Starting phenix.real_space_refine on Tue Aug 26 10:20:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wk3_37594/08_2025/8wk3_37594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wk3_37594/08_2025/8wk3_37594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wk3_37594/08_2025/8wk3_37594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wk3_37594/08_2025/8wk3_37594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wk3_37594/08_2025/8wk3_37594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wk3_37594/08_2025/8wk3_37594.map" } resolution = 3.3 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= -0.003 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 235 5.16 5 C 23026 2.51 5 N 6159 2.21 5 O 6823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.04s 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: 36243 Number of models: 1 Model: "" Number of chains: 43 Chain: "K" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 300 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Chain: "L" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 557 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 557 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 557 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "P" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 550 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 848 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "S" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 848 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "T" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 863 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain breaks: 1 Chain: "U" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "E" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1945 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 15, 'TRANS': 237} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1614 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "C" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "c" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "e" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "g" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "i" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "k" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 103 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 4, 'TRANS': 11} Chain: "a" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "m" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1804 Classifications: {'peptide': 248} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 231} Chain: "n" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain: "o" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1820 Classifications: {'peptide': 250} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 233} Chain: "p" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1820 Classifications: {'peptide': 250} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 233} Chain: "q" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1812 Classifications: {'peptide': 249} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 232} Chain: "Y" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1614 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "A" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "Z" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "b" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 81 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Chain: "F" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "d" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 133 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 5, 'TRANS': 14} Chain: "f" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "j" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 133 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 5, 'TRANS': 14} Chain: "l" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "J" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "V" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "D" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "X" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 969 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "W" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 964 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Time building chain proxies: 8.01, per 1000 atoms: 0.22 Number of scatterers: 36243 At special positions: 0 Unit cell: (127.2, 128.4, 250.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 235 16.00 O 6823 8.00 N 6159 7.00 C 23026 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 476.8 nanoseconds 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8992 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 56 sheets defined 61.0% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'K' and resid 67 through 101 Processing helix chain 'L' and resid 34 through 61 Processing helix chain 'L' and resid 67 through 101 Processing helix chain 'M' and resid 33 through 61 Processing helix chain 'M' and resid 67 through 100 Processing helix chain 'N' and resid 33 through 61 Processing helix chain 'N' and resid 67 through 101 Processing helix chain 'O' and resid 33 through 62 Processing helix chain 'O' and resid 67 through 101 Processing helix chain 'P' and resid 33 through 62 Processing helix chain 'P' and resid 67 through 101 Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 9 through 32 Processing helix chain 'Q' and resid 44 through 55 Processing helix chain 'Q' and resid 101 through 135 removed outlier: 4.208A pdb=" N VAL Q 133 " --> pdb=" O GLY Q 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 32 removed outlier: 3.613A pdb=" N LEU R 9 " --> pdb=" O LEU R 5 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN R 12 " --> pdb=" O ALA R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 55 Processing helix chain 'R' and resid 101 through 135 removed outlier: 3.598A pdb=" N LEU R 134 " --> pdb=" O MET R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 9 through 32 Processing helix chain 'S' and resid 44 through 55 Processing helix chain 'S' and resid 101 through 135 removed outlier: 3.516A pdb=" N LEU S 134 " --> pdb=" O MET S 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 32 removed outlier: 3.645A pdb=" N LEU T 9 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN T 12 " --> pdb=" O ALA T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 56 Processing helix chain 'T' and resid 101 through 135 Processing helix chain 'U' and resid 4 through 32 removed outlier: 4.770A pdb=" N PHE U 11 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN U 12 " --> pdb=" O ALA U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 44 through 54 Processing helix chain 'U' and resid 101 through 135 removed outlier: 3.598A pdb=" N LEU U 134 " --> pdb=" O MET U 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 28 removed outlier: 3.730A pdb=" N TRP E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TRP E 18 " --> pdb=" O HIS E 14 " (cutoff:3.500A) Proline residue: E 19 - end of helix Processing helix chain 'E' and resid 39 through 55 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 67 through 106 removed outlier: 4.396A pdb=" N ALA E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 4.010A pdb=" N VAL E 114 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 140 Processing helix chain 'E' and resid 141 through 157 removed outlier: 4.284A pdb=" N PHE E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS E 155 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 156 " --> pdb=" O ASP E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.913A pdb=" N MET E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 206 removed outlier: 3.715A pdb=" N ILE E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Proline residue: E 189 - end of helix removed outlier: 3.557A pdb=" N THR E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU E 193 " --> pdb=" O PRO E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 233 removed outlier: 3.652A pdb=" N LEU E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.754A pdb=" N PHE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER E 256 " --> pdb=" O ALA E 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 51 removed outlier: 3.568A pdb=" N LEU I 51 " --> pdb=" O PHE I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 62 removed outlier: 3.646A pdb=" N THR I 62 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 78 Processing helix chain 'I' and resid 85 through 112 Proline residue: I 103 - end of helix Processing helix chain 'I' and resid 112 through 118 Processing helix chain 'I' and resid 122 through 141 removed outlier: 4.045A pdb=" N GLN I 132 " --> pdb=" O ASP I 128 " (cutoff:3.500A) Proline residue: I 133 - end of helix removed outlier: 3.716A pdb=" N GLN I 141 " --> pdb=" O PHE I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 154 Processing helix chain 'I' and resid 161 through 165 removed outlier: 4.057A pdb=" N VAL I 165 " --> pdb=" O PRO I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 190 Proline residue: I 172 - end of helix removed outlier: 3.703A pdb=" N THR I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 208 Processing helix chain 'I' and resid 213 through 229 removed outlier: 3.653A pdb=" N ILE I 217 " --> pdb=" O PRO I 213 " (cutoff:3.500A) Proline residue: I 220 - end of helix Processing helix chain 'I' and resid 230 through 242 Processing helix chain 'C' and resid 2 through 42 removed outlier: 4.483A pdb=" N MET C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 50 through 88 Proline residue: C 67 - end of helix Proline residue: C 85 - end of helix removed outlier: 3.914A pdb=" N ILE C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 315 through 319 removed outlier: 3.882A pdb=" N GLN c 319 " --> pdb=" O LEU c 316 " (cutoff:3.500A) Processing helix chain 'g' and resid 314 through 318 removed outlier: 3.550A pdb=" N ASN g 318 " --> pdb=" O ALA g 315 " (cutoff:3.500A) Processing helix chain 'k' and resid 315 through 319 removed outlier: 3.689A pdb=" N GLN k 319 " --> pdb=" O LEU k 316 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 30 Processing helix chain 'a' and resid 97 through 130 removed outlier: 3.693A pdb=" N GLU a 101 " --> pdb=" O ASP a 97 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER a 124 " --> pdb=" O ASN a 120 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET a 125 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU a 130 " --> pdb=" O MET a 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 28 removed outlier: 3.635A pdb=" N ASN m 28 " --> pdb=" O SER m 24 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 155 removed outlier: 3.949A pdb=" N VAL m 155 " --> pdb=" O PRO m 152 " (cutoff:3.500A) Processing helix chain 'm' and resid 182 through 190 removed outlier: 3.749A pdb=" N GLU m 188 " --> pdb=" O GLU m 184 " (cutoff:3.500A) Processing helix chain 'm' and resid 212 through 249 Processing helix chain 'n' and resid 4 through 28 removed outlier: 3.764A pdb=" N GLY n 10 " --> pdb=" O TYR n 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU n 16 " --> pdb=" O ALA n 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 151 through 155 removed outlier: 3.639A pdb=" N VAL n 155 " --> pdb=" O PRO n 152 " (cutoff:3.500A) Processing helix chain 'n' and resid 182 through 190 removed outlier: 3.560A pdb=" N GLU n 188 " --> pdb=" O GLU n 184 " (cutoff:3.500A) Processing helix chain 'n' and resid 212 through 247 removed outlier: 3.967A pdb=" N MET n 229 " --> pdb=" O ARG n 225 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY n 242 " --> pdb=" O ASP n 238 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG n 243 " --> pdb=" O GLU n 239 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA n 244 " --> pdb=" O ASN n 240 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 28 removed outlier: 3.702A pdb=" N GLY o 10 " --> pdb=" O TYR o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 151 through 155 Processing helix chain 'o' and resid 167 through 169 No H-bonds generated for 'chain 'o' and resid 167 through 169' Processing helix chain 'o' and resid 182 through 190 Processing helix chain 'o' and resid 212 through 245 Processing helix chain 'o' and resid 246 through 249 Processing helix chain 'p' and resid 3 through 28 removed outlier: 3.646A pdb=" N THR p 7 " --> pdb=" O HIS p 3 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN p 28 " --> pdb=" O SER p 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 155 removed outlier: 3.891A pdb=" N VAL p 155 " --> pdb=" O PRO p 152 " (cutoff:3.500A) Processing helix chain 'p' and resid 167 through 169 No H-bonds generated for 'chain 'p' and resid 167 through 169' Processing helix chain 'p' and resid 182 through 190 Processing helix chain 'p' and resid 212 through 245 Processing helix chain 'p' and resid 246 through 249 Processing helix chain 'q' and resid 3 through 27 removed outlier: 3.691A pdb=" N ALA q 8 " --> pdb=" O ALA q 4 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET q 9 " --> pdb=" O ILE q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 167 through 169 No H-bonds generated for 'chain 'q' and resid 167 through 169' Processing helix chain 'q' and resid 182 through 190 Processing helix chain 'q' and resid 212 through 245 Processing helix chain 'Y' and resid 4 through 30 removed outlier: 3.831A pdb=" N ASP Y 8 " --> pdb=" O LEU Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 130 Processing helix chain 'H' and resid 39 through 53 removed outlier: 3.635A pdb=" N PHE H 53 " --> pdb=" O THR H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 62 removed outlier: 3.663A pdb=" N THR H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 78 Processing helix chain 'H' and resid 85 through 112 Proline residue: H 103 - end of helix Processing helix chain 'H' and resid 112 through 118 Processing helix chain 'H' and resid 122 through 141 removed outlier: 3.774A pdb=" N GLN H 132 " --> pdb=" O ASP H 128 " (cutoff:3.500A) Proline residue: H 133 - end of helix Processing helix chain 'H' and resid 143 through 154 Processing helix chain 'H' and resid 166 through 190 Proline residue: H 172 - end of helix Processing helix chain 'H' and resid 190 through 207 removed outlier: 3.558A pdb=" N LEU H 207 " --> pdb=" O VAL H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 229 removed outlier: 4.397A pdb=" N ILE H 217 " --> pdb=" O PRO H 213 " (cutoff:3.500A) Proline residue: H 220 - end of helix Processing helix chain 'H' and resid 230 through 242 Processing helix chain 'A' and resid 2 through 43 Proline residue: A 23 - end of helix removed outlier: 3.689A pdb=" N VAL A 27 " --> pdb=" O PRO A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 84 Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'B' and resid 2 through 43 Proline residue: B 23 - end of helix removed outlier: 4.055A pdb=" N VAL B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.751A pdb=" N LEU B 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 50 through 83 removed outlier: 3.985A pdb=" N LYS B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Proline residue: B 67 - end of helix removed outlier: 3.868A pdb=" N LEU B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 removed outlier: 4.218A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 30 removed outlier: 4.096A pdb=" N ASP Z 8 " --> pdb=" O LEU Z 4 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 130 removed outlier: 3.905A pdb=" N LEU Z 130 " --> pdb=" O MET Z 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 51 Processing helix chain 'G' and resid 53 through 62 Processing helix chain 'G' and resid 63 through 78 removed outlier: 3.549A pdb=" N ILE G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 112 Proline residue: G 103 - end of helix Processing helix chain 'G' and resid 112 through 118 Processing helix chain 'G' and resid 122 through 141 removed outlier: 3.750A pdb=" N ALA G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN G 132 " --> pdb=" O ASP G 128 " (cutoff:3.500A) Proline residue: G 133 - end of helix removed outlier: 3.662A pdb=" N GLN G 141 " --> pdb=" O PHE G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 154 Processing helix chain 'G' and resid 161 through 165 Processing helix chain 'G' and resid 166 through 190 Proline residue: G 172 - end of helix Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 213 through 229 removed outlier: 4.144A pdb=" N ILE G 217 " --> pdb=" O PRO G 213 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing helix chain 'G' and resid 230 through 244 removed outlier: 3.535A pdb=" N TYR G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 53 removed outlier: 3.598A pdb=" N THR F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.710A pdb=" N GLY F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 112 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 112 through 119 removed outlier: 3.900A pdb=" N SER F 117 " --> pdb=" O TYR F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 142 removed outlier: 3.651A pdb=" N ALA F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 143 through 153 removed outlier: 3.646A pdb=" N LEU F 147 " --> pdb=" O ARG F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 207 Proline residue: F 172 - end of helix Proline residue: F 192 - end of helix Processing helix chain 'F' and resid 213 through 229 removed outlier: 4.114A pdb=" N ILE F 217 " --> pdb=" O PRO F 213 " (cutoff:3.500A) Proline residue: F 220 - end of helix Processing helix chain 'F' and resid 230 through 242 removed outlier: 3.770A pdb=" N LEU F 234 " --> pdb=" O ASP F 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 51 Processing helix chain 'J' and resid 53 through 61 Processing helix chain 'J' and resid 63 through 79 removed outlier: 3.668A pdb=" N ILE J 67 " --> pdb=" O SER J 63 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY J 79 " --> pdb=" O ARG J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 101 Processing helix chain 'J' and resid 101 through 112 Processing helix chain 'J' and resid 112 through 118 Processing helix chain 'J' and resid 122 through 141 removed outlier: 3.796A pdb=" N LEU J 127 " --> pdb=" O MET J 123 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP J 128 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN J 132 " --> pdb=" O ASP J 128 " (cutoff:3.500A) Proline residue: J 133 - end of helix removed outlier: 3.643A pdb=" N GLN J 141 " --> pdb=" O PHE J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 154 removed outlier: 3.601A pdb=" N ALA J 154 " --> pdb=" O PHE J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 Processing helix chain 'J' and resid 166 through 207 Proline residue: J 172 - end of helix removed outlier: 3.883A pdb=" N ILE J 191 " --> pdb=" O PHE J 187 " (cutoff:3.500A) Proline residue: J 192 - end of helix removed outlier: 3.749A pdb=" N ASP J 197 " --> pdb=" O PHE J 193 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU J 207 " --> pdb=" O VAL J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 229 removed outlier: 4.057A pdb=" N ILE J 217 " --> pdb=" O PRO J 213 " (cutoff:3.500A) Proline residue: J 220 - end of helix Processing helix chain 'J' and resid 230 through 244 removed outlier: 3.644A pdb=" N LEU J 235 " --> pdb=" O GLY J 231 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 30 removed outlier: 3.788A pdb=" N ASP V 8 " --> pdb=" O LEU V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 131 Processing helix chain 'D' and resid 2 through 43 Proline residue: D 23 - end of helix Processing helix chain 'D' and resid 50 through 84 removed outlier: 4.149A pdb=" N LYS D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 56 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'X' and resid 3 through 30 removed outlier: 3.857A pdb=" N PHE X 7 " --> pdb=" O LEU X 3 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP X 8 " --> pdb=" O LEU X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 130 removed outlier: 3.578A pdb=" N LEU X 130 " --> pdb=" O MET X 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 30 Processing helix chain 'W' and resid 97 through 130 Processing sheet with id=AA1, first strand: chain 'Q' and resid 41 through 42 Processing sheet with id=AA2, first strand: chain 'R' and resid 41 through 42 Processing sheet with id=AA3, first strand: chain 'S' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'T' and resid 41 through 42 Processing sheet with id=AA5, first strand: chain 'U' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'a' and resid 33 through 35 removed outlier: 7.333A pdb=" N ALA q 43 " --> pdb=" O VAL a 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 45 through 52 removed outlier: 5.972A pdb=" N GLN a 46 " --> pdb=" O VAL a 67 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL a 67 " --> pdb=" O GLN a 46 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL a 48 " --> pdb=" O ALA a 65 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA a 65 " --> pdb=" O VAL a 48 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY a 61 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 75 through 78 Processing sheet with id=AA9, first strand: chain 'm' and resid 40 through 45 Processing sheet with id=AB1, first strand: chain 'm' and resid 71 through 73 Processing sheet with id=AB2, first strand: chain 'm' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'm' and resid 97 through 100 Processing sheet with id=AB4, first strand: chain 'm' and resid 106 through 107 Processing sheet with id=AB5, first strand: chain 'm' and resid 134 through 137 removed outlier: 6.847A pdb=" N ILE m 143 " --> pdb=" O VAL m 158 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA m 156 " --> pdb=" O ALA m 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'n' and resid 55 through 60 removed outlier: 6.709A pdb=" N LEU n 41 " --> pdb=" O SER X 33 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR X 35 " --> pdb=" O LEU n 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 71 through 72 Processing sheet with id=AB9, first strand: chain 'n' and resid 80 through 82 Processing sheet with id=AC1, first strand: chain 'n' and resid 97 through 100 Processing sheet with id=AC2, first strand: chain 'n' and resid 106 through 107 Processing sheet with id=AC3, first strand: chain 'n' and resid 121 through 122 Processing sheet with id=AC4, first strand: chain 'n' and resid 134 through 137 removed outlier: 3.807A pdb=" N GLY n 159 " --> pdb=" O ILE n 143 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA n 145 " --> pdb=" O PRO n 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'n' and resid 171 through 173 Processing sheet with id=AC6, first strand: chain 'o' and resid 40 through 45 Processing sheet with id=AC7, first strand: chain 'o' and resid 71 through 73 Processing sheet with id=AC8, first strand: chain 'o' and resid 80 through 82 Processing sheet with id=AC9, first strand: chain 'o' and resid 97 through 100 Processing sheet with id=AD1, first strand: chain 'o' and resid 105 through 107 Processing sheet with id=AD2, first strand: chain 'o' and resid 121 through 122 Processing sheet with id=AD3, first strand: chain 'o' and resid 134 through 137 removed outlier: 6.732A pdb=" N ILE o 143 " --> pdb=" O VAL o 158 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA o 156 " --> pdb=" O ALA o 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'o' and resid 171 through 173 Processing sheet with id=AD5, first strand: chain 'p' and resid 55 through 60 removed outlier: 7.792A pdb=" N LEU p 41 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'p' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'p' and resid 80 through 82 Processing sheet with id=AD8, first strand: chain 'p' and resid 97 through 100 Processing sheet with id=AD9, first strand: chain 'p' and resid 106 through 107 Processing sheet with id=AE1, first strand: chain 'p' and resid 121 through 122 Processing sheet with id=AE2, first strand: chain 'p' and resid 134 through 137 removed outlier: 3.896A pdb=" N GLY p 159 " --> pdb=" O ILE p 143 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA p 145 " --> pdb=" O PRO p 157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'p' and resid 171 through 173 Processing sheet with id=AE4, first strand: chain 'q' and resid 71 through 72 Processing sheet with id=AE5, first strand: chain 'q' and resid 80 through 82 Processing sheet with id=AE6, first strand: chain 'q' and resid 97 through 100 Processing sheet with id=AE7, first strand: chain 'q' and resid 105 through 107 Processing sheet with id=AE8, first strand: chain 'q' and resid 121 through 122 removed outlier: 3.509A pdb=" N GLY q 125 " --> pdb=" O GLY q 122 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'q' and resid 134 through 137 removed outlier: 3.506A pdb=" N LEU q 146 " --> pdb=" O GLU q 134 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE q 143 " --> pdb=" O VAL q 158 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'q' and resid 171 through 173 Processing sheet with id=AF2, first strand: chain 'Y' and resid 45 through 51 removed outlier: 4.245A pdb=" N SER Y 66 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN Y 50 " --> pdb=" O VAL Y 64 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL Y 64 " --> pdb=" O GLN Y 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 75 through 78 Processing sheet with id=AF4, first strand: chain 'Z' and resid 45 through 52 removed outlier: 6.204A pdb=" N GLN Z 46 " --> pdb=" O VAL Z 67 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL Z 67 " --> pdb=" O GLN Z 46 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL Z 48 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 75 through 78 Processing sheet with id=AF6, first strand: chain 'V' and resid 45 through 52 removed outlier: 4.337A pdb=" N SER V 66 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLN V 50 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL V 64 " --> pdb=" O GLN V 50 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP V 52 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL V 62 " --> pdb=" O ASP V 52 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 75 through 78 Processing sheet with id=AF8, first strand: chain 'X' and resid 45 through 50 removed outlier: 4.225A pdb=" N SER X 66 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN X 50 " --> pdb=" O VAL X 64 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL X 64 " --> pdb=" O GLN X 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 75 through 78 Processing sheet with id=AG1, first strand: chain 'W' and resid 45 through 51 removed outlier: 6.131A pdb=" N GLN W 46 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL W 67 " --> pdb=" O GLN W 46 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL W 48 " --> pdb=" O ALA W 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 75 through 78 2383 hydrogen bonds defined for protein. 6993 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: 7.04 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 4 1.19 - 1.35: 12123 1.35 - 1.51: 10183 1.51 - 1.67: 14041 1.67 - 1.84: 470 Bond restraints: 36821 Sorted by residual: bond pdb=" CG PRO f 331 " pdb=" CD PRO f 331 " ideal model delta sigma weight residual 1.503 1.032 0.471 3.40e-02 8.65e+02 1.92e+02 bond pdb=" CG PRO X 73 " pdb=" CD PRO X 73 " ideal model delta sigma weight residual 1.503 1.082 0.421 3.40e-02 8.65e+02 1.53e+02 bond pdb=" C MET E 185 " pdb=" O MET E 185 " ideal model delta sigma weight residual 1.236 1.349 -0.112 1.15e-02 7.56e+03 9.56e+01 bond pdb=" CB PRO X 73 " pdb=" CG PRO X 73 " ideal model delta sigma weight residual 1.492 1.113 0.379 5.00e-02 4.00e+02 5.75e+01 bond pdb=" C ASN E 182 " pdb=" O ASN E 182 " ideal model delta sigma weight residual 1.236 1.319 -0.083 1.25e-02 6.40e+03 4.41e+01 ... (remaining 36816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.75: 50049 14.75 - 29.51: 5 29.51 - 44.26: 0 44.26 - 59.01: 0 59.01 - 73.77: 1 Bond angle restraints: 50055 Sorted by residual: angle pdb=" CB PRO X 73 " pdb=" CG PRO X 73 " pdb=" CD PRO X 73 " ideal model delta sigma weight residual 106.10 179.87 -73.77 3.20e+00 9.77e-02 5.31e+02 angle pdb=" N PRO X 73 " pdb=" CD PRO X 73 " pdb=" CG PRO X 73 " ideal model delta sigma weight residual 103.20 75.01 28.19 1.50e+00 4.44e-01 3.53e+02 angle pdb=" N PRO f 331 " pdb=" CD PRO f 331 " pdb=" CG PRO f 331 " ideal model delta sigma weight residual 103.20 79.05 24.15 1.50e+00 4.44e-01 2.59e+02 angle pdb=" CA PRO X 73 " pdb=" CB PRO X 73 " pdb=" CG PRO X 73 " ideal model delta sigma weight residual 104.50 77.42 27.08 1.90e+00 2.77e-01 2.03e+02 angle pdb=" CA PRO F 162 " pdb=" N PRO F 162 " pdb=" CD PRO F 162 " ideal model delta sigma weight residual 112.00 94.66 17.34 1.40e+00 5.10e-01 1.53e+02 ... (remaining 50050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 19395 18.06 - 36.11: 2472 36.11 - 54.17: 549 54.17 - 72.23: 142 72.23 - 90.28: 23 Dihedral angle restraints: 22581 sinusoidal: 8703 harmonic: 13878 Sorted by residual: dihedral pdb=" CD ARG a 110 " pdb=" NE ARG a 110 " pdb=" CZ ARG a 110 " pdb=" NH1 ARG a 110 " ideal model delta sinusoidal sigma weight residual 0.00 -64.36 64.36 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" CD ARG Q 106 " pdb=" NE ARG Q 106 " pdb=" CZ ARG Q 106 " pdb=" NH1 ARG Q 106 " ideal model delta sinusoidal sigma weight residual 0.00 -55.57 55.57 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CD ARG q 160 " pdb=" NE ARG q 160 " pdb=" CZ ARG q 160 " pdb=" NH1 ARG q 160 " ideal model delta sinusoidal sigma weight residual 0.00 51.79 -51.79 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 22578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4800 0.051 - 0.103: 997 0.103 - 0.154: 171 0.154 - 0.206: 28 0.206 - 0.257: 5 Chirality restraints: 6001 Sorted by residual: chirality pdb=" CB VAL q 155 " pdb=" CA VAL q 155 " pdb=" CG1 VAL q 155 " pdb=" CG2 VAL q 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASN n 153 " pdb=" N ASN n 153 " pdb=" C ASN n 153 " pdb=" CB ASN n 153 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA PRO E 189 " pdb=" N PRO E 189 " pdb=" C PRO E 189 " pdb=" CB PRO E 189 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 5998 not shown) Planarity restraints: 6520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG a 110 " 0.994 9.50e-02 1.11e+02 4.45e-01 1.20e+02 pdb=" NE ARG a 110 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG a 110 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG a 110 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG a 110 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 106 " -0.890 9.50e-02 1.11e+02 3.99e-01 9.65e+01 pdb=" NE ARG Q 106 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG Q 106 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 106 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 106 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG q 160 " 0.866 9.50e-02 1.11e+02 3.88e-01 9.15e+01 pdb=" NE ARG q 160 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG q 160 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG q 160 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG q 160 " 0.025 2.00e-02 2.50e+03 ... (remaining 6517 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 369 2.62 - 3.19: 32086 3.19 - 3.76: 57071 3.76 - 4.33: 73428 4.33 - 4.90: 126953 Nonbonded interactions: 289907 Sorted by model distance: nonbonded pdb=" O VAL e 312 " pdb=" OG SER e 317 " model vdw 2.049 3.040 nonbonded pdb=" O ALA I 206 " pdb=" OG1 THR D 48 " model vdw 2.083 3.040 nonbonded pdb=" NH1 ARG Q 88 " pdb=" OE2 GLU Q 105 " model vdw 2.099 3.120 nonbonded pdb=" OG SER p 249 " pdb=" OE1 GLU Y 117 " model vdw 2.106 3.040 nonbonded pdb=" OD1 ASN P 69 " pdb=" OH TYR V 112 " model vdw 2.112 3.040 ... (remaining 289902 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' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 37 through 243) selection = (chain 'H' and resid 37 through 243) selection = (chain 'I' and resid 37 through 243) selection = (chain 'J' and resid 37 through 243) } ncs_group { reference = chain 'L' selection = (chain 'M' and resid 33 through 104) selection = (chain 'N' and resid 33 through 104) selection = (chain 'O' and resid 33 through 104) selection = (chain 'P' and resid 33 through 104) } ncs_group { reference = (chain 'Q' and (resid 3 through 54 or resid 83 through 136)) selection = (chain 'R' and (resid 3 through 54 or resid 83 through 136)) selection = (chain 'S' and (resid 3 through 54 or resid 83 through 136)) selection = (chain 'T' and (resid 3 through 54 or resid 83 through 136)) selection = chain 'U' } ncs_group { reference = (chain 'V' and resid 3 through 134) selection = chain 'W' selection = (chain 'X' and resid 3 through 134) selection = (chain 'Y' and resid 3 through 134) selection = (chain 'Z' and resid 3 through 134) selection = (chain 'a' and resid 3 through 134) } ncs_group { reference = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain 'd' selection = (chain 'f' and resid 311 through 330) selection = (chain 'h' and resid 311 through 330) selection = chain 'j' selection = (chain 'l' and resid 311 through 330) } ncs_group { reference = chain 'm' selection = (chain 'n' and resid 2 through 249) selection = (chain 'o' and resid 2 through 249) selection = (chain 'p' and resid 2 through 249) selection = (chain 'q' and resid 2 through 249) } 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: 10.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 30.730 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.270 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.471 36821 Z= 0.273 Angle : 0.846 73.765 50055 Z= 0.470 Chirality : 0.044 0.257 6001 Planarity : 0.014 0.445 6520 Dihedral : 17.012 90.284 13589 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.09 % Favored : 96.57 % Rotamer: Outliers : 1.11 % Allowed : 21.49 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.85 (0.12), residues: 4751 helix: 2.41 (0.10), residues: 2786 sheet: -0.15 (0.28), residues: 317 loop : -0.60 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 10 TYR 0.017 0.001 TYR Z 112 PHE 0.034 0.002 PHE E 101 TRP 0.029 0.002 TRP B 68 HIS 0.004 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00590 (36821) covalent geometry : angle 0.84568 (50055) hydrogen bonds : bond 0.12180 ( 2383) hydrogen bonds : angle 5.00785 ( 6993) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 858 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: U 96 ASP cc_start: 0.8329 (p0) cc_final: 0.7804 (p0) REVERT: E 96 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7722 (mtt180) REVERT: m 150 ASP cc_start: 0.4518 (OUTLIER) cc_final: 0.4311 (m-30) REVERT: m 239 GLU cc_start: 0.8013 (tt0) cc_final: 0.7598 (tp30) REVERT: m 247 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7248 (mp) REVERT: n 225 ARG cc_start: 0.8283 (mpt-90) cc_final: 0.7117 (mmm-85) REVERT: n 231 MET cc_start: 0.8820 (mmp) cc_final: 0.8587 (mmm) REVERT: o 217 MET cc_start: 0.8349 (mmt) cc_final: 0.7993 (mmt) REVERT: o 232 LYS cc_start: 0.8396 (tptp) cc_final: 0.6979 (mttt) REVERT: o 243 ARG cc_start: 0.8467 (ptp-170) cc_final: 0.8234 (ptp90) REVERT: Y 101 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: H 143 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.6309 (mpt180) REVERT: A 15 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7854 (ttpp) REVERT: G 140 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7773 (tpt170) REVERT: G 162 PRO cc_start: 0.7315 (OUTLIER) cc_final: 0.6892 (Cg_endo) REVERT: G 236 MET cc_start: 0.8583 (mtp) cc_final: 0.8147 (mtp) outliers start: 43 outliers final: 11 residues processed: 874 average time/residue: 0.2064 time to fit residues: 297.8008 Evaluate side-chains 846 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 828 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 97 GLN Chi-restraints excluded: chain Q residue 101 ASP Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 150 ASP Chi-restraints excluded: chain m residue 247 LEU Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 143 ARG Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain G residue 140 ARG Chi-restraints excluded: chain G residue 162 PRO Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain l residue 318 ASN Chi-restraints excluded: chain J residue 230 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0870 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 103 GLN L 90 ASN M 103 GLN O 39 HIS O 55 GLN O 97 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN R 23 GLN R 29 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN S 32 ASN S 92 GLN T 17 ASN T 21 GLN T 32 ASN U 13 GLN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 318 ASN a 5 ASN a 57 GLN a 115 ASN m 102 ASN n 210 ASN n 240 ASN o 14 GLN o 18 GLN o 28 ASN o 116 GLN o 186 GLN p 28 ASN p 37 GLN p 210 ASN p 240 ASN q 18 GLN q 112 GLN q 246 GLN Y 30 ASN H 36 GLN B 39 GLN Z 17 GLN Z 30 ASN Z 71 GLN G 87 GLN F 119 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 324 ASN l 318 ASN l 324 ASN J 114 GLN J 155 ASN V 30 ASN D 39 GLN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 50 GLN X 57 GLN W 22 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130880 restraints weight = 48753.397| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.66 r_work: 0.3386 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36821 Z= 0.120 Angle : 0.558 7.940 50055 Z= 0.278 Chirality : 0.039 0.170 6001 Planarity : 0.005 0.079 6520 Dihedral : 4.705 60.409 5130 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 2.49 % Allowed : 20.20 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.34 (0.12), residues: 4751 helix: 2.81 (0.10), residues: 2817 sheet: -0.06 (0.28), residues: 322 loop : -0.42 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG q 180 TYR 0.020 0.001 TYR Z 112 PHE 0.023 0.001 PHE E 101 TRP 0.012 0.001 TRP B 68 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00267 (36821) covalent geometry : angle 0.55808 (50055) hydrogen bonds : bond 0.04273 ( 2383) hydrogen bonds : angle 3.77277 ( 6993) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 873 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: P 69 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8203 (m-40) REVERT: P 75 MET cc_start: 0.8143 (tpp) cc_final: 0.7639 (mmt) REVERT: S 96 ASP cc_start: 0.8357 (p0) cc_final: 0.8125 (p0) REVERT: U 87 TYR cc_start: 0.9294 (m-80) cc_final: 0.9042 (m-80) REVERT: U 103 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: E 96 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7649 (mtt180) REVERT: E 170 MET cc_start: 0.7275 (mmt) cc_final: 0.6630 (mmt) REVERT: E 185 MET cc_start: 0.7291 (mmt) cc_final: 0.7053 (mmt) REVERT: E 229 MET cc_start: 0.7690 (ppp) cc_final: 0.7422 (ppp) REVERT: a 123 LYS cc_start: 0.8041 (tppt) cc_final: 0.7737 (tptt) REVERT: n 165 LYS cc_start: 0.8751 (tttt) cc_final: 0.8279 (ttmt) REVERT: n 225 ARG cc_start: 0.8464 (mpt-90) cc_final: 0.7021 (mmm160) REVERT: o 94 ASP cc_start: 0.8811 (p0) cc_final: 0.8582 (p0) REVERT: o 184 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: o 217 MET cc_start: 0.8300 (mmt) cc_final: 0.7974 (mmt) REVERT: o 232 LYS cc_start: 0.8262 (tptp) cc_final: 0.6820 (mttt) REVERT: p 66 MET cc_start: 0.8707 (mmt) cc_final: 0.8481 (mmt) REVERT: p 202 MET cc_start: 0.8145 (ttm) cc_final: 0.7541 (ttm) REVERT: Y 101 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: A 15 LYS cc_start: 0.8208 (tmmm) cc_final: 0.7764 (ttpp) REVERT: G 138 MET cc_start: 0.9047 (mtm) cc_final: 0.8683 (mtp) REVERT: G 140 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7592 (tpt170) REVERT: G 178 GLU cc_start: 0.8534 (tp30) cc_final: 0.8273 (tp30) REVERT: G 236 MET cc_start: 0.8555 (mtp) cc_final: 0.8349 (mtp) REVERT: F 211 MET cc_start: 0.7597 (mmp) cc_final: 0.7133 (mmp) REVERT: j 324 ASN cc_start: 0.7288 (OUTLIER) cc_final: 0.6849 (p0) REVERT: J 146 ASP cc_start: 0.6833 (m-30) cc_final: 0.6603 (m-30) REVERT: J 205 MET cc_start: 0.8147 (tpt) cc_final: 0.7614 (tpp) REVERT: X 52 ASP cc_start: 0.7618 (p0) cc_final: 0.7351 (p0) outliers start: 97 outliers final: 49 residues processed: 927 average time/residue: 0.2007 time to fit residues: 307.9247 Evaluate side-chains 877 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 822 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain g residue 316 LEU Chi-restraints excluded: chain a residue 125 MET Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 184 GLU Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain q residue 163 LEU Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain Y residue 30 ASN Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain G residue 140 ARG Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain l residue 330 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 256 optimal weight: 0.6980 chunk 371 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 76 GLN L 90 ASN O 55 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN R 23 GLN R 92 GLN T 32 ASN T 132 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 230 GLN p 37 GLN Y 30 ASN Y 115 ASN B 39 GLN Z 30 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN X 22 ASN X 50 GLN X 57 GLN X 113 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.148220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127269 restraints weight = 49190.031| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.69 r_work: 0.3326 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36821 Z= 0.164 Angle : 0.561 6.860 50055 Z= 0.277 Chirality : 0.041 0.144 6001 Planarity : 0.005 0.069 6520 Dihedral : 4.163 60.041 5098 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.57 % Favored : 97.35 % Rotamer: Outliers : 3.01 % Allowed : 20.25 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.38 (0.12), residues: 4751 helix: 2.84 (0.10), residues: 2813 sheet: -0.18 (0.27), residues: 333 loop : -0.37 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 180 TYR 0.021 0.001 TYR X 112 PHE 0.017 0.001 PHE E 101 TRP 0.007 0.001 TRP p 87 HIS 0.003 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00396 (36821) covalent geometry : angle 0.56131 (50055) hydrogen bonds : bond 0.04435 ( 2383) hydrogen bonds : angle 3.74316 ( 6993) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 853 time to evaluate : 1.414 Fit side-chains REVERT: P 69 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8181 (m-40) REVERT: P 75 MET cc_start: 0.8266 (tpp) cc_final: 0.7740 (mmt) REVERT: S 96 ASP cc_start: 0.8461 (p0) cc_final: 0.8210 (p0) REVERT: T 117 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: E 88 MET cc_start: 0.8007 (tpt) cc_final: 0.7394 (mmm) REVERT: E 96 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7721 (mtt180) REVERT: I 106 ASP cc_start: 0.8388 (m-30) cc_final: 0.8035 (m-30) REVERT: C 8 MET cc_start: 0.7592 (tpt) cc_final: 0.7234 (tpp) REVERT: a 82 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8914 (m-40) REVERT: a 123 LYS cc_start: 0.8196 (tppt) cc_final: 0.7920 (tppt) REVERT: n 225 ARG cc_start: 0.8517 (mpt-90) cc_final: 0.7001 (mmm160) REVERT: o 217 MET cc_start: 0.8398 (mmt) cc_final: 0.8029 (mmt) REVERT: o 232 LYS cc_start: 0.8332 (tptp) cc_final: 0.6931 (mttt) REVERT: p 202 MET cc_start: 0.8239 (ttm) cc_final: 0.7680 (ttm) REVERT: p 243 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7790 (mtt90) REVERT: q 228 GLU cc_start: 0.7926 (mt-10) cc_final: 0.6875 (tt0) REVERT: Y 101 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: A 15 LYS cc_start: 0.8269 (tmmm) cc_final: 0.7789 (ttpp) REVERT: B 39 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6596 (tt0) REVERT: Z 127 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8429 (mp) REVERT: G 140 ARG cc_start: 0.8211 (ptt-90) cc_final: 0.7560 (tpt170) REVERT: j 324 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6896 (p0) REVERT: J 146 ASP cc_start: 0.6844 (m-30) cc_final: 0.6612 (m-30) REVERT: J 205 MET cc_start: 0.8392 (tpt) cc_final: 0.7774 (tpp) REVERT: X 52 ASP cc_start: 0.7690 (p0) cc_final: 0.7398 (p0) outliers start: 117 outliers final: 72 residues processed: 917 average time/residue: 0.1985 time to fit residues: 302.8354 Evaluate side-chains 908 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 828 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 132 ASN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain g residue 316 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 125 MET Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain n residue 209 SER Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 201 ILE Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain p residue 9 MET Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 30 ASN Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain l residue 330 THR Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 227 optimal weight: 2.9990 chunk 407 optimal weight: 6.9990 chunk 134 optimal weight: 0.1980 chunk 252 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 309 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 403 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN O 55 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN T 132 ASN U 108 GLN E 61 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 ASN p 37 GLN Y 30 ASN B 39 GLN Z 30 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN V 30 ASN X 57 GLN X 113 GLN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.129663 restraints weight = 49029.433| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.61 r_work: 0.3192 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 36821 Z= 0.189 Angle : 0.580 6.863 50055 Z= 0.287 Chirality : 0.041 0.145 6001 Planarity : 0.005 0.067 6520 Dihedral : 3.951 49.211 5088 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 3.91 % Allowed : 20.10 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.26 (0.12), residues: 4751 helix: 2.75 (0.10), residues: 2812 sheet: -0.22 (0.27), residues: 323 loop : -0.42 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG m 54 TYR 0.023 0.002 TYR X 112 PHE 0.019 0.002 PHE C 51 TRP 0.008 0.001 TRP p 87 HIS 0.004 0.001 HIS n 3 Details of bonding type rmsd covalent geometry : bond 0.00458 (36821) covalent geometry : angle 0.58021 (50055) hydrogen bonds : bond 0.04628 ( 2383) hydrogen bonds : angle 3.78688 ( 6993) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 837 time to evaluate : 1.444 Fit side-chains REVERT: L 82 MET cc_start: 0.8336 (tpt) cc_final: 0.8028 (tpp) REVERT: P 69 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: S 48 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: S 96 ASP cc_start: 0.8546 (p0) cc_final: 0.8284 (p0) REVERT: T 117 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: E 96 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7718 (mtt180) REVERT: E 179 ILE cc_start: 0.8541 (mt) cc_final: 0.8334 (mp) REVERT: C 8 MET cc_start: 0.7694 (tpt) cc_final: 0.7365 (tpp) REVERT: a 82 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8859 (m-40) REVERT: a 123 LYS cc_start: 0.8041 (tppt) cc_final: 0.7834 (tppt) REVERT: m 56 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8517 (mt) REVERT: m 186 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: n 225 ARG cc_start: 0.8506 (mpt180) cc_final: 0.6893 (mmm160) REVERT: o 232 LYS cc_start: 0.8495 (tptp) cc_final: 0.7103 (mttt) REVERT: p 202 MET cc_start: 0.8343 (ttm) cc_final: 0.7814 (ttm) REVERT: p 243 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7788 (mtt90) REVERT: q 42 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8667 (ptp-110) REVERT: q 228 GLU cc_start: 0.8021 (mt-10) cc_final: 0.6925 (tt0) REVERT: Y 52 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8169 (t0) REVERT: Y 101 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: A 15 LYS cc_start: 0.8280 (tmmm) cc_final: 0.7779 (ttpp) REVERT: Z 127 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8424 (mp) REVERT: G 140 ARG cc_start: 0.8324 (ptt-90) cc_final: 0.7513 (tpt170) REVERT: J 121 ILE cc_start: 0.8178 (mt) cc_final: 0.7888 (tt) REVERT: J 146 ASP cc_start: 0.7106 (m-30) cc_final: 0.6860 (m-30) REVERT: J 205 MET cc_start: 0.8582 (tpt) cc_final: 0.7926 (tpp) REVERT: D 9 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: X 52 ASP cc_start: 0.7668 (p0) cc_final: 0.7348 (p0) outliers start: 152 outliers final: 109 residues processed: 921 average time/residue: 0.2054 time to fit residues: 315.0805 Evaluate side-chains 940 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 819 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain O residue 101 SER Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 132 ASN Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain g residue 316 LEU Chi-restraints excluded: chain a residue 38 ASP Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 125 MET Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 16 LEU Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 186 GLN Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain n residue 209 SER Chi-restraints excluded: chain n residue 237 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 201 ILE Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain p residue 9 MET Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 249 SER Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 201 ILE Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain h residue 328 ILE Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain l residue 330 THR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 84 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 197 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 377 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 132 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 GLN Z 30 ASN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN X 57 GLN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131175 restraints weight = 48695.891| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.60 r_work: 0.3198 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36821 Z= 0.138 Angle : 0.546 8.054 50055 Z= 0.269 Chirality : 0.040 0.155 6001 Planarity : 0.005 0.068 6520 Dihedral : 3.874 49.537 5088 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.36 % Favored : 97.56 % Rotamer: Outliers : 3.60 % Allowed : 21.18 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.39 (0.12), residues: 4751 helix: 2.87 (0.10), residues: 2813 sheet: -0.21 (0.28), residues: 313 loop : -0.39 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 66 TYR 0.019 0.001 TYR Z 112 PHE 0.022 0.001 PHE F 99 TRP 0.007 0.001 TRP E 12 HIS 0.002 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00327 (36821) covalent geometry : angle 0.54632 (50055) hydrogen bonds : bond 0.04258 ( 2383) hydrogen bonds : angle 3.67064 ( 6993) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 850 time to evaluate : 1.398 Fit side-chains REVERT: L 82 MET cc_start: 0.8339 (tpt) cc_final: 0.8097 (tpp) REVERT: P 69 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8160 (m-40) REVERT: Q 34 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: S 48 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: S 96 ASP cc_start: 0.8520 (p0) cc_final: 0.8286 (p0) REVERT: T 117 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: U 87 TYR cc_start: 0.9238 (m-80) cc_final: 0.9013 (m-80) REVERT: E 96 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7711 (mtt180) REVERT: C 8 MET cc_start: 0.7679 (tpt) cc_final: 0.7349 (tpp) REVERT: a 82 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8870 (m-40) REVERT: a 123 LYS cc_start: 0.8056 (tppt) cc_final: 0.7838 (tppt) REVERT: n 225 ARG cc_start: 0.8467 (mpt180) cc_final: 0.6710 (mmm160) REVERT: o 217 MET cc_start: 0.8412 (mmt) cc_final: 0.8097 (mmt) REVERT: o 232 LYS cc_start: 0.8444 (tptp) cc_final: 0.7074 (mttt) REVERT: p 202 MET cc_start: 0.8372 (ttm) cc_final: 0.7811 (ttm) REVERT: p 243 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7807 (mtt90) REVERT: q 228 GLU cc_start: 0.8004 (mt-10) cc_final: 0.6898 (tt0) REVERT: Y 101 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6403 (mp0) REVERT: A 15 LYS cc_start: 0.8245 (tmmm) cc_final: 0.7737 (ttpp) REVERT: Z 127 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8386 (mp) REVERT: G 138 MET cc_start: 0.9127 (mtm) cc_final: 0.8761 (mtp) REVERT: G 140 ARG cc_start: 0.8283 (ptt-90) cc_final: 0.7536 (tpt170) REVERT: j 324 ASN cc_start: 0.6931 (OUTLIER) cc_final: 0.6226 (p0) REVERT: J 121 ILE cc_start: 0.8240 (mt) cc_final: 0.7966 (tt) REVERT: J 146 ASP cc_start: 0.7071 (m-30) cc_final: 0.6819 (m-30) REVERT: J 205 MET cc_start: 0.8567 (tpt) cc_final: 0.7948 (tpp) REVERT: X 52 ASP cc_start: 0.7594 (p0) cc_final: 0.7230 (p0) outliers start: 140 outliers final: 104 residues processed: 933 average time/residue: 0.1985 time to fit residues: 309.4598 Evaluate side-chains 929 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 816 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 34 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 132 ASN Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain g residue 316 LEU Chi-restraints excluded: chain a residue 38 ASP Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 125 MET Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain n residue 209 SER Chi-restraints excluded: chain n residue 237 VAL Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 201 ILE Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain o residue 243 ARG Chi-restraints excluded: chain p residue 9 MET Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 247 LEU Chi-restraints excluded: chain p residue 249 SER Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 201 ILE Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain l residue 330 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 134 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 236 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 348 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 372 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 402 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN T 132 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 GLN Z 30 ASN F 141 GLN J 155 ASN X 113 GLN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132140 restraints weight = 48732.911| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.62 r_work: 0.3233 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36821 Z= 0.124 Angle : 0.537 8.186 50055 Z= 0.264 Chirality : 0.039 0.163 6001 Planarity : 0.004 0.072 6520 Dihedral : 3.756 50.823 5085 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 3.78 % Allowed : 21.18 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.50 (0.12), residues: 4751 helix: 2.95 (0.10), residues: 2816 sheet: -0.17 (0.28), residues: 313 loop : -0.35 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 66 TYR 0.020 0.001 TYR Z 112 PHE 0.024 0.001 PHE F 99 TRP 0.010 0.001 TRP E 9 HIS 0.002 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00291 (36821) covalent geometry : angle 0.53678 (50055) hydrogen bonds : bond 0.04017 ( 2383) hydrogen bonds : angle 3.59446 ( 6993) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 854 time to evaluate : 1.140 Fit side-chains REVERT: M 74 ASP cc_start: 0.8622 (m-30) cc_final: 0.8388 (m-30) REVERT: O 84 MET cc_start: 0.8507 (tpt) cc_final: 0.8207 (tpt) REVERT: P 69 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8122 (m-40) REVERT: P 75 MET cc_start: 0.8300 (tpp) cc_final: 0.7766 (mmt) REVERT: Q 34 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: S 48 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: S 96 ASP cc_start: 0.8505 (p0) cc_final: 0.8276 (p0) REVERT: T 53 MET cc_start: 0.8167 (mmm) cc_final: 0.7722 (mmm) REVERT: T 117 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: U 87 TYR cc_start: 0.9238 (m-80) cc_final: 0.8992 (m-80) REVERT: E 88 MET cc_start: 0.7931 (tpt) cc_final: 0.7360 (mmm) REVERT: E 96 ARG cc_start: 0.8002 (mtt-85) cc_final: 0.7715 (mtt180) REVERT: E 179 ILE cc_start: 0.8465 (mt) cc_final: 0.8238 (mp) REVERT: I 106 ASP cc_start: 0.8566 (m-30) cc_final: 0.8107 (m-30) REVERT: C 8 MET cc_start: 0.7697 (tpt) cc_final: 0.7357 (tpp) REVERT: a 82 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8878 (m-40) REVERT: a 123 LYS cc_start: 0.8080 (tppt) cc_final: 0.7855 (tppt) REVERT: m 56 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8466 (mt) REVERT: m 174 SER cc_start: 0.8528 (t) cc_final: 0.7925 (p) REVERT: n 165 LYS cc_start: 0.8790 (tttt) cc_final: 0.8279 (ttmt) REVERT: n 225 ARG cc_start: 0.8464 (mpt180) cc_final: 0.6702 (mmm160) REVERT: o 217 MET cc_start: 0.8341 (mmt) cc_final: 0.8060 (mmt) REVERT: o 232 LYS cc_start: 0.8399 (tptp) cc_final: 0.7008 (mttt) REVERT: p 202 MET cc_start: 0.8327 (ttm) cc_final: 0.7788 (ttm) REVERT: p 243 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7689 (mtt90) REVERT: q 42 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8656 (ptp-110) REVERT: q 228 GLU cc_start: 0.7989 (mt-10) cc_final: 0.6858 (tt0) REVERT: Y 52 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7988 (t0) REVERT: Y 101 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: Y 113 GLN cc_start: 0.8604 (mt0) cc_final: 0.8322 (mt0) REVERT: H 153 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8737 (tt) REVERT: A 15 LYS cc_start: 0.8264 (tmmm) cc_final: 0.7747 (ttpp) REVERT: G 140 ARG cc_start: 0.8270 (ptt-90) cc_final: 0.7549 (tpt170) REVERT: F 197 ASP cc_start: 0.8040 (t0) cc_final: 0.7771 (t0) REVERT: j 324 ASN cc_start: 0.6946 (OUTLIER) cc_final: 0.6224 (p0) REVERT: J 121 ILE cc_start: 0.8244 (mt) cc_final: 0.7982 (tt) REVERT: J 146 ASP cc_start: 0.7037 (m-30) cc_final: 0.6781 (m-30) REVERT: J 205 MET cc_start: 0.8506 (tpt) cc_final: 0.7960 (tpp) REVERT: D 9 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7686 (ttm) REVERT: X 52 ASP cc_start: 0.7569 (p0) cc_final: 0.7245 (p0) REVERT: W 117 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8229 (mm-30) outliers start: 147 outliers final: 111 residues processed: 940 average time/residue: 0.2041 time to fit residues: 320.0948 Evaluate side-chains 949 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 825 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 97 GLN Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 34 ASP Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 132 ASN Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain g residue 316 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain n residue 237 VAL Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 201 ILE Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain p residue 9 MET Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 247 LEU Chi-restraints excluded: chain p residue 249 SER Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 201 ILE Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain Z residue 3 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain l residue 330 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 134 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 226 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 chunk 365 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 442 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 375 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 HIS L 90 ASN M 103 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN T 132 ASN E 182 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 ASN Z 71 GLN J 155 ASN X 113 GLN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128946 restraints weight = 49155.948| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.63 r_work: 0.3198 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 36821 Z= 0.155 Angle : 0.556 7.482 50055 Z= 0.273 Chirality : 0.040 0.163 6001 Planarity : 0.005 0.070 6520 Dihedral : 3.786 50.503 5085 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 4.06 % Allowed : 21.13 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.42 (0.12), residues: 4751 helix: 2.85 (0.10), residues: 2832 sheet: -0.20 (0.28), residues: 311 loop : -0.33 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 66 TYR 0.017 0.001 TYR Z 112 PHE 0.022 0.001 PHE F 99 TRP 0.010 0.001 TRP E 12 HIS 0.002 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00375 (36821) covalent geometry : angle 0.55619 (50055) hydrogen bonds : bond 0.04208 ( 2383) hydrogen bonds : angle 3.63752 ( 6993) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 833 time to evaluate : 1.463 Fit side-chains REVERT: M 74 ASP cc_start: 0.8631 (m-30) cc_final: 0.8339 (m-30) REVERT: P 69 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8135 (m-40) REVERT: S 48 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: S 96 ASP cc_start: 0.8559 (p0) cc_final: 0.8325 (p0) REVERT: T 53 MET cc_start: 0.8194 (mmm) cc_final: 0.7763 (mmm) REVERT: T 117 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: E 96 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7791 (mtt180) REVERT: E 179 ILE cc_start: 0.8531 (mt) cc_final: 0.8287 (mp) REVERT: C 8 MET cc_start: 0.7689 (tpt) cc_final: 0.7347 (tpp) REVERT: a 82 ASN cc_start: 0.9145 (OUTLIER) cc_final: 0.8875 (m-40) REVERT: a 123 LYS cc_start: 0.8096 (tppt) cc_final: 0.7629 (tppt) REVERT: m 56 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (mt) REVERT: n 225 ARG cc_start: 0.8483 (mpt180) cc_final: 0.6692 (mmm160) REVERT: o 217 MET cc_start: 0.8389 (mmt) cc_final: 0.8097 (mmt) REVERT: o 232 LYS cc_start: 0.8483 (tptp) cc_final: 0.7065 (mttt) REVERT: p 202 MET cc_start: 0.8374 (ttm) cc_final: 0.7824 (ttm) REVERT: p 243 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7701 (mtt90) REVERT: q 42 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8620 (ptp-110) REVERT: q 228 GLU cc_start: 0.7992 (mt-10) cc_final: 0.6886 (tt0) REVERT: Y 52 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8022 (t0) REVERT: Y 101 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: H 153 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 15 LYS cc_start: 0.8258 (tmmm) cc_final: 0.7934 (ttpt) REVERT: B 7 MET cc_start: 0.7010 (mmm) cc_final: 0.6678 (mmm) REVERT: Z 127 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8315 (mp) REVERT: G 140 ARG cc_start: 0.8328 (ptt-90) cc_final: 0.7485 (tpt170) REVERT: F 197 ASP cc_start: 0.8139 (t0) cc_final: 0.7877 (t0) REVERT: J 121 ILE cc_start: 0.8247 (mt) cc_final: 0.7974 (tt) REVERT: J 146 ASP cc_start: 0.7052 (m-30) cc_final: 0.6797 (m-30) REVERT: J 205 MET cc_start: 0.8553 (tpt) cc_final: 0.7893 (tpp) REVERT: D 9 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: X 52 ASP cc_start: 0.7545 (p0) cc_final: 0.7215 (p0) REVERT: W 117 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8260 (mm-30) outliers start: 158 outliers final: 124 residues processed: 933 average time/residue: 0.2034 time to fit residues: 318.5807 Evaluate side-chains 956 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 820 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 132 ASN Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 103 ASP Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain U residue 125 SER Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 159 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain g residue 316 LEU Chi-restraints excluded: chain a residue 38 ASP Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 110 THR Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 235 THR Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 174 SER Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain n residue 209 SER Chi-restraints excluded: chain n residue 237 VAL Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 201 ILE Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain p residue 9 MET Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 247 LEU Chi-restraints excluded: chain p residue 249 SER Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 114 THR Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 201 ILE Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 84 LEU Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 129 LYS Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 236 MET Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain j residue 312 VAL Chi-restraints excluded: chain j residue 324 ASN Chi-restraints excluded: chain l residue 330 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 134 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 105 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 402 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 206 optimal weight: 0.0970 chunk 266 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 106 optimal weight: 0.0000 chunk 255 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN M 103 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN S 112 ASN T 21 GLN T 112 ASN T 132 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 182 ASN E 205 ASN C 39 GLN p 37 GLN Y 113 GLN H 132 GLN Z 30 ASN J 155 ASN X 134 GLN ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132047 restraints weight = 48686.025| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.62 r_work: 0.3244 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36821 Z= 0.109 Angle : 0.531 9.021 50055 Z= 0.262 Chirality : 0.039 0.173 6001 Planarity : 0.004 0.073 6520 Dihedral : 3.700 51.825 5085 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.68 % Rotamer: Outliers : 3.34 % Allowed : 22.13 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.64 (0.12), residues: 4751 helix: 3.01 (0.10), residues: 2835 sheet: -0.13 (0.28), residues: 313 loop : -0.21 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 66 TYR 0.021 0.001 TYR Z 112 PHE 0.030 0.001 PHE F 99 TRP 0.008 0.001 TRP E 9 HIS 0.001 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00244 (36821) covalent geometry : angle 0.53129 (50055) hydrogen bonds : bond 0.03733 ( 2383) hydrogen bonds : angle 3.51877 ( 6993) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 859 time to evaluate : 1.011 Fit side-chains REVERT: L 72 MET cc_start: 0.9107 (mmm) cc_final: 0.8885 (mmm) REVERT: M 74 ASP cc_start: 0.8534 (m-30) cc_final: 0.8233 (m-30) REVERT: O 84 MET cc_start: 0.8473 (tpt) cc_final: 0.8163 (tpt) REVERT: P 69 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: P 75 MET cc_start: 0.8256 (tpp) cc_final: 0.7733 (mmt) REVERT: R 55 ARG cc_start: 0.6908 (ppt170) cc_final: 0.6706 (tmm160) REVERT: S 48 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: S 96 ASP cc_start: 0.8484 (p0) cc_final: 0.8259 (p0) REVERT: T 53 MET cc_start: 0.8062 (mmm) cc_final: 0.7667 (mmm) REVERT: T 117 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: E 88 MET cc_start: 0.7887 (tpt) cc_final: 0.7578 (mmm) REVERT: E 96 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7751 (mtt180) REVERT: E 158 PRO cc_start: 0.8552 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: E 205 ASN cc_start: 0.6790 (OUTLIER) cc_final: 0.6578 (t160) REVERT: E 229 MET cc_start: 0.7765 (ppp) cc_final: 0.7553 (ppp) REVERT: E 240 CYS cc_start: 0.7866 (OUTLIER) cc_final: 0.6582 (m) REVERT: I 106 ASP cc_start: 0.8550 (m-30) cc_final: 0.8115 (m-30) REVERT: C 8 MET cc_start: 0.7681 (tpt) cc_final: 0.7337 (tpp) REVERT: a 123 LYS cc_start: 0.8036 (tppt) cc_final: 0.7641 (tppt) REVERT: m 56 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8417 (mt) REVERT: m 186 GLN cc_start: 0.7564 (tt0) cc_final: 0.7342 (mt0) REVERT: m 232 LYS cc_start: 0.8391 (tppt) cc_final: 0.8096 (tppt) REVERT: n 165 LYS cc_start: 0.8812 (tttt) cc_final: 0.8257 (ttmt) REVERT: n 225 ARG cc_start: 0.8426 (mpt180) cc_final: 0.6615 (mmm160) REVERT: o 217 MET cc_start: 0.8280 (mmt) cc_final: 0.8022 (mmt) REVERT: o 232 LYS cc_start: 0.8349 (tptp) cc_final: 0.6921 (mttt) REVERT: p 123 GLU cc_start: 0.6059 (mt-10) cc_final: 0.5787 (mm-30) REVERT: p 140 ASP cc_start: 0.7755 (t70) cc_final: 0.7503 (t70) REVERT: p 202 MET cc_start: 0.8327 (ttm) cc_final: 0.7796 (ttm) REVERT: p 243 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7478 (mtt90) REVERT: q 228 GLU cc_start: 0.8125 (mt-10) cc_final: 0.6933 (tt0) REVERT: Y 52 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7981 (t0) REVERT: Y 101 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: Y 113 GLN cc_start: 0.8609 (mt0) cc_final: 0.8207 (mt0) REVERT: H 153 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8761 (tt) REVERT: A 1 MET cc_start: 0.8471 (mmm) cc_final: 0.8086 (mmm) REVERT: A 15 LYS cc_start: 0.8248 (tmmm) cc_final: 0.7722 (ttpp) REVERT: B 7 MET cc_start: 0.6977 (mmm) cc_final: 0.6649 (mmm) REVERT: B 14 MET cc_start: 0.7403 (ptp) cc_final: 0.6809 (mtp) REVERT: G 140 ARG cc_start: 0.8240 (ptt-90) cc_final: 0.7532 (tpt170) REVERT: F 197 ASP cc_start: 0.8131 (t0) cc_final: 0.7851 (t0) REVERT: l 319 GLN cc_start: 0.8506 (mp10) cc_final: 0.8243 (mm-40) REVERT: J 121 ILE cc_start: 0.8251 (mt) cc_final: 0.7987 (tt) REVERT: J 146 ASP cc_start: 0.7090 (m-30) cc_final: 0.6827 (m-30) REVERT: J 205 MET cc_start: 0.8551 (tpt) cc_final: 0.7912 (tpp) REVERT: V 74 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: D 9 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7545 (ttm) REVERT: X 52 ASP cc_start: 0.7511 (p0) cc_final: 0.7160 (p0) REVERT: W 117 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8176 (mm-30) outliers start: 130 outliers final: 98 residues processed: 939 average time/residue: 0.1977 time to fit residues: 310.2745 Evaluate side-chains 940 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 830 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 97 GLN Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 110 THR Chi-restraints excluded: chain m residue 235 THR Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 188 GLU Chi-restraints excluded: chain n residue 209 SER Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain o residue 236 SER Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 250 MET Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 30 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain X residue 134 GLN Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 134 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 104 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 136 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 317 optimal weight: 0.9990 chunk 406 optimal weight: 0.9990 chunk 271 optimal weight: 0.0020 chunk 48 optimal weight: 0.7980 chunk 178 optimal weight: 0.0980 chunk 380 optimal weight: 6.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN M 103 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN T 117 GLN T 132 ASN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 182 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 230 GLN Z 17 GLN Z 30 ASN J 155 ASN W 22 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133217 restraints weight = 48866.603| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.62 r_work: 0.3254 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36821 Z= 0.108 Angle : 0.532 8.795 50055 Z= 0.262 Chirality : 0.039 0.177 6001 Planarity : 0.004 0.074 6520 Dihedral : 3.640 52.557 5085 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 2.93 % Allowed : 22.69 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.71 (0.12), residues: 4751 helix: 3.04 (0.10), residues: 2837 sheet: -0.03 (0.28), residues: 313 loop : -0.15 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 66 TYR 0.020 0.001 TYR a 112 PHE 0.042 0.001 PHE E 101 TRP 0.012 0.001 TRP E 12 HIS 0.001 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00239 (36821) covalent geometry : angle 0.53244 (50055) hydrogen bonds : bond 0.03545 ( 2383) hydrogen bonds : angle 3.47226 ( 6993) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 850 time to evaluate : 0.951 Fit side-chains REVERT: L 72 MET cc_start: 0.9083 (mmm) cc_final: 0.8853 (mmm) REVERT: M 74 ASP cc_start: 0.8509 (m-30) cc_final: 0.8218 (m-30) REVERT: O 84 MET cc_start: 0.8459 (tpt) cc_final: 0.8083 (tpt) REVERT: P 69 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7908 (m-40) REVERT: P 75 MET cc_start: 0.8258 (tpp) cc_final: 0.7746 (mmt) REVERT: S 48 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: S 96 ASP cc_start: 0.8495 (p0) cc_final: 0.8272 (p0) REVERT: T 53 MET cc_start: 0.8041 (mmm) cc_final: 0.7685 (mmm) REVERT: T 117 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7877 (mp-120) REVERT: E 36 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6071 (mtm-85) REVERT: E 61 ASN cc_start: 0.6926 (OUTLIER) cc_final: 0.6615 (t0) REVERT: E 88 MET cc_start: 0.7901 (tpt) cc_final: 0.7629 (mmm) REVERT: E 96 ARG cc_start: 0.8015 (mtt-85) cc_final: 0.7727 (mtt180) REVERT: E 129 MET cc_start: 0.8027 (ptp) cc_final: 0.7688 (ptp) REVERT: E 229 MET cc_start: 0.7806 (ppp) cc_final: 0.7423 (ppp) REVERT: I 106 ASP cc_start: 0.8638 (m-30) cc_final: 0.8226 (m-30) REVERT: C 8 MET cc_start: 0.7663 (tpt) cc_final: 0.7317 (tpp) REVERT: a 123 LYS cc_start: 0.7978 (tppt) cc_final: 0.7605 (tppt) REVERT: m 186 GLN cc_start: 0.7522 (tt0) cc_final: 0.7314 (mt0) REVERT: n 165 LYS cc_start: 0.8813 (tttt) cc_final: 0.8267 (ttmt) REVERT: n 225 ARG cc_start: 0.8308 (mpt180) cc_final: 0.6639 (mmm160) REVERT: o 232 LYS cc_start: 0.8313 (tptp) cc_final: 0.6690 (mttt) REVERT: p 140 ASP cc_start: 0.7732 (t70) cc_final: 0.7430 (t70) REVERT: p 202 MET cc_start: 0.8304 (ttm) cc_final: 0.7774 (ttm) REVERT: p 243 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7439 (mtt90) REVERT: Y 52 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7974 (t0) REVERT: Y 101 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: Y 113 GLN cc_start: 0.8480 (mt0) cc_final: 0.8158 (mt0) REVERT: H 153 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8773 (tt) REVERT: A 1 MET cc_start: 0.8480 (mmm) cc_final: 0.8078 (mmm) REVERT: A 15 LYS cc_start: 0.8232 (tmmm) cc_final: 0.7994 (ttpt) REVERT: B 7 MET cc_start: 0.6920 (mmm) cc_final: 0.6671 (mmm) REVERT: G 101 MET cc_start: 0.8681 (mmm) cc_final: 0.8155 (mtm) REVERT: G 140 ARG cc_start: 0.8185 (ptt-90) cc_final: 0.7518 (tpt170) REVERT: F 197 ASP cc_start: 0.8081 (t0) cc_final: 0.7800 (t0) REVERT: l 319 GLN cc_start: 0.8454 (mp10) cc_final: 0.8090 (mm-40) REVERT: J 121 ILE cc_start: 0.8249 (mt) cc_final: 0.7982 (tt) REVERT: J 146 ASP cc_start: 0.7159 (m-30) cc_final: 0.6894 (m-30) REVERT: J 205 MET cc_start: 0.8545 (tpt) cc_final: 0.7879 (tpp) REVERT: D 55 ILE cc_start: 0.7228 (mm) cc_final: 0.6914 (mt) REVERT: X 52 ASP cc_start: 0.7451 (p0) cc_final: 0.7094 (p0) REVERT: W 102 MET cc_start: 0.8415 (mmm) cc_final: 0.8176 (mtp) REVERT: W 117 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8140 (mm-30) outliers start: 114 outliers final: 92 residues processed: 920 average time/residue: 0.2030 time to fit residues: 311.6467 Evaluate side-chains 926 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 825 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 97 GLN Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 117 GLN Chi-restraints excluded: chain T residue 132 ASN Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain a residue 38 ASP Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 110 THR Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 201 ILE Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 250 MET Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 134 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 265 optimal weight: 0.7980 chunk 165 optimal weight: 0.0770 chunk 173 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 274 optimal weight: 0.9990 chunk 234 optimal weight: 0.0170 chunk 358 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 286 optimal weight: 2.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN M 103 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 115 ASN J 155 ASN W 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133454 restraints weight = 48818.004| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.60 r_work: 0.3248 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 36821 Z= 0.139 Angle : 0.679 59.197 50055 Z= 0.376 Chirality : 0.040 0.664 6001 Planarity : 0.005 0.139 6520 Dihedral : 3.645 52.564 5085 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 2.75 % Allowed : 22.92 % Favored : 74.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.72 (0.12), residues: 4751 helix: 3.05 (0.10), residues: 2837 sheet: -0.01 (0.28), residues: 313 loop : -0.15 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG q 180 TYR 0.019 0.001 TYR a 112 PHE 0.037 0.001 PHE E 101 TRP 0.010 0.001 TRP E 12 HIS 0.001 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00284 (36821) covalent geometry : angle 0.67945 (50055) hydrogen bonds : bond 0.03547 ( 2383) hydrogen bonds : angle 3.47297 ( 6993) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9502 Ramachandran restraints generated. 4751 Oldfield, 0 Emsley, 4751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 822 time to evaluate : 1.391 Fit side-chains REVERT: L 72 MET cc_start: 0.9067 (mmm) cc_final: 0.8835 (mmm) REVERT: M 74 ASP cc_start: 0.8491 (m-30) cc_final: 0.8198 (m-30) REVERT: O 84 MET cc_start: 0.8455 (tpt) cc_final: 0.8089 (tpt) REVERT: P 69 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7913 (m-40) REVERT: P 75 MET cc_start: 0.8264 (tpp) cc_final: 0.7749 (mmt) REVERT: S 48 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: S 96 ASP cc_start: 0.8491 (p0) cc_final: 0.8273 (p0) REVERT: T 53 MET cc_start: 0.8056 (mmm) cc_final: 0.7684 (mmm) REVERT: T 132 ASN cc_start: 0.8557 (p0) cc_final: 0.8210 (p0) REVERT: E 36 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6063 (mtm-85) REVERT: E 88 MET cc_start: 0.7891 (tpt) cc_final: 0.7615 (mmm) REVERT: E 96 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7720 (mtt180) REVERT: E 129 MET cc_start: 0.8023 (ptp) cc_final: 0.7677 (ptp) REVERT: E 229 MET cc_start: 0.7752 (ppp) cc_final: 0.6894 (ptm) REVERT: I 106 ASP cc_start: 0.8641 (m-30) cc_final: 0.8222 (m-30) REVERT: C 8 MET cc_start: 0.7645 (tpt) cc_final: 0.7298 (tpp) REVERT: a 123 LYS cc_start: 0.7968 (tppt) cc_final: 0.7594 (tppt) REVERT: m 186 GLN cc_start: 0.7520 (tt0) cc_final: 0.7311 (mt0) REVERT: n 165 LYS cc_start: 0.8813 (tttt) cc_final: 0.8264 (ttmt) REVERT: n 225 ARG cc_start: 0.8308 (mpt180) cc_final: 0.6634 (mmm160) REVERT: o 232 LYS cc_start: 0.8306 (tptp) cc_final: 0.6739 (mttt) REVERT: p 140 ASP cc_start: 0.7725 (t70) cc_final: 0.7417 (t70) REVERT: p 202 MET cc_start: 0.8311 (ttm) cc_final: 0.7778 (ttm) REVERT: p 243 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7426 (mtt90) REVERT: Y 52 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7961 (t0) REVERT: Y 101 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: Y 113 GLN cc_start: 0.8481 (mt0) cc_final: 0.8151 (mt0) REVERT: H 153 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8775 (tt) REVERT: A 1 MET cc_start: 0.8476 (mmm) cc_final: 0.8078 (mmm) REVERT: A 15 LYS cc_start: 0.8227 (tmmm) cc_final: 0.7983 (ttpt) REVERT: B 7 MET cc_start: 0.6918 (mmm) cc_final: 0.6664 (mmm) REVERT: G 101 MET cc_start: 0.8674 (mmm) cc_final: 0.8135 (mtm) REVERT: G 140 ARG cc_start: 0.8185 (ptt-90) cc_final: 0.7482 (tpt170) REVERT: F 197 ASP cc_start: 0.8074 (t0) cc_final: 0.7793 (t0) REVERT: l 319 GLN cc_start: 0.8441 (mp10) cc_final: 0.8103 (mm-40) REVERT: J 121 ILE cc_start: 0.8242 (mt) cc_final: 0.7968 (tt) REVERT: J 146 ASP cc_start: 0.7151 (m-30) cc_final: 0.6894 (m-30) REVERT: J 205 MET cc_start: 0.8547 (tpt) cc_final: 0.7870 (tpp) REVERT: D 55 ILE cc_start: 0.7209 (mm) cc_final: 0.6901 (mt) REVERT: X 52 ASP cc_start: 0.7446 (p0) cc_final: 0.7095 (p0) REVERT: W 102 MET cc_start: 0.8434 (mmm) cc_final: 0.8203 (mtp) REVERT: W 117 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8128 (mm-30) outliers start: 107 outliers final: 95 residues processed: 890 average time/residue: 0.1994 time to fit residues: 297.9671 Evaluate side-chains 922 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 820 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 97 GLN Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain S residue 48 GLU Chi-restraints excluded: chain S residue 126 GLN Chi-restraints excluded: chain T residue 133 VAL Chi-restraints excluded: chain U residue 102 MET Chi-restraints excluded: chain U residue 113 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 86 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 187 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain a residue 38 ASP Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 107 SER Chi-restraints excluded: chain a residue 127 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 110 THR Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 201 ILE Chi-restraints excluded: chain m residue 245 ASN Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain n residue 120 VAL Chi-restraints excluded: chain n residue 129 VAL Chi-restraints excluded: chain n residue 246 GLN Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 110 THR Chi-restraints excluded: chain o residue 112 GLN Chi-restraints excluded: chain o residue 129 VAL Chi-restraints excluded: chain o residue 233 VAL Chi-restraints excluded: chain p residue 201 ILE Chi-restraints excluded: chain p residue 243 ARG Chi-restraints excluded: chain p residue 250 MET Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 170 GLU Chi-restraints excluded: chain q residue 205 VAL Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 66 SER Chi-restraints excluded: chain Y residue 101 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 187 PHE Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 VAL Chi-restraints excluded: chain Z residue 119 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 178 GLU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain d residue 317 SER Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 38 ASP Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 126 MET Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 70 SER Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 134 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 34 optimal weight: 4.9990 chunk 198 optimal weight: 0.0970 chunk 124 optimal weight: 0.3980 chunk 159 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 342 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 ASN M 103 GLN ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN T 117 GLN ** U 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN ** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN W 22 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133361 restraints weight = 48457.401| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.61 r_work: 0.3261 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 36821 Z= 0.139 Angle : 0.679 59.197 50055 Z= 0.376 Chirality : 0.040 0.664 6001 Planarity : 0.005 0.139 6520 Dihedral : 3.645 52.564 5085 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 2.62 % Allowed : 23.03 % Favored : 74.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 2.72 (0.12), residues: 4751 helix: 3.05 (0.10), residues: 2837 sheet: -0.01 (0.28), residues: 313 loop : -0.15 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG q 180 TYR 0.019 0.001 TYR a 112 PHE 0.037 0.001 PHE E 101 TRP 0.010 0.001 TRP E 12 HIS 0.001 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00284 (36821) covalent geometry : angle 0.67945 (50055) hydrogen bonds : bond 0.03547 ( 2383) hydrogen bonds : angle 3.47297 ( 6993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9780.72 seconds wall clock time: 167 minutes 32.40 seconds (10052.40 seconds total)