT: F 12 ASP cc_start: 0.9234 (m-30) cc_final: 0.8824 (p0) REVERT: F 65 TYR cc_start: 0.8705 (t80) cc_final: 0.7949 (t80) REVERT: A 11 LYS cc_start: 0.9454 (mppt) cc_final: 0.9151 (mptt) REVERT: A 97 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8694 (ttp80) REVERT: A 101 ASP cc_start: 0.9215 (t0) cc_final: 0.8869 (t0) REVERT: A 107 ASP cc_start: 0.9575 (m-30) cc_final: 0.9229 (p0) REVERT: A 203 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8892 (m-30) REVERT: C 67 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9049 (mptm) REVERT: C 255 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9053 (t) REVERT: D 132 ARG cc_start: 0.8479 (tmm160) cc_final: 0.8227 (tmm160) REVERT: D 148 ARG cc_start: 0.8761 (mpp80) cc_final: 0.8471 (mpp80) REVERT: I 97 ARG cc_start: 0.9418 (OUTLIER) cc_final: 0.8896 (tpt-90) REVERT: I 119 ARG cc_start: 0.9337 (ptp90) cc_final: 0.8875 (ptp90) REVERT: I 139 GLU cc_start: 0.9454 (tp30) cc_final: 0.9135 (tp30) REVERT: J 112 PHE cc_start: 0.8385 (t80) cc_final: 0.7953 (t80) REVERT: J 185 LYS cc_start: 0.9115 (mmpt) cc_final: 0.8734 (mppt) REVERT: K 3 GLN cc_start: 0.8029 (mp10) cc_final: 0.7809 (mp10) REVERT: K 183 ASP cc_start: 0.9292 (p0) cc_final: 0.9046 (p0) REVERT: L 112 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8440 (t80) REVERT: L 132 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8639 (tmm-80) REVERT: L 154 MET cc_start: 0.8467 (mmm) cc_final: 0.7936 (tmm) REVERT: M 3 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8680 (mm-40) REVERT: M 47 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8211 (tp) REVERT: N 154 MET cc_start: 0.9040 (tpp) cc_final: 0.8760 (tpp) REVERT: N 185 LYS cc_start: 0.9537 (mmmt) cc_final: 0.9279 (mmpt) REVERT: N 195 ASN cc_start: 0.9437 (m-40) cc_final: 0.9157 (p0) REVERT: O 101 ASP cc_start: 0.9306 (t0) cc_final: 0.9086 (t0) REVERT: O 132 ARG cc_start: 0.8539 (ttp80) cc_final: 0.8289 (ttp80) REVERT: O 139 GLU cc_start: 0.9348 (tm-30) cc_final: 0.9144 (tm-30) REVERT: O 196 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8860 (tp30) REVERT: P 26 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8430 (t) REVERT: P 90 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9053 (pp) REVERT: P 132 ARG cc_start: 0.9370 (tmm160) cc_final: 0.9135 (tmm160) REVERT: P 187 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.9005 (mp0) REVERT: R 148 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8609 (ttm110) REVERT: U 99 GLN cc_start: 0.9089 (mp10) cc_final: 0.8781 (mp10) REVERT: U 107 ASP cc_start: 0.9386 (m-30) cc_final: 0.9067 (p0) REVERT: U 130 MET cc_start: 0.9260 (tpt) cc_final: 0.8896 (tpp) REVERT: U 156 LYS cc_start: 0.9340 (tttt) cc_final: 0.8886 (tttm) REVERT: V 132 ARG cc_start: 0.8526 (tmm-80) cc_final: 0.8103 (tmm160) REVERT: V 187 GLU cc_start: 0.9265 (mp0) cc_final: 0.8939 (mp0) REVERT: S 11 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9114 (mmpt) REVERT: S 96 ASN cc_start: 0.8860 (t0) cc_final: 0.8620 (t0) REVERT: S 101 ASP cc_start: 0.9274 (t0) cc_final: 0.9007 (t0) REVERT: S 154 MET cc_start: 0.8934 (mmm) cc_final: 0.8656 (mmm) REVERT: S 161 GLU cc_start: 0.8497 (tp30) cc_final: 0.7972 (tp30) REVERT: S 239 GLU cc_start: 0.8970 (mp0) cc_final: 0.8729 (mp0) REVERT: T 97 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7928 (tpm170) REVERT: T 161 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8873 (mm-30) outliers start: 243 outliers final: 94 residues processed: 704 average time/residue: 0.7667 time to fit residues: 669.9235 Evaluate side-chains 548 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 437 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 123 VAL Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 254 MET Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 141 LEU Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 188 ASP Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 154 MET Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 161 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 490 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 387 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 306 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 405 optimal weight: 0.9990 chunk 265 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 ASN ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 129 ASN ** Q 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN V 144 ASN ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044007 restraints weight = 174904.408| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.73 r_work: 0.2818 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46717 Z= 0.144 Angle : 0.627 11.214 63602 Z= 0.308 Chirality : 0.045 0.349 7106 Planarity : 0.004 0.066 7876 Dihedral : 8.312 73.440 6377 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.93 % Allowed : 28.15 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.12), residues: 5390 helix: 1.50 (0.13), residues: 1562 sheet: -0.89 (0.15), residues: 1276 loop : 0.60 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 132 TYR 0.017 0.001 TYR N 56 PHE 0.016 0.001 PHE B 5 TRP 0.020 0.001 TRP M 31 HIS 0.003 0.001 HIS T 8 Details of bonding type rmsd covalent geometry : bond 0.00342 (46717) covalent geometry : angle 0.62739 (63602) hydrogen bonds : bond 0.03742 ( 1592) hydrogen bonds : angle 4.96763 ( 4269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 490 time to evaluate : 1.964 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: G 14 LYS cc_start: 0.9663 (tptp) cc_final: 0.9398 (tptp) REVERT: G 25 GLN cc_start: 0.9442 (tp40) cc_final: 0.8862 (mm-40) REVERT: G 88 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8605 (ptpt) REVERT: G 119 ARG cc_start: 0.9055 (mtm110) cc_final: 0.8762 (ptm-80) REVERT: G 148 ARG cc_start: 0.8530 (mpt-90) cc_final: 0.8061 (mpt-90) REVERT: G 185 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8275 (ttpp) REVERT: H 122 TYR cc_start: 0.8394 (p90) cc_final: 0.8112 (p90) REVERT: H 132 ARG cc_start: 0.9195 (tmm160) cc_final: 0.8908 (tmm160) REVERT: H 183 ASP cc_start: 0.8243 (p0) cc_final: 0.8040 (p0) REVERT: E 77 GLN cc_start: 0.9615 (mt0) cc_final: 0.9333 (mt0) REVERT: E 99 GLN cc_start: 0.9079 (pm20) cc_final: 0.8848 (pm20) REVERT: E 132 ARG cc_start: 0.8867 (tmm-80) cc_final: 0.8618 (tmm-80) REVERT: E 143 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8733 (pm20) REVERT: E 184 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9221 (tm) REVERT: E 185 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9147 (ptpp) REVERT: E 203 ASP cc_start: 0.9171 (t0) cc_final: 0.8964 (p0) REVERT: F 12 ASP cc_start: 0.9245 (m-30) cc_final: 0.8802 (p0) REVERT: F 65 TYR cc_start: 0.8633 (t80) cc_final: 0.7882 (t80) REVERT: F 177 ASP cc_start: 0.9469 (p0) cc_final: 0.9065 (p0) REVERT: F 195 ASN cc_start: 0.9419 (m-40) cc_final: 0.8937 (p0) REVERT: F 239 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: A 11 LYS cc_start: 0.9461 (mppt) cc_final: 0.9076 (mptt) REVERT: A 97 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8615 (ttp80) REVERT: A 101 ASP cc_start: 0.9214 (t0) cc_final: 0.8853 (t0) REVERT: A 107 ASP cc_start: 0.9557 (m-30) cc_final: 0.9254 (p0) REVERT: A 129 ASN cc_start: 0.8690 (t0) cc_final: 0.8029 (t0) REVERT: A 143 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8867 (tm-30) REVERT: A 203 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8910 (m-30) REVERT: B 128 HIS cc_start: 0.9224 (OUTLIER) cc_final: 0.8984 (p-80) REVERT: C 97 ARG cc_start: 0.8833 (ttm-80) cc_final: 0.8520 (ttm-80) REVERT: C 244 TYR cc_start: 0.8168 (t80) cc_final: 0.7865 (t80) REVERT: C 255 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9090 (t) REVERT: D 31 TRP cc_start: 0.9219 (m100) cc_final: 0.8718 (m100) REVERT: D 132 ARG cc_start: 0.8489 (tmm160) cc_final: 0.8277 (tmm160) REVERT: D 148 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8515 (mpp80) REVERT: I 11 LYS cc_start: 0.9634 (mmmm) cc_final: 0.9351 (mmpt) REVERT: I 139 GLU cc_start: 0.9434 (tp30) cc_final: 0.9096 (tp30) REVERT: J 112 PHE cc_start: 0.8414 (t80) cc_final: 0.8006 (t80) REVERT: J 185 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8721 (mppt) REVERT: K 24 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.9086 (mtm-85) REVERT: K 66 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8809 (pp) REVERT: K 73 ASP cc_start: 0.9085 (p0) cc_final: 0.8785 (p0) REVERT: K 77 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8877 (mp10) REVERT: K 101 ASP cc_start: 0.9117 (t0) cc_final: 0.7940 (p0) REVERT: K 132 ARG cc_start: 0.9053 (tmm-80) cc_final: 0.8703 (ttp80) REVERT: K 183 ASP cc_start: 0.9310 (p0) cc_final: 0.9050 (p0) REVERT: K 195 ASN cc_start: 0.9369 (m110) cc_final: 0.8780 (p0) REVERT: L 17 LEU cc_start: 0.9270 (mt) cc_final: 0.9027 (pp) REVERT: L 112 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8434 (t80) REVERT: L 132 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8651 (tmm-80) REVERT: L 148 ARG cc_start: 0.9189 (ptm160) cc_final: 0.8819 (ptm160) REVERT: L 154 MET cc_start: 0.8483 (mmm) cc_final: 0.7999 (tmm) REVERT: M 3 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8465 (mm-40) REVERT: M 47 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8207 (tp) REVERT: N 154 MET cc_start: 0.9019 (tpp) cc_final: 0.8736 (tpp) REVERT: N 185 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9159 (mppt) REVERT: N 195 ASN cc_start: 0.9451 (m-40) cc_final: 0.9166 (p0) REVERT: O 3 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9138 (mp10) REVERT: O 101 ASP cc_start: 0.9309 (t0) cc_final: 0.9082 (t0) REVERT: O 139 GLU cc_start: 0.9354 (tm-30) cc_final: 0.9112 (tm-30) REVERT: O 196 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8743 (tp30) REVERT: P 90 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9122 (pp) REVERT: P 132 ARG cc_start: 0.9313 (ttm170) cc_final: 0.8898 (ttp80) REVERT: P 187 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9033 (mp0) REVERT: Q 11 LYS cc_start: 0.9451 (tppp) cc_final: 0.9027 (tmmm) REVERT: Q 73 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (p0) REVERT: R 55 GLN cc_start: 0.6277 (pt0) cc_final: 0.5843 (pt0) REVERT: R 148 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8668 (ttm110) REVERT: R 154 MET cc_start: 0.8907 (mmm) cc_final: 0.8695 (mmm) REVERT: U 94 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9369 (mm) REVERT: U 96 ASN cc_start: 0.8401 (t0) cc_final: 0.8013 (t0) REVERT: U 99 GLN cc_start: 0.9179 (mp10) cc_final: 0.8803 (mp10) REVERT: U 107 ASP cc_start: 0.9393 (m-30) cc_final: 0.9090 (p0) REVERT: U 130 MET cc_start: 0.9249 (tpt) cc_final: 0.8921 (tpp) REVERT: U 156 LYS cc_start: 0.9371 (tttt) cc_final: 0.8824 (tppp) REVERT: V 132 ARG cc_start: 0.8553 (tmm-80) cc_final: 0.8153 (tmm-80) REVERT: V 187 GLU cc_start: 0.9293 (mp0) cc_final: 0.8975 (mp0) REVERT: S 11 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9113 (mmpt) REVERT: S 96 ASN cc_start: 0.8769 (t0) cc_final: 0.8497 (t0) REVERT: S 101 ASP cc_start: 0.9314 (t0) cc_final: 0.9066 (t0) REVERT: S 154 MET cc_start: 0.9000 (mmm) cc_final: 0.8700 (mmm) REVERT: S 161 GLU cc_start: 0.8588 (tp30) cc_final: 0.8009 (tp30) REVERT: S 239 GLU cc_start: 0.8940 (mp0) cc_final: 0.8680 (mp0) REVERT: T 26 SER cc_start: 0.9315 (OUTLIER) cc_final: 0.8907 (t) REVERT: T 161 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8904 (mm-30) outliers start: 241 outliers final: 107 residues processed: 687 average time/residue: 0.7568 time to fit residues: 645.2605 Evaluate side-chains 556 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 427 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 238 SER Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 90 ILE Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 266 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 329 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 173 optimal weight: 30.0000 chunk 403 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 HIS V 234 ASN S 234 ASN ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.062082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041759 restraints weight = 176744.404| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.66 r_work: 0.2747 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 46717 Z= 0.253 Angle : 0.672 12.399 63602 Z= 0.334 Chirality : 0.047 0.383 7106 Planarity : 0.004 0.063 7876 Dihedral : 8.452 74.597 6364 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 6.00 % Allowed : 27.40 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.12), residues: 5390 helix: 1.51 (0.13), residues: 1562 sheet: -1.01 (0.15), residues: 1276 loop : 0.49 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 132 TYR 0.020 0.002 TYR M 122 PHE 0.020 0.001 PHE H 60 TRP 0.014 0.001 TRP O 215 HIS 0.005 0.001 HIS K 8 Details of bonding type rmsd covalent geometry : bond 0.00584 (46717) covalent geometry : angle 0.67189 (63602) hydrogen bonds : bond 0.03768 ( 1592) hydrogen bonds : angle 4.87638 ( 4269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 293 poor density : 460 time to evaluate : 1.810 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: G 14 LYS cc_start: 0.9652 (tptp) cc_final: 0.9377 (tptp) REVERT: G 25 GLN cc_start: 0.9471 (tp40) cc_final: 0.8950 (mm-40) REVERT: G 88 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8540 (ptpt) REVERT: G 107 ASP cc_start: 0.9536 (m-30) cc_final: 0.9178 (t0) REVERT: G 119 ARG cc_start: 0.9049 (mtm110) cc_final: 0.8739 (ptm-80) REVERT: G 148 ARG cc_start: 0.8598 (mpt-90) cc_final: 0.8274 (mpt-90) REVERT: G 185 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: H 60 PHE cc_start: 0.8757 (m-10) cc_final: 0.8438 (m-80) REVERT: H 122 TYR cc_start: 0.8508 (p90) cc_final: 0.8216 (p90) REVERT: H 132 ARG cc_start: 0.9175 (tmm160) cc_final: 0.8945 (tmm160) REVERT: E 26 SER cc_start: 0.9492 (OUTLIER) cc_final: 0.9263 (t) REVERT: E 77 GLN cc_start: 0.9601 (mt0) cc_final: 0.9293 (mt0) REVERT: E 101 ASP cc_start: 0.9335 (t0) cc_final: 0.8690 (t0) REVERT: E 119 ARG cc_start: 0.9260 (ptp90) cc_final: 0.8748 (ptp90) REVERT: E 132 ARG cc_start: 0.8899 (tmm-80) cc_final: 0.8591 (tmm-80) REVERT: E 143 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8756 (pm20) REVERT: E 184 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9264 (tm) REVERT: F 12 ASP cc_start: 0.9254 (m-30) cc_final: 0.8800 (p0) REVERT: F 107 ASP cc_start: 0.9223 (p0) cc_final: 0.8895 (t0) REVERT: F 239 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: A 11 LYS cc_start: 0.9434 (mppt) cc_final: 0.9055 (mptt) REVERT: A 77 GLN cc_start: 0.9493 (mt0) cc_final: 0.9199 (mt0) REVERT: A 97 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8626 (ttp80) REVERT: A 101 ASP cc_start: 0.9270 (t0) cc_final: 0.8882 (t0) REVERT: A 107 ASP cc_start: 0.9530 (m-30) cc_final: 0.9324 (p0) REVERT: A 129 ASN cc_start: 0.8713 (t0) cc_final: 0.7070 (t0) REVERT: A 132 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8679 (ttp80) REVERT: A 143 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8777 (tm-30) REVERT: A 203 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8935 (m-30) REVERT: B 128 HIS cc_start: 0.9259 (OUTLIER) cc_final: 0.8990 (p-80) REVERT: C 107 ASP cc_start: 0.9548 (m-30) cc_final: 0.9279 (t0) REVERT: D 31 TRP cc_start: 0.9248 (m100) cc_final: 0.8873 (m100) REVERT: D 132 ARG cc_start: 0.8468 (tmm160) cc_final: 0.8216 (tmm160) REVERT: D 203 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8628 (m-30) REVERT: D 217 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8577 (m-10) REVERT: I 3 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8431 (mm-40) REVERT: I 11 LYS cc_start: 0.9652 (mmmm) cc_final: 0.9392 (mmpt) REVERT: I 55 GLN cc_start: 0.7725 (pm20) cc_final: 0.7325 (mp10) REVERT: I 97 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8695 (tpt-90) REVERT: I 129 ASN cc_start: 0.8740 (t0) cc_final: 0.8346 (t0) REVERT: I 139 GLU cc_start: 0.9438 (tp30) cc_final: 0.9135 (tp30) REVERT: J 112 PHE cc_start: 0.8492 (t80) cc_final: 0.8107 (OUTLIER) REVERT: J 185 LYS cc_start: 0.9154 (mmpt) cc_final: 0.8844 (mppt) REVERT: K 24 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8998 (ttm110) REVERT: K 66 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8950 (pp) REVERT: K 101 ASP cc_start: 0.9205 (t0) cc_final: 0.8173 (p0) REVERT: K 110 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8654 (ttm110) REVERT: K 148 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8356 (mmt90) REVERT: K 195 ASN cc_start: 0.9387 (m110) cc_final: 0.8791 (p0) REVERT: L 17 LEU cc_start: 0.9286 (mt) cc_final: 0.9060 (pp) REVERT: L 112 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8454 (t80) REVERT: L 132 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8660 (tmm-80) REVERT: L 154 MET cc_start: 0.8390 (mmm) cc_final: 0.7933 (tmm) REVERT: M 3 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8666 (mm-40) REVERT: N 97 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8249 (tpm170) REVERT: N 154 MET cc_start: 0.8971 (tpp) cc_final: 0.8671 (tpp) REVERT: N 185 LYS cc_start: 0.9526 (mmmt) cc_final: 0.9179 (mppt) REVERT: N 195 ASN cc_start: 0.9479 (m-40) cc_final: 0.9201 (p0) REVERT: O 101 ASP cc_start: 0.9335 (t0) cc_final: 0.9073 (t0) REVERT: O 132 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8382 (ttp80) REVERT: O 139 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9109 (tm-30) REVERT: O 143 GLN cc_start: 0.9250 (tm-30) cc_final: 0.8870 (pp30) REVERT: O 196 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8999 (tt0) REVERT: P 26 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8468 (t) REVERT: P 132 ARG cc_start: 0.9357 (ttm170) cc_final: 0.9023 (tmm160) REVERT: P 187 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.9093 (mp0) REVERT: Q 11 LYS cc_start: 0.9447 (tppp) cc_final: 0.9073 (tmmm) REVERT: Q 17 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9165 (mp) REVERT: Q 166 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: R 120 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7815 (tm) REVERT: R 148 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8706 (ttm110) REVERT: U 94 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9313 (mm) REVERT: U 96 ASN cc_start: 0.8476 (t0) cc_final: 0.8079 (t0) REVERT: U 99 GLN cc_start: 0.9249 (mp10) cc_final: 0.8917 (mp10) REVERT: U 107 ASP cc_start: 0.9411 (m-30) cc_final: 0.9129 (p0) REVERT: V 26 SER cc_start: 0.9290 (OUTLIER) cc_final: 0.8981 (t) REVERT: V 187 GLU cc_start: 0.9283 (mp0) cc_final: 0.8950 (mp0) REVERT: S 11 LYS cc_start: 0.9342 (mmtm) cc_final: 0.9126 (mmpt) REVERT: S 101 ASP cc_start: 0.9407 (t0) cc_final: 0.9146 (t0) REVERT: S 139 GLU cc_start: 0.9414 (tp30) cc_final: 0.9205 (tp30) REVERT: S 154 MET cc_start: 0.9094 (mmm) cc_final: 0.8719 (mmm) REVERT: S 161 GLU cc_start: 0.8794 (tp30) cc_final: 0.8194 (tp30) REVERT: S 239 GLU cc_start: 0.8957 (mp0) cc_final: 0.8614 (mp0) REVERT: T 26 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8896 (t) REVERT: T 161 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8841 (mm-30) REVERT: T 203 ASP cc_start: 0.8963 (t0) cc_final: 0.8454 (p0) outliers start: 293 outliers final: 139 residues processed: 705 average time/residue: 0.6938 time to fit residues: 612.6787 Evaluate side-chains 590 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 423 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 181 HIS Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 97 ARG Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 187 GLU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 95 THR Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 130 MET Chi-restraints excluded: chain U residue 154 MET Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 15 ILE Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 229 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain T residue 161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 361 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 368 optimal weight: 8.9990 chunk 303 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 385 optimal weight: 10.0000 chunk 526 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 459 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042441 restraints weight = 176425.044| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.68 r_work: 0.2769 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 46717 Z= 0.168 Angle : 0.653 12.913 63602 Z= 0.320 Chirality : 0.046 0.436 7106 Planarity : 0.004 0.056 7876 Dihedral : 8.373 73.667 6361 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.47 % Allowed : 28.17 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.12), residues: 5390 helix: 1.59 (0.13), residues: 1562 sheet: -0.99 (0.15), residues: 1276 loop : 0.51 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 132 TYR 0.021 0.001 TYR N 56 PHE 0.016 0.001 PHE B 5 TRP 0.015 0.001 TRP O 215 HIS 0.004 0.001 HIS V 8 Details of bonding type rmsd covalent geometry : bond 0.00396 (46717) covalent geometry : angle 0.65331 (63602) hydrogen bonds : bond 0.03367 ( 1592) hydrogen bonds : angle 4.75061 ( 4269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 267 poor density : 489 time to evaluate : 1.589 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: G 11 LYS cc_start: 0.9590 (ttpt) cc_final: 0.9249 (ttpp) REVERT: G 14 LYS cc_start: 0.9670 (tptp) cc_final: 0.9381 (tptp) REVERT: G 25 GLN cc_start: 0.9460 (tp40) cc_final: 0.8941 (mm-40) REVERT: G 88 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8488 (ptpt) REVERT: G 97 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8146 (ttt-90) REVERT: G 107 ASP cc_start: 0.9498 (m-30) cc_final: 0.9165 (t0) REVERT: G 119 ARG cc_start: 0.9049 (mtm110) cc_final: 0.8566 (ptt-90) REVERT: G 132 ARG cc_start: 0.9053 (tmm-80) cc_final: 0.8846 (tmm-80) REVERT: G 148 ARG cc_start: 0.8591 (mpt-90) cc_final: 0.8241 (mpt-90) REVERT: G 185 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8284 (ttpp) REVERT: H 122 TYR cc_start: 0.8609 (p90) cc_final: 0.8342 (p90) REVERT: H 141 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9178 (tm) REVERT: H 154 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8461 (mmm) REVERT: E 77 GLN cc_start: 0.9593 (mt0) cc_final: 0.9284 (mt0) REVERT: E 94 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9051 (mm) REVERT: E 97 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8532 (ttp80) REVERT: E 101 ASP cc_start: 0.9340 (t0) cc_final: 0.8687 (t0) REVERT: E 132 ARG cc_start: 0.8946 (tmm-80) cc_final: 0.8705 (tmm-80) REVERT: E 143 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8720 (pm20) REVERT: F 3 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: F 12 ASP cc_start: 0.9242 (m-30) cc_final: 0.8785 (p0) REVERT: F 107 ASP cc_start: 0.9221 (p0) cc_final: 0.8894 (t0) REVERT: F 119 ARG cc_start: 0.9432 (mtm110) cc_final: 0.8808 (ptt90) REVERT: F 132 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8334 (tmm-80) REVERT: F 195 ASN cc_start: 0.9429 (m-40) cc_final: 0.8955 (p0) REVERT: F 239 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: A 11 LYS cc_start: 0.9452 (mppt) cc_final: 0.9105 (mptt) REVERT: A 77 GLN cc_start: 0.9483 (mt0) cc_final: 0.9182 (mt0) REVERT: A 97 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8812 (ttp80) REVERT: A 101 ASP cc_start: 0.9263 (t0) cc_final: 0.8912 (t0) REVERT: A 129 ASN cc_start: 0.8811 (t0) cc_final: 0.6915 (t0) REVERT: A 132 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8676 (ttp80) REVERT: A 143 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 203 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8936 (m-30) REVERT: B 128 HIS cc_start: 0.9207 (OUTLIER) cc_final: 0.8935 (p-80) REVERT: D 31 TRP cc_start: 0.9286 (m100) cc_final: 0.8927 (m100) REVERT: D 76 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9131 (mt-10) REVERT: D 79 TYR cc_start: 0.9276 (t80) cc_final: 0.9025 (t80) REVERT: D 110 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8429 (mpp80) REVERT: D 132 ARG cc_start: 0.8476 (tmm160) cc_final: 0.8104 (tmm160) REVERT: D 148 ARG cc_start: 0.8810 (mpp80) cc_final: 0.8369 (tpp80) REVERT: D 203 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8575 (m-30) REVERT: D 217 TYR cc_start: 0.9272 (OUTLIER) cc_final: 0.8584 (m-10) REVERT: I 3 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8234 (mm-40) REVERT: I 11 LYS cc_start: 0.9646 (mmmm) cc_final: 0.9437 (mmpt) REVERT: I 97 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8645 (tpt-90) REVERT: I 119 ARG cc_start: 0.9551 (ptm-80) cc_final: 0.9051 (ptp90) REVERT: I 129 ASN cc_start: 0.8744 (t0) cc_final: 0.8399 (t0) REVERT: I 139 GLU cc_start: 0.9424 (tp30) cc_final: 0.9121 (tp30) REVERT: J 112 PHE cc_start: 0.8539 (t80) cc_final: 0.8163 (OUTLIER) REVERT: J 185 LYS cc_start: 0.9146 (mmpt) cc_final: 0.8803 (mppt) REVERT: K 24 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.9015 (ttm110) REVERT: K 58 LEU cc_start: 0.9454 (mm) cc_final: 0.9190 (mp) REVERT: K 66 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8935 (pp) REVERT: K 73 ASP cc_start: 0.9123 (p0) cc_final: 0.8699 (p0) REVERT: K 77 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8784 (mp10) REVERT: K 101 ASP cc_start: 0.9222 (t0) cc_final: 0.8173 (p0) REVERT: K 110 ARG cc_start: 0.8881 (ttm110) cc_final: 0.8660 (ttm110) REVERT: K 132 ARG cc_start: 0.9334 (mmm160) cc_final: 0.8647 (tpm170) REVERT: K 148 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8320 (mmt90) REVERT: K 195 ASN cc_start: 0.9378 (m110) cc_final: 0.8765 (p0) REVERT: L 17 LEU cc_start: 0.9296 (mt) cc_final: 0.9076 (pp) REVERT: L 112 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8436 (t80) REVERT: L 132 ARG cc_start: 0.8987 (ttp80) cc_final: 0.8665 (tmm-80) REVERT: L 153 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8205 (mtp85) REVERT: L 154 MET cc_start: 0.8448 (mmm) cc_final: 0.7946 (tmm) REVERT: M 3 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8594 (mm-40) REVERT: M 14 LYS cc_start: 0.9703 (tptp) cc_final: 0.9461 (tptp) REVERT: M 47 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8357 (tp) REVERT: M 70 TRP cc_start: 0.8636 (m-90) cc_final: 0.8078 (t60) REVERT: M 97 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8871 (tpp80) REVERT: N 97 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8262 (tpm170) REVERT: N 154 MET cc_start: 0.8953 (tpp) cc_final: 0.8631 (tpp) REVERT: N 195 ASN cc_start: 0.9496 (m-40) cc_final: 0.9198 (p0) REVERT: O 101 ASP cc_start: 0.9344 (t0) cc_final: 0.9070 (t0) REVERT: O 132 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8439 (ttp80) REVERT: O 139 GLU cc_start: 0.9366 (tm-30) cc_final: 0.9094 (tm-30) REVERT: O 143 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8981 (tm-30) REVERT: O 150 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9231 (mp0) REVERT: O 196 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8738 (tp30) REVERT: P 26 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8376 (t) REVERT: P 132 ARG cc_start: 0.9348 (ttm170) cc_final: 0.8957 (ttp80) REVERT: Q 3 GLN cc_start: 0.8670 (mp10) cc_final: 0.8309 (mp10) REVERT: Q 11 LYS cc_start: 0.9448 (tppp) cc_final: 0.9062 (tmmm) REVERT: Q 17 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9185 (mp) REVERT: Q 73 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.9126 (p0) REVERT: Q 99 GLN cc_start: 0.9142 (mp10) cc_final: 0.8844 (mp10) REVERT: Q 101 ASP cc_start: 0.9074 (t0) cc_final: 0.8619 (t0) REVERT: Q 148 ARG cc_start: 0.8614 (mtt90) cc_final: 0.8406 (mtt-85) REVERT: Q 166 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: Q 209 TYR cc_start: 0.7942 (t80) cc_final: 0.7654 (t80) REVERT: R 120 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7836 (tm) REVERT: U 94 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9341 (mm) REVERT: U 96 ASN cc_start: 0.8490 (t0) cc_final: 0.8184 (t0) REVERT: U 99 GLN cc_start: 0.9280 (mp10) cc_final: 0.9054 (mm-40) REVERT: U 107 ASP cc_start: 0.9397 (m-30) cc_final: 0.9103 (p0) REVERT: U 130 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8920 (tpp) REVERT: U 156 LYS cc_start: 0.9354 (tttt) cc_final: 0.9031 (tttm) REVERT: V 119 ARG cc_start: 0.9398 (ptm-80) cc_final: 0.8994 (mtm110) REVERT: V 132 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8118 (tmm-80) REVERT: V 187 GLU cc_start: 0.9282 (mp0) cc_final: 0.8935 (mp0) REVERT: S 11 LYS cc_start: 0.9357 (mmtm) cc_final: 0.9137 (mmpt) REVERT: S 14 LYS cc_start: 0.9482 (tptp) cc_final: 0.9266 (tppp) REVERT: S 84 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8734 (ptmm) REVERT: S 101 ASP cc_start: 0.9433 (t0) cc_final: 0.9156 (t0) REVERT: S 139 GLU cc_start: 0.9432 (tp30) cc_final: 0.9149 (tp30) REVERT: S 154 MET cc_start: 0.9111 (mmm) cc_final: 0.8673 (mmm) REVERT: S 161 GLU cc_start: 0.8864 (tp30) cc_final: 0.8201 (tp30) REVERT: T 26 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.8944 (t) REVERT: T 161 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8847 (mm-30) outliers start: 267 outliers final: 131 residues processed: 711 average time/residue: 0.6953 time to fit residues: 613.3312 Evaluate side-chains 602 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 435 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 27 LEU Chi-restraints excluded: chain N residue 31 TRP Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 97 ARG Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 222 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 94 LEU Chi-restraints excluded: chain U residue 95 THR Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 121 LYS Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 130 MET Chi-restraints excluded: chain U residue 154 MET Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 161 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 154 optimal weight: 4.9990 chunk 528 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 510 optimal weight: 8.9990 chunk 427 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 273 optimal weight: 7.9990 chunk 518 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN K 8 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 ASN ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040579 restraints weight = 177308.839| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.63 r_work: 0.2702 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 46717 Z= 0.292 Angle : 0.723 12.057 63602 Z= 0.359 Chirality : 0.048 0.463 7106 Planarity : 0.004 0.071 7876 Dihedral : 8.569 74.889 6359 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.96 % Allowed : 28.05 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 5390 helix: 1.50 (0.13), residues: 1562 sheet: -1.10 (0.15), residues: 1276 loop : 0.37 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG T 132 TYR 0.025 0.002 TYR K 79 PHE 0.025 0.001 PHE O 5 TRP 0.014 0.001 TRP M 31 HIS 0.006 0.001 HIS K 8 Details of bonding type rmsd covalent geometry : bond 0.00672 (46717) covalent geometry : angle 0.72287 (63602) hydrogen bonds : bond 0.03766 ( 1592) hydrogen bonds : angle 4.84754 ( 4269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 452 time to evaluate : 1.112 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: G 11 LYS cc_start: 0.9578 (ttpt) cc_final: 0.9354 (ttpp) REVERT: G 14 LYS cc_start: 0.9670 (tptp) cc_final: 0.9462 (tmmt) REVERT: G 25 GLN cc_start: 0.9497 (tp40) cc_final: 0.8987 (mm-40) REVERT: G 88 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8562 (ptpt) REVERT: G 97 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8228 (ttt-90) REVERT: G 107 ASP cc_start: 0.9447 (m-30) cc_final: 0.9204 (t0) REVERT: G 119 ARG cc_start: 0.9043 (mtm110) cc_final: 0.8717 (ptm-80) REVERT: G 132 ARG cc_start: 0.9064 (tmm-80) cc_final: 0.8636 (tmm-80) REVERT: G 148 ARG cc_start: 0.8634 (mpt-90) cc_final: 0.8248 (mpt-90) REVERT: G 185 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8512 (ttpp) REVERT: H 122 TYR cc_start: 0.8651 (p90) cc_final: 0.8394 (p90) REVERT: E 26 SER cc_start: 0.9542 (OUTLIER) cc_final: 0.9278 (t) REVERT: E 77 GLN cc_start: 0.9596 (mt0) cc_final: 0.9297 (mt0) REVERT: E 94 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9071 (mm) REVERT: E 97 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8602 (ttp80) REVERT: E 101 ASP cc_start: 0.9374 (t0) cc_final: 0.8749 (t0) REVERT: E 119 ARG cc_start: 0.9255 (ptp90) cc_final: 0.8834 (ptp90) REVERT: E 132 ARG cc_start: 0.8948 (tmm-80) cc_final: 0.8617 (tmm-80) REVERT: F 12 ASP cc_start: 0.9267 (m-30) cc_final: 0.8846 (p0) REVERT: F 107 ASP cc_start: 0.9215 (p0) cc_final: 0.8896 (t0) REVERT: F 239 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: A 11 LYS cc_start: 0.9410 (mppt) cc_final: 0.9008 (mptt) REVERT: A 77 GLN cc_start: 0.9504 (mt0) cc_final: 0.9218 (mt0) REVERT: A 97 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8591 (tpp80) REVERT: A 129 ASN cc_start: 0.8906 (t0) cc_final: 0.7055 (t0) REVERT: A 132 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8690 (ttp80) REVERT: A 143 GLN cc_start: 0.9227 (tm-30) cc_final: 0.8803 (tm-30) REVERT: B 128 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.8914 (p-80) REVERT: C 67 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9051 (mmtp) REVERT: C 107 ASP cc_start: 0.9527 (m-30) cc_final: 0.9260 (t0) REVERT: D 31 TRP cc_start: 0.9315 (m100) cc_final: 0.9003 (m100) REVERT: D 76 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (mt-10) REVERT: D 203 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8581 (m-30) REVERT: D 217 TYR cc_start: 0.9309 (OUTLIER) cc_final: 0.8636 (m-10) REVERT: I 3 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8940 (mp10) REVERT: I 119 ARG cc_start: 0.9535 (ptm-80) cc_final: 0.9017 (ptp90) REVERT: I 129 ASN cc_start: 0.8828 (t0) cc_final: 0.8523 (t0) REVERT: I 197 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.9024 (pp30) REVERT: J 112 PHE cc_start: 0.8664 (t80) cc_final: 0.8302 (t80) REVERT: J 185 LYS cc_start: 0.9182 (mmpt) cc_final: 0.8912 (mppt) REVERT: K 24 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.9020 (ttm110) REVERT: K 110 ARG cc_start: 0.8867 (ttm110) cc_final: 0.8632 (ttm110) REVERT: K 148 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8403 (mmt90) REVERT: K 195 ASN cc_start: 0.9404 (m110) cc_final: 0.8807 (p0) REVERT: L 101 ASP cc_start: 0.9109 (t70) cc_final: 0.8770 (p0) REVERT: L 112 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8404 (t80) REVERT: L 132 ARG cc_start: 0.8995 (ttp80) cc_final: 0.8750 (ttp80) REVERT: L 154 MET cc_start: 0.8399 (mmm) cc_final: 0.7996 (tmm) REVERT: M 3 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8748 (mm-40) REVERT: M 14 LYS cc_start: 0.9678 (tptp) cc_final: 0.9345 (tptp) REVERT: M 18 GLU cc_start: 0.8495 (pm20) cc_final: 0.8208 (pm20) REVERT: N 15 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9378 (tp) REVERT: N 154 MET cc_start: 0.8926 (tpp) cc_final: 0.8642 (tpp) REVERT: N 185 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9162 (mppt) REVERT: N 195 ASN cc_start: 0.9474 (m-40) cc_final: 0.9213 (p0) REVERT: O 101 ASP cc_start: 0.9394 (t0) cc_final: 0.9101 (t0) REVERT: O 132 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8392 (ttp80) REVERT: O 139 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9119 (tm-30) REVERT: O 143 GLN cc_start: 0.9255 (tm-30) cc_final: 0.9010 (tm-30) REVERT: O 150 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9201 (mp0) REVERT: O 166 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: O 196 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9040 (tt0) REVERT: P 26 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8452 (t) REVERT: P 101 ASP cc_start: 0.9186 (t0) cc_final: 0.8953 (t0) REVERT: P 132 ARG cc_start: 0.9300 (ttm170) cc_final: 0.9009 (tmm160) REVERT: P 177 ASP cc_start: 0.9653 (p0) cc_final: 0.9442 (p0) REVERT: Q 3 GLN cc_start: 0.8799 (mp10) cc_final: 0.8501 (mp10) REVERT: Q 11 LYS cc_start: 0.9449 (tppp) cc_final: 0.9114 (tmmm) REVERT: Q 17 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9203 (mp) REVERT: Q 101 ASP cc_start: 0.9086 (t0) cc_final: 0.8684 (t0) REVERT: Q 166 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: Q 209 TYR cc_start: 0.8073 (t80) cc_final: 0.7709 (t80) REVERT: R 120 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7856 (tm) REVERT: R 148 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8713 (ttm110) REVERT: U 96 ASN cc_start: 0.8582 (t0) cc_final: 0.8242 (t0) REVERT: U 99 GLN cc_start: 0.9277 (mp10) cc_final: 0.9018 (mm-40) REVERT: U 107 ASP cc_start: 0.9428 (m-30) cc_final: 0.9137 (p0) REVERT: U 121 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8689 (tptt) REVERT: U 130 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8907 (tpp) REVERT: V 26 SER cc_start: 0.9320 (OUTLIER) cc_final: 0.9049 (t) REVERT: V 119 ARG cc_start: 0.9418 (ptm-80) cc_final: 0.9048 (mtm110) REVERT: V 132 ARG cc_start: 0.8641 (tmm-80) cc_final: 0.8006 (tmm160) REVERT: V 187 GLU cc_start: 0.9249 (mp0) cc_final: 0.8923 (mp0) REVERT: S 11 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9180 (mmpt) REVERT: S 101 ASP cc_start: 0.9475 (t0) cc_final: 0.9198 (t0) REVERT: S 139 GLU cc_start: 0.9448 (tp30) cc_final: 0.9172 (tp30) REVERT: S 154 MET cc_start: 0.9150 (mmm) cc_final: 0.8664 (mmm) REVERT: S 161 GLU cc_start: 0.9093 (tp30) cc_final: 0.8517 (tp30) REVERT: S 229 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.8945 (p) REVERT: T 26 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.8914 (t) REVERT: T 161 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8827 (mm-30) outliers start: 291 outliers final: 144 residues processed: 690 average time/residue: 0.4878 time to fit residues: 423.2003 Evaluate side-chains 587 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 409 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 181 HIS Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 197 GLN Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 247 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 188 ASP Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 229 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 20 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 95 THR Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 121 LYS Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 130 MET Chi-restraints excluded: chain U residue 147 VAL Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 181 HIS Chi-restraints excluded: chain S residue 11 LYS Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 229 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain T residue 161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 511 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 201 optimal weight: 0.0270 chunk 447 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 483 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.062859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042799 restraints weight = 174230.370| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.63 r_work: 0.2775 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46717 Z= 0.131 Angle : 0.687 14.893 63602 Z= 0.330 Chirality : 0.046 0.452 7106 Planarity : 0.004 0.090 7876 Dihedral : 8.390 73.838 6357 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.81 % Allowed : 29.75 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.12), residues: 5390 helix: 1.53 (0.13), residues: 1584 sheet: -1.02 (0.15), residues: 1276 loop : 0.48 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 132 TYR 0.025 0.001 TYR T 79 PHE 0.012 0.001 PHE L 57 TRP 0.015 0.001 TRP O 215 HIS 0.008 0.000 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00314 (46717) covalent geometry : angle 0.68741 (63602) hydrogen bonds : bond 0.03207 ( 1592) hydrogen bonds : angle 4.70590 ( 4269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 474 time to evaluate : 1.103 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: G 11 LYS cc_start: 0.9599 (ttpt) cc_final: 0.9375 (ttpp) REVERT: G 25 GLN cc_start: 0.9456 (tp40) cc_final: 0.8982 (mm-40) REVERT: G 88 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8525 (ptpt) REVERT: G 97 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8148 (ttt-90) REVERT: G 119 ARG cc_start: 0.9010 (mtm110) cc_final: 0.8755 (ptm-80) REVERT: G 124 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8979 (tp30) REVERT: G 132 ARG cc_start: 0.9052 (tmm-80) cc_final: 0.8780 (tmm-80) REVERT: G 148 ARG cc_start: 0.8581 (mpt-90) cc_final: 0.8194 (mpt-90) REVERT: G 185 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8291 (ttpp) REVERT: H 110 ARG cc_start: 0.8889 (ttm110) cc_final: 0.8598 (mtm110) REVERT: H 122 TYR cc_start: 0.8699 (p90) cc_final: 0.8454 (p90) REVERT: H 132 ARG cc_start: 0.9246 (tmm160) cc_final: 0.9025 (ppt170) REVERT: H 154 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8420 (mmm) REVERT: E 77 GLN cc_start: 0.9568 (mt0) cc_final: 0.9216 (mt0) REVERT: E 94 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9011 (mm) REVERT: E 97 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8595 (ttp80) REVERT: E 101 ASP cc_start: 0.9371 (t0) cc_final: 0.8735 (t0) REVERT: E 132 ARG cc_start: 0.8989 (tmm-80) cc_final: 0.8716 (tmm-80) REVERT: F 12 ASP cc_start: 0.9224 (m-30) cc_final: 0.8769 (p0) REVERT: F 107 ASP cc_start: 0.9255 (p0) cc_final: 0.8941 (t0) REVERT: F 119 ARG cc_start: 0.9468 (mtm110) cc_final: 0.8949 (ptt90) REVERT: F 195 ASN cc_start: 0.9414 (m-40) cc_final: 0.8962 (p0) REVERT: F 239 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8679 (pm20) REVERT: A 11 LYS cc_start: 0.9457 (mppt) cc_final: 0.9098 (mptt) REVERT: A 77 GLN cc_start: 0.9468 (mt0) cc_final: 0.9167 (mt0) REVERT: A 101 ASP cc_start: 0.9239 (t0) cc_final: 0.9030 (t0) REVERT: A 129 ASN cc_start: 0.8978 (t0) cc_final: 0.7134 (t0) REVERT: A 132 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8637 (ttp80) REVERT: A 143 GLN cc_start: 0.9144 (tm-30) cc_final: 0.8835 (tm-30) REVERT: A 203 ASP cc_start: 0.9208 (t0) cc_final: 0.8898 (m-30) REVERT: C 107 ASP cc_start: 0.9517 (m-30) cc_final: 0.9167 (t0) REVERT: D 31 TRP cc_start: 0.9347 (m100) cc_final: 0.8984 (m100) REVERT: D 76 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9180 (mp0) REVERT: D 120 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7517 (tp) REVERT: D 203 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8565 (m-30) REVERT: I 3 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8665 (mm-40) REVERT: I 97 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8632 (tpt-90) REVERT: I 119 ARG cc_start: 0.9519 (ptm-80) cc_final: 0.8983 (ptp90) REVERT: I 129 ASN cc_start: 0.8730 (t0) cc_final: 0.8494 (t0) REVERT: I 197 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8975 (pp30) REVERT: I 209 TYR cc_start: 0.9253 (t80) cc_final: 0.9026 (t80) REVERT: J 112 PHE cc_start: 0.8653 (t80) cc_final: 0.8296 (OUTLIER) REVERT: J 154 MET cc_start: 0.9358 (mpp) cc_final: 0.8999 (mmm) REVERT: J 185 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8867 (mppt) REVERT: K 24 ARG cc_start: 0.9303 (mtm-85) cc_final: 0.9017 (ttm110) REVERT: K 73 ASP cc_start: 0.9149 (p0) cc_final: 0.8779 (p0) REVERT: K 77 GLN cc_start: 0.9323 (OUTLIER) cc_final: 0.8923 (mp10) REVERT: K 101 ASP cc_start: 0.9178 (t0) cc_final: 0.8028 (p0) REVERT: K 110 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8653 (ttm110) REVERT: K 132 ARG cc_start: 0.9349 (mmm160) cc_final: 0.8647 (tpm170) REVERT: K 148 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8299 (mmt90) REVERT: K 195 ASN cc_start: 0.9370 (m110) cc_final: 0.8754 (p0) REVERT: L 3 GLN cc_start: 0.7975 (mp10) cc_final: 0.7751 (mp10) REVERT: L 112 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8364 (t80) REVERT: L 132 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8589 (tmm-80) REVERT: L 154 MET cc_start: 0.8445 (mmm) cc_final: 0.7890 (tmm) REVERT: M 3 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8589 (mm-40) REVERT: M 14 LYS cc_start: 0.9667 (tptp) cc_final: 0.9386 (tptp) REVERT: M 69 ASP cc_start: 0.9559 (m-30) cc_final: 0.8951 (m-30) REVERT: M 70 TRP cc_start: 0.8646 (m-90) cc_final: 0.8075 (t60) REVERT: M 97 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8882 (tpp80) REVERT: N 154 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8634 (tpp) REVERT: N 185 LYS cc_start: 0.9409 (mmmm) cc_final: 0.9130 (mppt) REVERT: N 195 ASN cc_start: 0.9477 (m-40) cc_final: 0.9178 (p0) REVERT: N 254 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8842 (mmm) REVERT: O 3 GLN cc_start: 0.9305 (mm-40) cc_final: 0.9101 (mp10) REVERT: O 101 ASP cc_start: 0.9354 (t0) cc_final: 0.9050 (t0) REVERT: O 132 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8424 (ttp80) REVERT: O 139 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9079 (tm-30) REVERT: O 143 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8915 (tm-30) REVERT: O 166 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8075 (tp30) REVERT: P 26 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8372 (t) REVERT: P 79 TYR cc_start: 0.9347 (t80) cc_final: 0.9143 (t80) REVERT: P 132 ARG cc_start: 0.9335 (ttm170) cc_final: 0.9010 (tmm160) REVERT: Q 3 GLN cc_start: 0.8780 (mp10) cc_final: 0.8348 (mp10) REVERT: Q 11 LYS cc_start: 0.9420 (tppp) cc_final: 0.9048 (tmmm) REVERT: Q 17 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9175 (mp) REVERT: Q 101 ASP cc_start: 0.9094 (t0) cc_final: 0.8662 (t0) REVERT: Q 148 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8361 (mtt-85) REVERT: Q 166 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: Q 209 TYR cc_start: 0.8101 (t80) cc_final: 0.7844 (t80) REVERT: R 120 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7866 (tm) REVERT: R 148 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8857 (ttm110) REVERT: U 12 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8530 (p0) REVERT: U 96 ASN cc_start: 0.8516 (t0) cc_final: 0.8101 (t0) REVERT: U 99 GLN cc_start: 0.9273 (mp10) cc_final: 0.8912 (mm-40) REVERT: U 107 ASP cc_start: 0.9411 (m-30) cc_final: 0.9128 (p0) REVERT: U 121 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8655 (tptt) REVERT: V 132 ARG cc_start: 0.8675 (tmm-80) cc_final: 0.8048 (tmm160) REVERT: S 11 LYS cc_start: 0.9373 (mmtm) cc_final: 0.9132 (mmpt) REVERT: S 101 ASP cc_start: 0.9452 (t0) cc_final: 0.9170 (t0) REVERT: S 139 GLU cc_start: 0.9429 (tp30) cc_final: 0.9137 (tp30) REVERT: S 154 MET cc_start: 0.9143 (mmm) cc_final: 0.8660 (mmm) REVERT: S 161 GLU cc_start: 0.9059 (tp30) cc_final: 0.8376 (tp30) REVERT: T 26 SER cc_start: 0.9357 (OUTLIER) cc_final: 0.8940 (t) outliers start: 235 outliers final: 120 residues processed: 666 average time/residue: 0.4607 time to fit residues: 385.6539 Evaluate side-chains 578 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 429 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 97 ARG Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 197 GLN Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 220 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 154 MET Chi-restraints excluded: chain N residue 254 MET Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 229 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 95 THR Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 121 LYS Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 130 MET Chi-restraints excluded: chain U residue 222 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 100 LEU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 229 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 164 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 196 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 389 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 382 optimal weight: 0.8980 chunk 496 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 GLN ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 ASN T 3 GLN ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041402 restraints weight = 175948.125| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.59 r_work: 0.2741 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 46717 Z= 0.216 Angle : 0.732 14.659 63602 Z= 0.355 Chirality : 0.047 0.449 7106 Planarity : 0.005 0.080 7876 Dihedral : 8.424 73.263 6356 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.81 % Allowed : 30.10 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.12), residues: 5390 helix: 1.51 (0.13), residues: 1584 sheet: -1.07 (0.15), residues: 1276 loop : 0.41 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 132 TYR 0.047 0.002 TYR L 79 PHE 0.021 0.001 PHE K 112 TRP 0.019 0.001 TRP T 72 HIS 0.007 0.001 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00504 (46717) covalent geometry : angle 0.73207 (63602) hydrogen bonds : bond 0.03425 ( 1592) hydrogen bonds : angle 4.69265 ( 4269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 454 time to evaluate : 1.202 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: G 11 LYS cc_start: 0.9592 (ttpt) cc_final: 0.9362 (ttpp) REVERT: G 25 GLN cc_start: 0.9474 (tp40) cc_final: 0.8984 (mm-40) REVERT: G 88 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8454 (ptpt) REVERT: G 97 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8165 (ttt-90) REVERT: G 107 ASP cc_start: 0.9412 (m-30) cc_final: 0.9206 (t0) REVERT: G 119 ARG cc_start: 0.9016 (mtm110) cc_final: 0.8738 (ptm-80) REVERT: G 132 ARG cc_start: 0.9065 (tmm-80) cc_final: 0.8575 (tmm-80) REVERT: G 148 ARG cc_start: 0.8587 (mpt-90) cc_final: 0.8279 (mpt-90) REVERT: H 122 TYR cc_start: 0.8722 (p90) cc_final: 0.8441 (p90) REVERT: H 153 ARG cc_start: 0.8398 (mtp-110) cc_final: 0.8127 (ttm-80) REVERT: E 26 SER cc_start: 0.9488 (OUTLIER) cc_final: 0.9275 (t) REVERT: E 46 GLN cc_start: 0.9498 (mt0) cc_final: 0.8785 (mp10) REVERT: E 94 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9040 (mm) REVERT: E 97 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8691 (ttp80) REVERT: E 101 ASP cc_start: 0.9381 (t0) cc_final: 0.8761 (t0) REVERT: E 119 ARG cc_start: 0.9236 (ptp90) cc_final: 0.8580 (ptp90) REVERT: E 132 ARG cc_start: 0.9008 (tmm-80) cc_final: 0.8729 (tmm-80) REVERT: F 12 ASP cc_start: 0.9247 (m-30) cc_final: 0.8790 (p0) REVERT: F 107 ASP cc_start: 0.9252 (p0) cc_final: 0.8934 (t0) REVERT: F 132 ARG cc_start: 0.8901 (ttp80) cc_final: 0.8620 (ttp80) REVERT: F 195 ASN cc_start: 0.9424 (m-40) cc_final: 0.8970 (p0) REVERT: F 239 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8644 (pm20) REVERT: A 11 LYS cc_start: 0.9431 (mppt) cc_final: 0.9028 (mptt) REVERT: A 77 GLN cc_start: 0.9469 (mt0) cc_final: 0.9157 (mt0) REVERT: A 129 ASN cc_start: 0.8978 (t0) cc_final: 0.7190 (t0) REVERT: A 132 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8676 (ttp80) REVERT: A 143 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 203 ASP cc_start: 0.9225 (t0) cc_final: 0.8923 (m-30) REVERT: B 132 ARG cc_start: 0.8712 (tmt-80) cc_final: 0.8448 (ttp80) REVERT: C 107 ASP cc_start: 0.9494 (m-30) cc_final: 0.9202 (t0) REVERT: D 31 TRP cc_start: 0.9379 (m100) cc_final: 0.9040 (m100) REVERT: D 76 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9114 (mt-10) REVERT: D 148 ARG cc_start: 0.8733 (mpp80) cc_final: 0.8387 (tpp80) REVERT: D 203 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8571 (m-30) REVERT: I 3 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8603 (mm-40) REVERT: I 95 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8546 (t) REVERT: I 119 ARG cc_start: 0.9526 (ptm-80) cc_final: 0.9192 (ttm110) REVERT: I 129 ASN cc_start: 0.8776 (t0) cc_final: 0.8256 (t0) REVERT: I 197 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9014 (pp30) REVERT: J 26 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.8735 (t) REVERT: J 112 PHE cc_start: 0.8703 (t80) cc_final: 0.8367 (t80) REVERT: J 185 LYS cc_start: 0.9149 (mmpt) cc_final: 0.8894 (mppt) REVERT: K 24 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8950 (ttm170) REVERT: K 110 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8611 (ttm110) REVERT: K 148 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8347 (mmt90) REVERT: K 195 ASN cc_start: 0.9381 (m110) cc_final: 0.8761 (p0) REVERT: L 112 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8391 (t80) REVERT: L 132 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8582 (tmm-80) REVERT: L 154 MET cc_start: 0.8446 (mmm) cc_final: 0.7942 (tmm) REVERT: M 3 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8637 (mm-40) REVERT: M 14 LYS cc_start: 0.9625 (tptp) cc_final: 0.9356 (tptp) REVERT: M 70 TRP cc_start: 0.8674 (m-90) cc_final: 0.8150 (t60) REVERT: M 95 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8341 (t) REVERT: M 97 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8808 (tpp80) REVERT: N 154 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8608 (tpp) REVERT: N 185 LYS cc_start: 0.9403 (mmmm) cc_final: 0.9146 (mppt) REVERT: N 195 ASN cc_start: 0.9476 (m-40) cc_final: 0.9188 (p0) REVERT: O 3 GLN cc_start: 0.9402 (mm-40) cc_final: 0.9202 (mp10) REVERT: O 101 ASP cc_start: 0.9366 (t0) cc_final: 0.9061 (t0) REVERT: O 132 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8447 (ttp80) REVERT: O 139 GLU cc_start: 0.9374 (tm-30) cc_final: 0.9087 (tm-30) REVERT: O 143 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8954 (tm-30) REVERT: O 166 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: P 26 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8404 (t) REVERT: P 69 ASP cc_start: 0.9159 (t0) cc_final: 0.8944 (p0) REVERT: P 79 TYR cc_start: 0.9352 (t80) cc_final: 0.9151 (t80) REVERT: P 101 ASP cc_start: 0.9180 (t0) cc_final: 0.8926 (t0) REVERT: P 132 ARG cc_start: 0.9302 (ttm170) cc_final: 0.8962 (tmm160) REVERT: P 177 ASP cc_start: 0.9634 (p0) cc_final: 0.9419 (p0) REVERT: Q 3 GLN cc_start: 0.8816 (mp10) cc_final: 0.8404 (mp10) REVERT: Q 11 LYS cc_start: 0.9435 (tppp) cc_final: 0.9090 (tmmm) REVERT: Q 17 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9191 (mp) REVERT: Q 69 ASP cc_start: 0.9249 (m-30) cc_final: 0.9022 (p0) REVERT: Q 101 ASP cc_start: 0.9097 (t0) cc_final: 0.8679 (t0) REVERT: Q 166 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: Q 209 TYR cc_start: 0.8260 (t80) cc_final: 0.7887 (t80) REVERT: R 120 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7823 (tm) REVERT: R 148 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8229 (mtp-110) REVERT: U 12 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8559 (p0) REVERT: U 26 SER cc_start: 0.9311 (OUTLIER) cc_final: 0.8518 (t) REVERT: U 96 ASN cc_start: 0.8543 (t0) cc_final: 0.8145 (t0) REVERT: U 99 GLN cc_start: 0.9267 (mp10) cc_final: 0.8892 (mm-40) REVERT: U 107 ASP cc_start: 0.9423 (m-30) cc_final: 0.9138 (p0) REVERT: U 121 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8680 (tptt) REVERT: V 119 ARG cc_start: 0.9386 (ptm-80) cc_final: 0.9059 (mtm110) REVERT: V 132 ARG cc_start: 0.8678 (tmm-80) cc_final: 0.8136 (tmm-80) REVERT: S 11 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9166 (mmpt) REVERT: S 101 ASP cc_start: 0.9463 (t0) cc_final: 0.9167 (t0) REVERT: S 139 GLU cc_start: 0.9445 (tp30) cc_final: 0.9163 (tp30) REVERT: S 154 MET cc_start: 0.9161 (mmm) cc_final: 0.8682 (mmm) REVERT: S 161 GLU cc_start: 0.9121 (tp30) cc_final: 0.8502 (tp30) REVERT: T 26 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.8896 (t) REVERT: T 101 ASP cc_start: 0.8935 (t0) cc_final: 0.8080 (p0) REVERT: T 161 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8828 (mm-30) outliers start: 235 outliers final: 142 residues processed: 646 average time/residue: 0.4479 time to fit residues: 363.4920 Evaluate side-chains 595 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 423 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ARG Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 197 GLN Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 128 HIS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 154 MET Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 229 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 95 THR Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 121 LYS Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 130 MET Chi-restraints excluded: chain U residue 222 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 229 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 161 GLU Chi-restraints excluded: chain T residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 53 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 511 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 chunk 349 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 491 optimal weight: 2.9990 chunk 398 optimal weight: 6.9990 chunk 518 optimal weight: 8.9990 chunk 483 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 8 HIS ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 GLN ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** N 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.041046 restraints weight = 176338.073| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.59 r_work: 0.2722 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 46717 Z= 0.234 Angle : 0.749 14.093 63602 Z= 0.366 Chirality : 0.048 0.487 7106 Planarity : 0.005 0.093 7876 Dihedral : 8.503 73.772 6356 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.38 % Allowed : 30.67 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 5390 helix: 1.45 (0.13), residues: 1584 sheet: -1.09 (0.15), residues: 1276 loop : 0.39 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 132 TYR 0.022 0.002 TYR K 79 PHE 0.052 0.001 PHE N 5 TRP 0.014 0.001 TRP O 215 HIS 0.004 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00545 (46717) covalent geometry : angle 0.74907 (63602) hydrogen bonds : bond 0.03521 ( 1592) hydrogen bonds : angle 4.73505 ( 4269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 439 time to evaluate : 1.142 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: G 11 LYS cc_start: 0.9592 (ttpt) cc_final: 0.9366 (ttpp) REVERT: G 25 GLN cc_start: 0.9482 (tp40) cc_final: 0.8989 (mm-40) REVERT: G 26 SER cc_start: 0.9577 (OUTLIER) cc_final: 0.9024 (p) REVERT: G 88 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8552 (ptpt) REVERT: G 119 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8728 (ptm-80) REVERT: G 132 ARG cc_start: 0.9066 (tmm-80) cc_final: 0.8578 (tmm-80) REVERT: G 148 ARG cc_start: 0.8597 (mpt-90) cc_final: 0.8281 (mpt-90) REVERT: H 110 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8675 (mtm110) REVERT: H 122 TYR cc_start: 0.8752 (p90) cc_final: 0.8428 (p90) REVERT: H 153 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8106 (ttm-80) REVERT: E 26 SER cc_start: 0.9502 (OUTLIER) cc_final: 0.9280 (t) REVERT: E 77 GLN cc_start: 0.9580 (mt0) cc_final: 0.9274 (mt0) REVERT: E 94 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9053 (mm) REVERT: E 97 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8575 (ttp80) REVERT: E 101 ASP cc_start: 0.9403 (t0) cc_final: 0.8795 (t0) REVERT: E 132 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8731 (tmm-80) REVERT: F 12 ASP cc_start: 0.9228 (m-30) cc_final: 0.8765 (p0) REVERT: F 107 ASP cc_start: 0.9225 (p0) cc_final: 0.8900 (t0) REVERT: F 119 ARG cc_start: 0.9432 (mtm110) cc_final: 0.8771 (ptt90) REVERT: F 195 ASN cc_start: 0.9418 (m-40) cc_final: 0.8973 (p0) REVERT: F 239 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8659 (pm20) REVERT: A 11 LYS cc_start: 0.9425 (mppt) cc_final: 0.9022 (mptt) REVERT: A 77 GLN cc_start: 0.9471 (mt0) cc_final: 0.9162 (mt0) REVERT: A 101 ASP cc_start: 0.9315 (t0) cc_final: 0.8999 (t0) REVERT: A 129 ASN cc_start: 0.9026 (t0) cc_final: 0.7825 (t0) REVERT: A 132 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8715 (ttp80) REVERT: A 143 GLN cc_start: 0.9203 (tm-30) cc_final: 0.8738 (tm-30) REVERT: B 17 LEU cc_start: 0.9290 (mm) cc_final: 0.9088 (mp) REVERT: C 107 ASP cc_start: 0.9498 (m-30) cc_final: 0.9209 (t0) REVERT: C 184 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9236 (tm) REVERT: D 31 TRP cc_start: 0.9388 (m100) cc_final: 0.9059 (m100) REVERT: D 76 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.9094 (mt-10) REVERT: D 203 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8523 (m-30) REVERT: I 3 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8772 (mp10) REVERT: I 95 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8591 (t) REVERT: I 119 ARG cc_start: 0.9518 (ptm-80) cc_final: 0.9201 (ttm110) REVERT: I 129 ASN cc_start: 0.8788 (t0) cc_final: 0.8259 (t0) REVERT: I 197 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8996 (pp30) REVERT: J 26 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.8745 (t) REVERT: J 112 PHE cc_start: 0.8722 (t80) cc_final: 0.8398 (t80) REVERT: J 132 ARG cc_start: 0.9125 (tmm-80) cc_final: 0.8884 (ttp80) REVERT: J 185 LYS cc_start: 0.9173 (mmpt) cc_final: 0.8930 (mppt) REVERT: K 24 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.8982 (ttm170) REVERT: K 110 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8628 (ttm110) REVERT: K 132 ARG cc_start: 0.9370 (mmm160) cc_final: 0.8714 (tpm170) REVERT: K 148 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8383 (mmt90) REVERT: K 195 ASN cc_start: 0.9386 (m110) cc_final: 0.8786 (p0) REVERT: L 112 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8257 (t80) REVERT: L 132 ARG cc_start: 0.8986 (ttp80) cc_final: 0.8593 (tmm-80) REVERT: L 154 MET cc_start: 0.8477 (mmm) cc_final: 0.7999 (tmm) REVERT: M 3 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8681 (mm-40) REVERT: M 14 LYS cc_start: 0.9612 (tptp) cc_final: 0.9312 (tptp) REVERT: M 70 TRP cc_start: 0.8695 (m-90) cc_final: 0.8135 (t60) REVERT: M 120 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8585 (tt) REVERT: N 154 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8608 (tpp) REVERT: N 185 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9142 (mppt) REVERT: N 195 ASN cc_start: 0.9479 (m-40) cc_final: 0.9194 (p0) REVERT: O 101 ASP cc_start: 0.9388 (t0) cc_final: 0.9084 (t0) REVERT: O 132 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8439 (ttp80) REVERT: O 139 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9091 (tm-30) REVERT: O 143 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8986 (tm-30) REVERT: O 150 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9124 (mp0) REVERT: O 166 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: O 185 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8912 (ptmt) REVERT: O 196 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8988 (tp30) REVERT: P 26 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8402 (t) REVERT: P 79 TYR cc_start: 0.9337 (t80) cc_final: 0.9129 (t80) REVERT: P 132 ARG cc_start: 0.9293 (ttm170) cc_final: 0.8940 (tmm160) REVERT: Q 3 GLN cc_start: 0.8784 (mp10) cc_final: 0.8281 (mp10) REVERT: Q 11 LYS cc_start: 0.9425 (tppp) cc_final: 0.9075 (tmmm) REVERT: Q 17 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9184 (mp) REVERT: Q 101 ASP cc_start: 0.9080 (t0) cc_final: 0.8661 (t0) REVERT: Q 148 ARG cc_start: 0.8674 (mtt90) cc_final: 0.8370 (mtt-85) REVERT: Q 166 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: Q 209 TYR cc_start: 0.8303 (t80) cc_final: 0.7970 (t80) REVERT: R 120 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7869 (tm) REVERT: R 132 ARG cc_start: 0.9315 (tmm160) cc_final: 0.9010 (pmt-80) REVERT: R 148 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8211 (mtp-110) REVERT: U 12 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8578 (p0) REVERT: U 26 SER cc_start: 0.9337 (OUTLIER) cc_final: 0.8546 (t) REVERT: U 96 ASN cc_start: 0.8558 (t0) cc_final: 0.8156 (t0) REVERT: U 99 GLN cc_start: 0.9273 (mp10) cc_final: 0.8880 (mm-40) REVERT: U 107 ASP cc_start: 0.9421 (m-30) cc_final: 0.9153 (p0) REVERT: U 121 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8691 (tptt) REVERT: U 130 MET cc_start: 0.9227 (tpt) cc_final: 0.8977 (tpp) REVERT: U 132 ARG cc_start: 0.9024 (tmm-80) cc_final: 0.8805 (tmm-80) REVERT: V 119 ARG cc_start: 0.9360 (ptm-80) cc_final: 0.9031 (mtm110) REVERT: V 132 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8108 (tmm160) REVERT: S 11 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9175 (mmpt) REVERT: S 101 ASP cc_start: 0.9472 (t0) cc_final: 0.9173 (t0) REVERT: S 124 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8799 (mm-30) REVERT: S 139 GLU cc_start: 0.9445 (tp30) cc_final: 0.9159 (tp30) REVERT: S 154 MET cc_start: 0.9176 (mmm) cc_final: 0.8683 (mmm) REVERT: S 161 GLU cc_start: 0.9155 (tp30) cc_final: 0.8537 (tp30) REVERT: T 26 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.8881 (t) REVERT: T 101 ASP cc_start: 0.8971 (t0) cc_final: 0.7920 (p0) REVERT: T 161 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8831 (mm-30) outliers start: 214 outliers final: 142 residues processed: 619 average time/residue: 0.4567 time to fit residues: 353.5928 Evaluate side-chains 575 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 401 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain I residue 197 GLN Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 128 HIS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 197 GLN Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 220 LEU Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain N residue 17 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 154 MET Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 229 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 229 THR Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 121 LYS Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 222 LEU Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 229 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 161 GLU Chi-restraints excluded: chain T residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 366 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 271 optimal weight: 0.9980 chunk 458 optimal weight: 7.9990 chunk 173 optimal weight: 0.3980 chunk 294 optimal weight: 7.9990 chunk 264 optimal weight: 0.3980 chunk 330 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN N 8 HIS ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041760 restraints weight = 176086.011| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.64 r_work: 0.2745 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 46717 Z= 0.174 Angle : 0.741 15.450 63602 Z= 0.359 Chirality : 0.047 0.457 7106 Planarity : 0.005 0.100 7876 Dihedral : 8.433 73.584 6355 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.79 % Allowed : 31.33 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.12), residues: 5390 helix: 1.46 (0.13), residues: 1584 sheet: -1.05 (0.15), residues: 1276 loop : 0.43 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG T 132 TYR 0.025 0.001 TYR M 122 PHE 0.043 0.001 PHE N 5 TRP 0.016 0.001 TRP C 70 HIS 0.003 0.000 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00414 (46717) covalent geometry : angle 0.74088 (63602) hydrogen bonds : bond 0.03336 ( 1592) hydrogen bonds : angle 4.69556 ( 4269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10780 Ramachandran restraints generated. 5390 Oldfield, 0 Emsley, 5390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 451 time to evaluate : 1.084 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: G 11 LYS cc_start: 0.9599 (ttpt) cc_final: 0.9384 (ttpp) REVERT: G 25 GLN cc_start: 0.9479 (tp40) cc_final: 0.8972 (mm-40) REVERT: G 26 SER cc_start: 0.9578 (OUTLIER) cc_final: 0.9029 (p) REVERT: G 88 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8568 (ptpt) REVERT: G 119 ARG cc_start: 0.8969 (mtm110) cc_final: 0.8739 (ptm-80) REVERT: G 132 ARG cc_start: 0.9073 (tmm-80) cc_final: 0.8851 (tmm-80) REVERT: G 148 ARG cc_start: 0.8587 (mpt-90) cc_final: 0.7925 (mmt90) REVERT: H 122 TYR cc_start: 0.8784 (p90) cc_final: 0.8429 (p90) REVERT: H 153 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8083 (ttm-80) REVERT: E 26 SER cc_start: 0.9477 (OUTLIER) cc_final: 0.9271 (t) REVERT: E 77 GLN cc_start: 0.9586 (mt0) cc_final: 0.9275 (mt0) REVERT: E 94 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9042 (mm) REVERT: E 97 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8625 (ttp80) REVERT: E 101 ASP cc_start: 0.9405 (t0) cc_final: 0.8885 (t0) REVERT: E 132 ARG cc_start: 0.9012 (tmm-80) cc_final: 0.8734 (tmm-80) REVERT: F 12 ASP cc_start: 0.9188 (m-30) cc_final: 0.8728 (p0) REVERT: F 107 ASP cc_start: 0.9237 (p0) cc_final: 0.8922 (t0) REVERT: F 127 PRO cc_start: 0.9590 (Cg_exo) cc_final: 0.9378 (Cg_endo) REVERT: F 132 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8667 (ttp80) REVERT: F 195 ASN cc_start: 0.9407 (m-40) cc_final: 0.8970 (p0) REVERT: F 239 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: A 11 LYS cc_start: 0.9446 (mppt) cc_final: 0.9040 (mptt) REVERT: A 77 GLN cc_start: 0.9457 (mt0) cc_final: 0.9139 (mt0) REVERT: A 119 ARG cc_start: 0.9109 (pmm-80) cc_final: 0.8883 (pmm-80) REVERT: A 129 ASN cc_start: 0.9067 (t0) cc_final: 0.7775 (t0) REVERT: A 132 ARG cc_start: 0.9138 (ttp80) cc_final: 0.8620 (ttp80) REVERT: A 143 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8877 (tm-30) REVERT: B 17 LEU cc_start: 0.9261 (mm) cc_final: 0.9045 (mp) REVERT: C 107 ASP cc_start: 0.9484 (m-30) cc_final: 0.9183 (t0) REVERT: C 184 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9238 (tm) REVERT: D 31 TRP cc_start: 0.9389 (m100) cc_final: 0.9124 (m100) REVERT: D 76 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9085 (mt-10) REVERT: D 203 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: I 3 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8816 (mp10) REVERT: I 95 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8610 (t) REVERT: I 119 ARG cc_start: 0.9500 (ptm-80) cc_final: 0.9176 (ttm110) REVERT: I 129 ASN cc_start: 0.8763 (t0) cc_final: 0.8270 (t0) REVERT: I 132 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8501 (ttp80) REVERT: I 197 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.9008 (pp30) REVERT: J 26 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.8695 (t) REVERT: J 112 PHE cc_start: 0.8739 (t80) cc_final: 0.8431 (t80) REVERT: J 132 ARG cc_start: 0.9144 (tmm-80) cc_final: 0.8907 (ttp80) REVERT: J 154 MET cc_start: 0.9358 (mpp) cc_final: 0.9007 (mmm) REVERT: J 185 LYS cc_start: 0.9163 (mmpt) cc_final: 0.8944 (mppt) REVERT: K 24 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.9051 (ttm110) REVERT: K 73 ASP cc_start: 0.9233 (p0) cc_final: 0.8771 (p0) REVERT: K 77 GLN cc_start: 0.9374 (mt0) cc_final: 0.8840 (mp10) REVERT: K 79 TYR cc_start: 0.9303 (t80) cc_final: 0.9052 (t80) REVERT: K 132 ARG cc_start: 0.9369 (mmm160) cc_final: 0.8648 (tpm170) REVERT: K 148 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8336 (mmt90) REVERT: K 195 ASN cc_start: 0.9362 (m110) cc_final: 0.8731 (p0) REVERT: L 112 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8264 (t80) REVERT: L 132 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8569 (tmm-80) REVERT: L 154 MET cc_start: 0.8497 (mmm) cc_final: 0.7976 (tmm) REVERT: M 3 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8603 (mm-40) REVERT: M 14 LYS cc_start: 0.9606 (tptp) cc_final: 0.9329 (tptp) REVERT: M 69 ASP cc_start: 0.9606 (m-30) cc_final: 0.8964 (m-30) REVERT: M 70 TRP cc_start: 0.8690 (m-90) cc_final: 0.8147 (t60) REVERT: M 120 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8597 (tt) REVERT: N 31 TRP cc_start: 0.9094 (OUTLIER) cc_final: 0.8876 (m100) REVERT: N 154 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8614 (tpp) REVERT: N 185 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9137 (mppt) REVERT: N 195 ASN cc_start: 0.9468 (m-40) cc_final: 0.9162 (p0) REVERT: O 101 ASP cc_start: 0.9388 (t0) cc_final: 0.9110 (t0) REVERT: O 132 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8450 (ttp80) REVERT: O 139 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9059 (tm-30) REVERT: O 143 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8947 (tm-30) REVERT: O 166 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: O 185 LYS cc_start: 0.9166 (ptmm) cc_final: 0.8923 (ptmt) REVERT: P 26 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8358 (t) REVERT: P 69 ASP cc_start: 0.9158 (t0) cc_final: 0.8937 (p0) REVERT: P 101 ASP cc_start: 0.9143 (t0) cc_final: 0.8858 (t0) REVERT: P 132 ARG cc_start: 0.9298 (ttm170) cc_final: 0.8951 (tmm160) REVERT: P 177 ASP cc_start: 0.9619 (p0) cc_final: 0.9408 (p0) REVERT: Q 3 GLN cc_start: 0.8818 (mp10) cc_final: 0.8324 (mp10) REVERT: Q 11 LYS cc_start: 0.9436 (tppp) cc_final: 0.9118 (tmmm) REVERT: Q 17 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9177 (mp) REVERT: Q 101 ASP cc_start: 0.9070 (t0) cc_final: 0.8653 (t0) REVERT: Q 148 ARG cc_start: 0.8677 (mtt90) cc_final: 0.8318 (mtt-85) REVERT: Q 166 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: Q 209 TYR cc_start: 0.8246 (t80) cc_final: 0.7939 (t80) REVERT: R 120 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7850 (tm) REVERT: R 132 ARG cc_start: 0.9319 (tmm160) cc_final: 0.9016 (pmt-80) REVERT: R 148 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8736 (mtp-110) REVERT: U 12 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8600 (p0) REVERT: U 26 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.8525 (t) REVERT: U 96 ASN cc_start: 0.8527 (t0) cc_final: 0.8109 (t0) REVERT: U 99 GLN cc_start: 0.9266 (mp10) cc_final: 0.8868 (mm-40) REVERT: U 107 ASP cc_start: 0.9412 (m-30) cc_final: 0.9155 (p0) REVERT: U 121 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8708 (tptt) REVERT: U 132 ARG cc_start: 0.9047 (tmm-80) cc_final: 0.8817 (tmm-80) REVERT: V 26 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8542 (p) REVERT: V 119 ARG cc_start: 0.9333 (ptm-80) cc_final: 0.9001 (mtm110) REVERT: V 132 ARG cc_start: 0.8728 (tmm-80) cc_final: 0.8127 (tmm160) REVERT: S 11 LYS cc_start: 0.9381 (mmtm) cc_final: 0.9143 (mmpt) REVERT: S 101 ASP cc_start: 0.9478 (t0) cc_final: 0.9184 (t0) REVERT: S 139 GLU cc_start: 0.9432 (tp30) cc_final: 0.9146 (tp30) REVERT: S 154 MET cc_start: 0.9179 (mmm) cc_final: 0.8733 (mmm) REVERT: S 155 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8764 (pp) REVERT: S 161 GLU cc_start: 0.9154 (tp30) cc_final: 0.8524 (tp30) REVERT: T 26 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.8902 (t) REVERT: T 84 LYS cc_start: 0.9649 (mmpt) cc_final: 0.9377 (mmtp) REVERT: T 101 ASP cc_start: 0.8875 (t0) cc_final: 0.7952 (p0) outliers start: 185 outliers final: 126 residues processed: 605 average time/residue: 0.4529 time to fit residues: 342.3133 Evaluate side-chains 581 residues out of total 4884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 423 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 97 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 197 GLN Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 222 LEU Chi-restraints excluded: chain L residue 11 LYS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 112 PHE Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 128 HIS Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 197 GLN Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 254 MET Chi-restraints excluded: chain N residue 31 TRP Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 147 VAL Chi-restraints excluded: chain N residue 154 MET Chi-restraints excluded: chain O residue 26 SER Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 106 THR Chi-restraints excluded: chain O residue 107 ASP Chi-restraints excluded: chain O residue 147 VAL Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 229 THR Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain P residue 147 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 229 THR Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 123 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 166 GLU Chi-restraints excluded: chain Q residue 176 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 148 ARG Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 62 SER Chi-restraints excluded: chain U residue 66 LEU Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain U residue 106 THR Chi-restraints excluded: chain U residue 121 LYS Chi-restraints excluded: chain U residue 123 VAL Chi-restraints excluded: chain U residue 222 LEU Chi-restraints excluded: chain V residue 26 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 66 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 106 THR Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 229 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 164 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 529 random chunks: chunk 526 optimal weight: 2.9990 chunk 435 optimal weight: 6.9990 chunk 512 optimal weight: 1.9990 chunk 322 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 493 optimal weight: 0.9980 chunk 477 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN B 55 GLN ** J 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 ASN K 63 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 ASN ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 195 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.063128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043088 restraints weight = 177225.845| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.68 r_work: 0.2776 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 46717 Z= 0.131 Angle : 0.735 15.621 63602 Z= 0.354 Chirality : 0.047 0.461 7106 Planarity : 0.005 0.097 7876 Dihedral : 8.265 72.842 6352 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.44 % Allowed : 31.92 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.12), residues: 5390 helix: 1.48 (0.13), residues: 1584 sheet: -0.98 (0.15), residues: 1276 loop : 0.47 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 132 TYR 0.029 0.001 TYR N 56 PHE 0.040 0.001 PHE N 5 TRP 0.017 0.001 TRP C 70 HIS 0.004 0.000 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00316 (46717) covalent geometry : angle 0.73528 (63602) hydrogen bonds : bond 0.03118 ( 1592) hydrogen bonds : angle 4.65449 ( 4269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13106.44 seconds wall clock time: 224 minutes 18.61 seconds (13458.61 seconds total)