Starting phenix.real_space_refine on Fri Oct 30 01:11:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qxf_4668/10_2026/6qxf_4668.cif" } resolution = 3.6 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= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 50 5.49 5 S 144 5.16 5 C 22240 2.51 5 N 5603 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34693 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "C" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "D" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "E" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "F" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "G" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1787 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "H" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1795 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "J" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "K" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "M" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "N" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "O" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "P" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "Q" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "R" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "S" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2369 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain: "T" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "X" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 500 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "Y" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 525 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.35, per 1000 atoms: 0.21 Number of scatterers: 34693 At special positions: 0 Unit cell: (126.945, 179.025, 185.535, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 144 16.00 P 50 15.00 O 6648 8.00 N 5603 7.00 C 22240 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7944 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 40 sheets defined 51.1% alpha, 13.2% beta 25 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.797A pdb=" N LYS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 115 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.913A pdb=" N LYS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 115 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 169 through 172 removed outlier: 3.705A pdb=" N TYR B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 174 through 189 removed outlier: 3.543A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 72 through 90 removed outlier: 3.796A pdb=" N LYS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 115 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.914A pdb=" N LYS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 115 Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 169 through 172 removed outlier: 3.710A pdb=" N TYR D 172 " --> pdb=" O SER D 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 169 through 172' Processing helix chain 'D' and resid 174 through 189 removed outlier: 3.540A pdb=" N LEU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 72 through 90 removed outlier: 3.797A pdb=" N LYS E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 115 Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE E 149 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 189 Processing helix chain 'F' and resid 24 through 37 Processing helix chain 'F' and resid 72 through 90 removed outlier: 3.890A pdb=" N LYS F 90 " --> pdb=" O GLN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 115 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 143 through 155 Processing helix chain 'F' and resid 169 through 172 removed outlier: 3.715A pdb=" N TYR F 172 " --> pdb=" O SER F 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 169 through 172' Processing helix chain 'F' and resid 174 through 189 removed outlier: 3.536A pdb=" N LEU F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 72 through 90 removed outlier: 3.797A pdb=" N LYS G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 115 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 143 through 158 removed outlier: 3.535A pdb=" N PHE G 149 " --> pdb=" O PHE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 189 Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'H' and resid 72 through 90 removed outlier: 3.907A pdb=" N LYS H 90 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 115 Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 143 through 155 Processing helix chain 'H' and resid 174 through 189 removed outlier: 3.538A pdb=" N LEU H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 62 Processing helix chain 'I' and resid 85 through 96 removed outlier: 3.964A pdb=" N LEU I 89 " --> pdb=" O HIS I 85 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA I 92 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN I 94 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 124 Processing helix chain 'I' and resid 126 through 140 Processing helix chain 'I' and resid 147 through 162 removed outlier: 3.856A pdb=" N ARG I 154 " --> pdb=" O GLY I 150 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE I 155 " --> pdb=" O HIS I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 196 Processing helix chain 'I' and resid 212 through 219 Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'I' and resid 223 through 233 removed outlier: 3.712A pdb=" N ASP I 227 " --> pdb=" O ARG I 223 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 247 removed outlier: 3.608A pdb=" N SER I 247 " --> pdb=" O LYS I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 279 Processing helix chain 'J' and resid 52 through 61 Processing helix chain 'J' and resid 85 through 96 removed outlier: 4.085A pdb=" N LEU J 89 " --> pdb=" O HIS J 85 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA J 92 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG J 93 " --> pdb=" O LEU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 124 Processing helix chain 'J' and resid 126 through 140 Processing helix chain 'J' and resid 147 through 162 Processing helix chain 'J' and resid 171 through 196 Processing helix chain 'J' and resid 212 through 220 Processing helix chain 'J' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE J 226 " --> pdb=" O PHE J 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE J 229 " --> pdb=" O ILE J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE J 248 " --> pdb=" O GLU J 244 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE J 249 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER J 250 " --> pdb=" O PHE J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 279 Processing helix chain 'L' and resid 52 through 62 Processing helix chain 'L' and resid 85 through 96 removed outlier: 3.965A pdb=" N LEU L 89 " --> pdb=" O HIS L 85 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA L 92 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG L 93 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 124 Processing helix chain 'L' and resid 126 through 140 Processing helix chain 'L' and resid 147 through 162 removed outlier: 3.853A pdb=" N ARG L 154 " --> pdb=" O GLY L 150 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE L 155 " --> pdb=" O HIS L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 196 Processing helix chain 'L' and resid 212 through 219 Processing helix chain 'L' and resid 220 through 222 No H-bonds generated for 'chain 'L' and resid 220 through 222' Processing helix chain 'L' and resid 223 through 233 removed outlier: 3.710A pdb=" N ASP L 227 " --> pdb=" O ARG L 223 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE L 229 " --> pdb=" O ILE L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 246 Processing helix chain 'L' and resid 247 through 249 No H-bonds generated for 'chain 'L' and resid 247 through 249' Processing helix chain 'L' and resid 262 through 279 Processing helix chain 'M' and resid 52 through 61 Processing helix chain 'M' and resid 85 through 96 removed outlier: 4.085A pdb=" N LEU M 89 " --> pdb=" O HIS M 85 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA M 92 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG M 93 " --> pdb=" O LEU M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 124 Processing helix chain 'M' and resid 126 through 140 Processing helix chain 'M' and resid 147 through 162 Processing helix chain 'M' and resid 171 through 196 Processing helix chain 'M' and resid 212 through 220 Processing helix chain 'M' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE M 226 " --> pdb=" O PHE M 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE M 229 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE M 249 " --> pdb=" O LEU M 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER M 250 " --> pdb=" O PHE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 262 through 279 Processing helix chain 'O' and resid 52 through 62 Processing helix chain 'O' and resid 85 through 96 removed outlier: 3.965A pdb=" N LEU O 89 " --> pdb=" O HIS O 85 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA O 92 " --> pdb=" O SER O 88 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN O 94 " --> pdb=" O GLN O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 124 Processing helix chain 'O' and resid 126 through 140 Processing helix chain 'O' and resid 147 through 162 removed outlier: 3.852A pdb=" N ARG O 154 " --> pdb=" O GLY O 150 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 196 Processing helix chain 'O' and resid 212 through 219 Processing helix chain 'O' and resid 220 through 222 No H-bonds generated for 'chain 'O' and resid 220 through 222' Processing helix chain 'O' and resid 223 through 233 removed outlier: 3.709A pdb=" N ASP O 227 " --> pdb=" O ARG O 223 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE O 229 " --> pdb=" O ILE O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 246 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 262 through 279 Processing helix chain 'P' and resid 52 through 61 Processing helix chain 'P' and resid 85 through 96 removed outlier: 4.085A pdb=" N LEU P 89 " --> pdb=" O HIS P 85 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG P 93 " --> pdb=" O LEU P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 124 Processing helix chain 'P' and resid 126 through 140 Processing helix chain 'P' and resid 147 through 162 Processing helix chain 'P' and resid 171 through 196 Processing helix chain 'P' and resid 212 through 220 Processing helix chain 'P' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE P 226 " --> pdb=" O PHE P 222 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE P 229 " --> pdb=" O ILE P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE P 248 " --> pdb=" O GLU P 244 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE P 249 " --> pdb=" O LEU P 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER P 250 " --> pdb=" O PHE P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 279 Processing helix chain 'R' and resid 52 through 62 Processing helix chain 'R' and resid 85 through 96 removed outlier: 3.965A pdb=" N LEU R 89 " --> pdb=" O HIS R 85 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA R 92 " --> pdb=" O SER R 88 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN R 94 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 124 Processing helix chain 'R' and resid 126 through 140 Processing helix chain 'R' and resid 147 through 162 removed outlier: 3.850A pdb=" N ARG R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE R 155 " --> pdb=" O HIS R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 196 Processing helix chain 'R' and resid 212 through 219 Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 223 through 233 removed outlier: 3.709A pdb=" N ASP R 227 " --> pdb=" O ARG R 223 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 247 removed outlier: 3.611A pdb=" N SER R 247 " --> pdb=" O LYS R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 279 Processing helix chain 'S' and resid 52 through 61 Processing helix chain 'S' and resid 85 through 96 removed outlier: 4.084A pdb=" N LEU S 89 " --> pdb=" O HIS S 85 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA S 92 " --> pdb=" O SER S 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG S 93 " --> pdb=" O LEU S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 124 Processing helix chain 'S' and resid 126 through 140 Processing helix chain 'S' and resid 147 through 162 Processing helix chain 'S' and resid 171 through 196 Processing helix chain 'S' and resid 212 through 220 Processing helix chain 'S' and resid 222 through 234 removed outlier: 4.074A pdb=" N ILE S 226 " --> pdb=" O PHE S 222 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE S 229 " --> pdb=" O ILE S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 251 removed outlier: 3.701A pdb=" N ILE S 248 " --> pdb=" O GLU S 244 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE S 249 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER S 250 " --> pdb=" O PHE S 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 262 through 279 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.667A pdb=" N VAL A 167 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.634A pdb=" N THR B 18 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU B 196 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 20 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 62 removed outlier: 3.667A pdb=" N VAL C 167 " --> pdb=" O ILE C 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB1, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.662A pdb=" N THR D 18 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU D 196 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU D 20 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AB3, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.666A pdb=" N VAL E 167 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 136 through 137 Processing sheet with id=AB5, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AB6, first strand: chain 'F' and resid 59 through 62 removed outlier: 6.648A pdb=" N THR F 18 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLU F 196 " --> pdb=" O THR F 18 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU F 20 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.667A pdb=" N VAL G 167 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AC2, first strand: chain 'H' and resid 59 through 62 removed outlier: 6.649A pdb=" N THR H 18 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLU H 196 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU H 20 " --> pdb=" O GLU H 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 5 through 9 removed outlier: 7.379A pdb=" N ARG I 5 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU I 41 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL I 7 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU I 43 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL I 9 " --> pdb=" O LEU I 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU I 64 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL I 65 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA I 76 " --> pdb=" O PHE I 67 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE J 67 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE J 77 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL J 65 " --> pdb=" O PHE J 77 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU J 64 " --> pdb=" O ASP J 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG J 5 " --> pdb=" O ASP J 39 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU J 41 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL J 7 " --> pdb=" O LEU J 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU J 43 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL J 9 " --> pdb=" O LEU J 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AC5, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.701A pdb=" N LEU I 50 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU J 50 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER J 13 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR J 51 " --> pdb=" O SER J 13 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU J 15 " --> pdb=" O THR J 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 252 through 254 Processing sheet with id=AC7, first strand: chain 'J' and resid 252 through 254 Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 9 removed outlier: 7.376A pdb=" N ARG L 5 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU L 41 " --> pdb=" O ARG L 5 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL L 7 " --> pdb=" O LEU L 41 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU L 43 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL L 9 " --> pdb=" O LEU L 43 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU L 64 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL L 65 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA L 76 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE M 67 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE M 77 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL M 65 " --> pdb=" O PHE M 77 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU M 64 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG M 5 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU M 41 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL M 7 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU M 43 " --> pdb=" O VAL M 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL M 9 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 14 through 18 Processing sheet with id=AD1, first strand: chain 'L' and resid 49 through 51 removed outlier: 3.652A pdb=" N LEU L 50 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU M 50 " --> pdb=" O LEU L 50 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER M 13 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR M 51 " --> pdb=" O SER M 13 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU M 15 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 252 through 254 Processing sheet with id=AD3, first strand: chain 'M' and resid 252 through 254 Processing sheet with id=AD4, first strand: chain 'O' and resid 5 through 9 removed outlier: 7.367A pdb=" N ARG O 5 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU O 41 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL O 7 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU O 43 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL O 9 " --> pdb=" O LEU O 43 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU O 64 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL O 65 " --> pdb=" O LEU O 78 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA O 76 " --> pdb=" O PHE O 67 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE P 67 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE P 77 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL P 65 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU P 64 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG P 5 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU P 41 " --> pdb=" O ARG P 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL P 7 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU P 43 " --> pdb=" O VAL P 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL P 9 " --> pdb=" O LEU P 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 14 through 18 Processing sheet with id=AD6, first strand: chain 'O' and resid 49 through 51 removed outlier: 3.716A pdb=" N LEU O 50 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU P 50 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER P 13 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR P 51 " --> pdb=" O SER P 13 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU P 15 " --> pdb=" O THR P 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'P' and resid 252 through 254 Processing sheet with id=AD9, first strand: chain 'R' and resid 5 through 9 removed outlier: 7.364A pdb=" N ARG R 5 " --> pdb=" O ASP R 39 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU R 41 " --> pdb=" O ARG R 5 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL R 7 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU R 43 " --> pdb=" O VAL R 7 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL R 9 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 64 " --> pdb=" O ASP R 39 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL R 65 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA R 76 " --> pdb=" O PHE R 67 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE S 67 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE S 77 " --> pdb=" O VAL S 65 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL S 65 " --> pdb=" O PHE S 77 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU S 64 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG S 5 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU S 41 " --> pdb=" O ARG S 5 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL S 7 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU S 43 " --> pdb=" O VAL S 7 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL S 9 " --> pdb=" O LEU S 43 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 14 through 18 Processing sheet with id=AE2, first strand: chain 'R' and resid 49 through 51 removed outlier: 3.646A pdb=" N LEU R 50 " --> pdb=" O LEU S 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU S 50 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER S 13 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N THR S 51 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU S 15 " --> pdb=" O THR S 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 252 through 254 Processing sheet with id=AE4, first strand: chain 'S' and resid 252 through 254 1816 hydrogen bonds defined for protein. 5304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 7.03 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9954 1.34 - 1.45: 5479 1.45 - 1.57: 19657 1.57 - 1.69: 98 1.69 - 1.81: 232 Bond restraints: 35420 Sorted by residual: bond pdb=" C1' DT X 20 " pdb=" N1 DT X 20 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.23e+00 bond pdb=" C1' DT X 19 " pdb=" N1 DT X 19 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.21e+00 bond pdb=" C1' DT X 13 " pdb=" N1 DT X 13 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.18e+00 bond pdb=" C1' DT X 9 " pdb=" N1 DT X 9 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.16e+00 bond pdb=" C1' DT X 6 " pdb=" N1 DT X 6 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.12e+00 ... (remaining 35415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 47139 1.34 - 2.68: 835 2.68 - 4.02: 82 4.02 - 5.37: 35 5.37 - 6.71: 8 Bond angle restraints: 48099 Sorted by residual: angle pdb=" N ALA I 206 " pdb=" CA ALA I 206 " pdb=" C ALA I 206 " ideal model delta sigma weight residual 111.28 117.99 -6.71 1.09e+00 8.42e-01 3.79e+01 angle pdb=" N ALA L 206 " pdb=" CA ALA L 206 " pdb=" C ALA L 206 " ideal model delta sigma weight residual 111.28 117.96 -6.68 1.09e+00 8.42e-01 3.75e+01 angle pdb=" N ALA O 206 " pdb=" CA ALA O 206 " pdb=" C ALA O 206 " ideal model delta sigma weight residual 111.28 117.94 -6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" N ALA R 206 " pdb=" CA ALA R 206 " pdb=" C ALA R 206 " ideal model delta sigma weight residual 111.28 117.84 -6.56 1.09e+00 8.42e-01 3.63e+01 angle pdb=" N ASN S 207 " pdb=" CA ASN S 207 " pdb=" C ASN S 207 " ideal model delta sigma weight residual 111.28 116.43 -5.15 1.09e+00 8.42e-01 2.23e+01 ... (remaining 48094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 20041 16.14 - 32.27: 889 32.27 - 48.41: 322 48.41 - 64.54: 102 64.54 - 80.68: 8 Dihedral angle restraints: 21362 sinusoidal: 9146 harmonic: 12216 Sorted by residual: dihedral pdb=" CA ASP M 69 " pdb=" CB ASP M 69 " pdb=" CG ASP M 69 " pdb=" OD1 ASP M 69 " ideal model delta sinusoidal sigma weight residual -30.00 -89.74 59.74 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP P 69 " pdb=" CB ASP P 69 " pdb=" CG ASP P 69 " pdb=" OD1 ASP P 69 " ideal model delta sinusoidal sigma weight residual -30.00 -89.71 59.71 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP J 69 " pdb=" CB ASP J 69 " pdb=" CG ASP J 69 " pdb=" OD1 ASP J 69 " ideal model delta sinusoidal sigma weight residual -30.00 -89.67 59.67 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 21359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4455 0.045 - 0.091: 797 0.091 - 0.136: 293 0.136 - 0.181: 11 0.181 - 0.227: 4 Chirality restraints: 5560 Sorted by residual: chirality pdb=" CA ALA I 206 " pdb=" N ALA I 206 " pdb=" C ALA I 206 " pdb=" CB ALA I 206 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ALA L 206 " pdb=" N ALA L 206 " pdb=" C ALA L 206 " pdb=" CB ALA L 206 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ALA O 206 " pdb=" N ALA O 206 " pdb=" C ALA O 206 " pdb=" CB ALA O 206 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5557 not shown) Planarity restraints: 5886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 203 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.27e+00 pdb=" C LEU I 203 " -0.019 2.00e-02 2.50e+03 pdb=" O LEU I 203 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS I 204 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 215 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO B 216 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 215 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO F 216 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 216 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 216 " -0.015 5.00e-02 4.00e+02 ... (remaining 5883 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2883 2.74 - 3.28: 35522 3.28 - 3.82: 56752 3.82 - 4.36: 69125 4.36 - 4.90: 117999 Nonbonded interactions: 282281 Sorted by model distance: nonbonded pdb=" O ARG M 5 " pdb=" N ASP M 39 " model vdw 2.203 3.120 nonbonded pdb=" O ARG S 5 " pdb=" N ASP S 39 " model vdw 2.204 3.120 nonbonded pdb=" O ARG J 5 " pdb=" N ASP J 39 " model vdw 2.204 3.120 nonbonded pdb=" O ARG P 5 " pdb=" N ASP P 39 " model vdw 2.205 3.120 nonbonded pdb=" O LEU O 183 " pdb=" OG SER O 186 " model vdw 2.272 3.040 ... (remaining 282276 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' and (resid 1 through 218 or resid 501)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 218 or resid 501)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 218 or resid 501)) selection = chain 'G' selection = (chain 'H' and (resid 1 through 218 or resid 501)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.040 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 : 0.002 0.035 35420 Z= 0.156 Angle : 0.444 6.708 48099 Z= 0.312 Chirality : 0.039 0.227 5560 Planarity : 0.002 0.028 5886 Dihedral : 11.229 80.681 13418 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.17 % Favored : 97.73 % Rotamer: Outliers : 0.73 % Allowed : 3.15 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.11), residues: 4048 helix: -1.07 (0.10), residues: 1972 sheet: 0.03 (0.18), residues: 660 loop : -0.42 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 190 TYR 0.006 0.001 TYR J 156 PHE 0.009 0.001 PHE D 5 TRP 0.007 0.001 TRP S 4 HIS 0.002 0.000 HIS P 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.16 (35420) covalent geometry : angle 0.44379 / 0.31 (48099) hydrogen bonds : bond 0.09067 / 5.83 ( 1866) hydrogen bonds : angle 8.07375 / 5.60 ( 5404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8190 (p) REVERT: A 162 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: A 217 TYR cc_start: 0.7422 (t80) cc_final: 0.7019 (t80) REVERT: B 217 TYR cc_start: 0.8703 (t80) cc_final: 0.8315 (t80) REVERT: C 72 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 215 MET cc_start: 0.8694 (ptm) cc_final: 0.8468 (ppp) REVERT: E 72 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.8063 (p) REVERT: E 122 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (p0) REVERT: E 160 LYS cc_start: 0.9586 (mttt) cc_final: 0.9281 (tppt) REVERT: E 210 LYS cc_start: 0.9565 (pttt) cc_final: 0.9310 (mmtt) REVERT: G 120 GLU cc_start: 0.9382 (tt0) cc_final: 0.9023 (tm-30) REVERT: H 52 ARG cc_start: 0.9280 (ttt90) cc_final: 0.9076 (ptm-80) REVERT: H 122 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8620 (p0) REVERT: I 151 HIS cc_start: 0.9484 (m90) cc_final: 0.9274 (t-170) REVERT: J 260 MET cc_start: 0.7961 (mtp) cc_final: 0.7132 (mtt) REVERT: M 19 ASN cc_start: 0.9663 (m110) cc_final: 0.9392 (t0) REVERT: O 163 ASN cc_start: 0.9507 (m-40) cc_final: 0.9248 (t0) REVERT: R 41 LEU cc_start: 0.9677 (tp) cc_final: 0.9371 (mm) REVERT: R 237 ASN cc_start: 0.9569 (m-40) cc_final: 0.9297 (p0) REVERT: S 279 GLN cc_start: 0.9266 (mm-40) cc_final: 0.9021 (pt0) outliers start: 28 outliers final: 7 residues processed: 412 average time/residue: 0.2333 time to fit residues: 149.0976 Evaluate side-chains 199 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 82 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 155, 244, 183] chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 40.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN A 86 GLN A 153 GLN B 86 GLN C 86 GLN C 153 GLN D 86 GLN D 180 GLN E 71 ASN E 86 GLN E 153 GLN F 86 GLN F 180 GLN G 71 ASN G 86 GLN G 153 GLN H 86 GLN H 180 GLN I 12 HIS I 90 GLN I 138 HIS I 174 ASN I 211 GLN J 12 HIS J 62 ASN L 12 HIS L 90 GLN L 174 ASN L 211 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS M 62 ASN ** O 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 174 ASN O 211 GLN P 12 HIS P 62 ASN P 138 HIS ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 GLN R 12 HIS R 19 ASN R 90 GLN R 174 ASN ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 12 HIS S 62 ASN S 138 HIS ** S 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.064618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042348 restraints weight = 217778.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.043632 restraints weight = 113186.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.044424 restraints weight = 75000.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.044935 restraints weight = 57885.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.045190 restraints weight = 49252.898| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35420 Z= 0.206 Angle : 0.598 7.416 48099 Z= 0.315 Chirality : 0.042 0.216 5560 Planarity : 0.004 0.092 5886 Dihedral : 12.454 59.731 5056 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.24 % Favored : 98.67 % Rotamer: Outliers : 0.96 % Allowed : 7.09 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 4048 helix: 0.98 (0.11), residues: 2000 sheet: 0.26 (0.20), residues: 660 loop : -0.12 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG M 84 TYR 0.018 0.001 TYR B 121 PHE 0.032 0.002 PHE R 246 TRP 0.020 0.001 TRP L 106 HIS 0.006 0.001 HIS O 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (35420) covalent geometry : angle 0.59839 / 0.31 (48099) hydrogen bonds : bond 0.04027 / 2.62 ( 1866) hydrogen bonds : angle 5.40612 / 3.74 ( 5404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8556 (p) REVERT: A 109 MET cc_start: 0.8504 (mtp) cc_final: 0.8100 (mtm) REVERT: A 179 TYR cc_start: 0.7973 (m-80) cc_final: 0.7703 (m-80) REVERT: B 217 TYR cc_start: 0.8260 (t80) cc_final: 0.7833 (t80) REVERT: C 50 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8190 (ptpp) REVERT: C 72 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8499 (p) REVERT: I 219 MET cc_start: 0.9062 (ppp) cc_final: 0.8500 (ppp) REVERT: J 53 MET cc_start: 0.8393 (tpp) cc_final: 0.8185 (tpp) REVERT: J 127 PHE cc_start: 0.8659 (m-80) cc_final: 0.8371 (m-80) REVERT: J 219 MET cc_start: 0.8353 (ppp) cc_final: 0.8079 (ppp) REVERT: M 53 MET cc_start: 0.8511 (ppp) cc_final: 0.8209 (tmm) REVERT: M 134 MET cc_start: 0.8884 (ttm) cc_final: 0.8439 (mtp) REVERT: M 198 MET cc_start: 0.7953 (mmp) cc_final: 0.7464 (mmm) REVERT: O 163 ASN cc_start: 0.9251 (m-40) cc_final: 0.8744 (t0) REVERT: P 219 MET cc_start: 0.7991 (ppp) cc_final: 0.7606 (ppp) REVERT: R 41 LEU cc_start: 0.9591 (tp) cc_final: 0.9376 (mm) REVERT: R 198 MET cc_start: 0.9063 (tpt) cc_final: 0.8542 (mtp) REVERT: R 219 MET cc_start: 0.8205 (ppp) cc_final: 0.7396 (ppp) REVERT: R 237 ASN cc_start: 0.9399 (m-40) cc_final: 0.9011 (p0) REVERT: S 53 MET cc_start: 0.8439 (tpp) cc_final: 0.8001 (tpp) REVERT: S 134 MET cc_start: 0.9064 (ttt) cc_final: 0.8786 (ppp) REVERT: S 219 MET cc_start: 0.8394 (ppp) cc_final: 0.8070 (ppp) REVERT: S 275 LYS cc_start: 0.9692 (tttt) cc_final: 0.9434 (pttp) outliers start: 37 outliers final: 17 residues processed: 217 average time/residue: 0.2218 time to fit residues: 76.8841 Evaluate side-chains 174 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain O residue 205 HIS Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain P residue 245 LEU Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 137 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [218, 286, 275, 253, 314, 11, 380, 342, 92, 195, 373] chunk 218 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 253 optimal weight: 0.0980 chunk 314 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 373 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 151 HIS ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 HIS ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.064561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.042267 restraints weight = 217147.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.043555 restraints weight = 111880.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.044360 restraints weight = 73853.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044787 restraints weight = 56840.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.045143 restraints weight = 48819.879| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35420 Z= 0.130 Angle : 0.512 9.009 48099 Z= 0.270 Chirality : 0.040 0.174 5560 Planarity : 0.003 0.035 5886 Dihedral : 12.503 59.279 5049 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.27 % Rotamer: Outliers : 1.15 % Allowed : 7.19 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.13), residues: 4048 helix: 1.76 (0.11), residues: 2020 sheet: 0.32 (0.20), residues: 660 loop : -0.11 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 55 TYR 0.024 0.001 TYR E 121 PHE 0.024 0.001 PHE R 209 TRP 0.008 0.001 TRP L 106 HIS 0.009 0.001 HIS O 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (35420) covalent geometry : angle 0.51210 / 0.27 (48099) hydrogen bonds : bond 0.03525 / 2.30 ( 1866) hydrogen bonds : angle 4.79549 / 3.31 ( 5404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 179 TYR cc_start: 0.7941 (m-80) cc_final: 0.7667 (m-80) REVERT: B 217 TYR cc_start: 0.8258 (t80) cc_final: 0.7808 (t80) REVERT: C 50 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8226 (ptpp) REVERT: C 72 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8628 (p) REVERT: H 122 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7750 (p0) REVERT: J 32 MET cc_start: 0.8186 (ttp) cc_final: 0.7888 (ttp) REVERT: J 53 MET cc_start: 0.8365 (tpp) cc_final: 0.8127 (tpp) REVERT: J 127 PHE cc_start: 0.8665 (m-80) cc_final: 0.8367 (m-80) REVERT: J 219 MET cc_start: 0.8367 (ppp) cc_final: 0.7928 (ppp) REVERT: L 198 MET cc_start: 0.8535 (mtt) cc_final: 0.8260 (mtt) REVERT: L 219 MET cc_start: 0.8344 (ptm) cc_final: 0.7758 (ptp) REVERT: M 53 MET cc_start: 0.8553 (ppp) cc_final: 0.8168 (tmm) REVERT: M 134 MET cc_start: 0.8929 (ttm) cc_final: 0.8514 (mtp) REVERT: M 198 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7473 (mmm) REVERT: O 163 ASN cc_start: 0.9237 (m-40) cc_final: 0.8747 (t0) REVERT: O 198 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7381 (mtp) REVERT: P 53 MET cc_start: 0.8386 (tpp) cc_final: 0.8169 (tpp) REVERT: P 219 MET cc_start: 0.8050 (ppp) cc_final: 0.7719 (ppp) REVERT: R 41 LEU cc_start: 0.9580 (tp) cc_final: 0.9366 (mm) REVERT: R 198 MET cc_start: 0.9126 (tpt) cc_final: 0.8717 (mtp) REVERT: R 219 MET cc_start: 0.8143 (ppp) cc_final: 0.7429 (ppp) REVERT: R 237 ASN cc_start: 0.9408 (m-40) cc_final: 0.9034 (p0) REVERT: R 260 MET cc_start: 0.7528 (ttp) cc_final: 0.7266 (ttt) REVERT: S 53 MET cc_start: 0.8376 (tpp) cc_final: 0.8139 (tpp) REVERT: S 134 MET cc_start: 0.9083 (ttt) cc_final: 0.8776 (ppp) REVERT: S 219 MET cc_start: 0.8609 (ppp) cc_final: 0.8267 (ppp) REVERT: S 260 MET cc_start: 0.8283 (ptp) cc_final: 0.7985 (ptt) outliers start: 44 outliers final: 19 residues processed: 196 average time/residue: 0.2011 time to fit residues: 65.2455 Evaluate side-chains 178 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 198 MET Chi-restraints excluded: chain O residue 198 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain P residue 197 CYS Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 137 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [81, 398, 293, 122, 52, 260, 48, 241, 31, 292, 390] chunk 81 optimal weight: 5.9990 chunk 398 optimal weight: 50.0000 chunk 293 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 241 optimal weight: 30.0000 chunk 31 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 390 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 211 GLN L 233 ASN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 HIS ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 HIS S 233 ASN S 236 ASN ** S 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.062977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.040688 restraints weight = 218697.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042188 restraints weight = 119931.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.042825 restraints weight = 69400.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.043011 restraints weight = 52221.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.043106 restraints weight = 53796.533| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35420 Z= 0.200 Angle : 0.561 7.093 48099 Z= 0.289 Chirality : 0.040 0.232 5560 Planarity : 0.003 0.046 5886 Dihedral : 12.630 59.401 5049 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.56 % Favored : 98.34 % Rotamer: Outliers : 1.38 % Allowed : 7.43 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.13), residues: 4048 helix: 2.16 (0.11), residues: 2056 sheet: 0.20 (0.20), residues: 660 loop : -0.11 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 154 TYR 0.024 0.001 TYR C 121 PHE 0.020 0.001 PHE S 24 TRP 0.008 0.001 TRP S 4 HIS 0.016 0.001 HIS O 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (35420) covalent geometry : angle 0.56101 / 0.29 (48099) hydrogen bonds : bond 0.03819 / 2.48 ( 1866) hydrogen bonds : angle 4.55554 / 3.15 ( 5404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8707 (p) REVERT: A 179 TYR cc_start: 0.7964 (m-80) cc_final: 0.7686 (m-80) REVERT: B 217 TYR cc_start: 0.8324 (t80) cc_final: 0.7876 (t80) REVERT: C 1 MET cc_start: 0.6585 (mtp) cc_final: 0.6187 (ttm) REVERT: C 50 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8378 (ptpp) REVERT: C 72 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (p) REVERT: D 12 MET cc_start: 0.8169 (ppp) cc_final: 0.7753 (ppp) REVERT: F 109 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8321 (mmm) REVERT: G 1 MET cc_start: 0.8003 (mmm) cc_final: 0.7717 (tpt) REVERT: H 122 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7886 (p0) REVERT: J 32 MET cc_start: 0.8260 (ttp) cc_final: 0.7913 (ttp) REVERT: J 45 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8493 (p) REVERT: J 53 MET cc_start: 0.8434 (tpp) cc_final: 0.8122 (tpp) REVERT: J 127 PHE cc_start: 0.8764 (m-80) cc_final: 0.8473 (m-80) REVERT: J 219 MET cc_start: 0.8372 (ppp) cc_final: 0.7936 (ppp) REVERT: L 219 MET cc_start: 0.8316 (ptm) cc_final: 0.7809 (ptp) REVERT: M 53 MET cc_start: 0.8697 (ppp) cc_final: 0.8305 (tmm) REVERT: M 134 MET cc_start: 0.8912 (ttm) cc_final: 0.8546 (mtp) REVERT: O 163 ASN cc_start: 0.9222 (m-40) cc_final: 0.8752 (t0) REVERT: O 198 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: P 198 MET cc_start: 0.5105 (mmm) cc_final: 0.4737 (mmm) REVERT: P 219 MET cc_start: 0.8091 (ppp) cc_final: 0.7796 (ppp) REVERT: R 41 LEU cc_start: 0.9585 (tp) cc_final: 0.9378 (mm) REVERT: R 198 MET cc_start: 0.9138 (tpt) cc_final: 0.8716 (mtp) REVERT: R 219 MET cc_start: 0.8214 (ppp) cc_final: 0.7380 (ppp) REVERT: R 237 ASN cc_start: 0.9400 (m-40) cc_final: 0.9031 (p0) REVERT: S 53 MET cc_start: 0.8494 (tpp) cc_final: 0.8190 (tpp) REVERT: S 134 MET cc_start: 0.9079 (ttt) cc_final: 0.8787 (ppp) REVERT: S 219 MET cc_start: 0.8720 (ppp) cc_final: 0.8378 (ppp) REVERT: S 260 MET cc_start: 0.8491 (ptp) cc_final: 0.7833 (ptt) outliers start: 53 outliers final: 24 residues processed: 192 average time/residue: 0.1994 time to fit residues: 63.7142 Evaluate side-chains 176 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain O residue 198 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [201, 292, 328, 364, 275, 219, 181, 390, 221, 258, 186] chunk 201 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 328 optimal weight: 5.9990 chunk 364 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 390 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 258 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 71 ASN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN O 138 HIS ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.039923 restraints weight = 218755.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041345 restraints weight = 120186.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042009 restraints weight = 69993.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.042181 restraints weight = 52401.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.042277 restraints weight = 54158.624| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35420 Z= 0.211 Angle : 0.548 9.756 48099 Z= 0.284 Chirality : 0.040 0.345 5560 Planarity : 0.003 0.069 5886 Dihedral : 12.792 59.302 5049 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 1.28 % Allowed : 7.59 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.13), residues: 4048 helix: 2.21 (0.11), residues: 2076 sheet: 0.15 (0.20), residues: 656 loop : -0.11 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG C 198 TYR 0.025 0.001 TYR C 121 PHE 0.020 0.001 PHE S 24 TRP 0.007 0.001 TRP S 106 HIS 0.018 0.001 HIS O 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (35420) covalent geometry : angle 0.54759 / 0.28 (48099) hydrogen bonds : bond 0.03607 / 2.35 ( 1866) hydrogen bonds : angle 4.41780 / 3.04 ( 5404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 109 MET cc_start: 0.8668 (mmp) cc_final: 0.8249 (mmt) REVERT: A 179 TYR cc_start: 0.7972 (m-80) cc_final: 0.7683 (m-80) REVERT: B 217 TYR cc_start: 0.8398 (t80) cc_final: 0.8021 (t80) REVERT: C 1 MET cc_start: 0.6853 (mtp) cc_final: 0.6427 (mtt) REVERT: C 50 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8421 (ptpp) REVERT: C 72 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 12 MET cc_start: 0.8237 (ppp) cc_final: 0.7852 (ppp) REVERT: H 122 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7839 (p0) REVERT: J 53 MET cc_start: 0.8436 (tpp) cc_final: 0.8126 (tpp) REVERT: J 127 PHE cc_start: 0.8832 (m-80) cc_final: 0.8549 (m-80) REVERT: J 198 MET cc_start: 0.5746 (OUTLIER) cc_final: 0.5509 (mmp) REVERT: J 219 MET cc_start: 0.8440 (ppp) cc_final: 0.7977 (ppp) REVERT: L 219 MET cc_start: 0.8315 (ptm) cc_final: 0.7790 (ptp) REVERT: M 53 MET cc_start: 0.8727 (ppp) cc_final: 0.8265 (tmm) REVERT: M 133 ILE cc_start: 0.5692 (OUTLIER) cc_final: 0.5268 (tt) REVERT: M 134 MET cc_start: 0.8926 (ttm) cc_final: 0.8398 (mtp) REVERT: M 198 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7833 (mmp) REVERT: O 53 MET cc_start: 0.8796 (mmm) cc_final: 0.8379 (tmm) REVERT: O 163 ASN cc_start: 0.9244 (m-40) cc_final: 0.8780 (t0) REVERT: P 146 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8666 (p) REVERT: P 219 MET cc_start: 0.8248 (ppp) cc_final: 0.7939 (ppp) REVERT: R 41 LEU cc_start: 0.9592 (tp) cc_final: 0.9385 (mm) REVERT: R 198 MET cc_start: 0.9146 (tpt) cc_final: 0.8789 (mtp) REVERT: R 219 MET cc_start: 0.8253 (ppp) cc_final: 0.7415 (ppp) REVERT: R 237 ASN cc_start: 0.9401 (m-40) cc_final: 0.9051 (p0) REVERT: S 53 MET cc_start: 0.8484 (tpp) cc_final: 0.8154 (tpp) REVERT: S 134 MET cc_start: 0.9094 (ttt) cc_final: 0.8815 (ppp) REVERT: S 219 MET cc_start: 0.8709 (ppp) cc_final: 0.8371 (ppp) REVERT: S 260 MET cc_start: 0.8570 (ptp) cc_final: 0.8314 (ptt) outliers start: 49 outliers final: 21 residues processed: 187 average time/residue: 0.1911 time to fit residues: 60.3595 Evaluate side-chains 168 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 198 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 82 TYR Chi-restraints excluded: chain P residue 146 SER Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 82 TYR Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [144, 317, 183, 284, 9, 351, 244, 348, 373, 157, 192] chunk 144 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 348 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 192 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 GLN J 138 HIS L 232 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.061597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039236 restraints weight = 218065.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040647 restraints weight = 120743.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.041229 restraints weight = 70924.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.041463 restraints weight = 54534.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.041553 restraints weight = 54265.064| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35420 Z= 0.223 Angle : 0.566 12.124 48099 Z= 0.293 Chirality : 0.040 0.214 5560 Planarity : 0.003 0.041 5886 Dihedral : 12.864 60.159 5047 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 1.36 % Allowed : 7.92 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.13), residues: 4048 helix: 2.31 (0.11), residues: 2076 sheet: 0.07 (0.20), residues: 656 loop : -0.07 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 198 TYR 0.029 0.001 TYR C 121 PHE 0.021 0.001 PHE S 24 TRP 0.008 0.001 TRP S 106 HIS 0.009 0.001 HIS O 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (35420) covalent geometry : angle 0.56595 / 0.29 (48099) hydrogen bonds : bond 0.03761 / 2.44 ( 1866) hydrogen bonds : angle 4.37157 / 3.01 ( 5404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 141 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 121 TYR cc_start: 0.8580 (p90) cc_final: 0.8317 (p90) REVERT: A 179 TYR cc_start: 0.8096 (m-80) cc_final: 0.7798 (m-80) REVERT: B 156 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9148 (ptpp) REVERT: B 179 TYR cc_start: 0.8380 (m-80) cc_final: 0.8112 (m-80) REVERT: C 1 MET cc_start: 0.6899 (mtp) cc_final: 0.6495 (mtt) REVERT: C 72 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 109 MET cc_start: 0.9123 (mmp) cc_final: 0.8886 (mmp) REVERT: D 12 MET cc_start: 0.8318 (ppp) cc_final: 0.7906 (ppp) REVERT: H 122 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.7813 (p0) REVERT: J 53 MET cc_start: 0.8449 (tpp) cc_final: 0.8168 (tpp) REVERT: J 219 MET cc_start: 0.8486 (ppp) cc_final: 0.8014 (ppp) REVERT: L 198 MET cc_start: 0.8618 (mmt) cc_final: 0.8362 (mtp) REVERT: L 219 MET cc_start: 0.8379 (ptm) cc_final: 0.7912 (ptp) REVERT: L 260 MET cc_start: 0.6782 (tmm) cc_final: 0.6544 (tmm) REVERT: M 53 MET cc_start: 0.8836 (ppp) cc_final: 0.8335 (tmm) REVERT: M 133 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5167 (tt) REVERT: M 134 MET cc_start: 0.8945 (ttm) cc_final: 0.8454 (mtp) REVERT: O 32 MET cc_start: 0.8206 (tpt) cc_final: 0.7330 (tpt) REVERT: O 53 MET cc_start: 0.8882 (mmm) cc_final: 0.8403 (tmm) REVERT: O 163 ASN cc_start: 0.9265 (m-40) cc_final: 0.8802 (t0) REVERT: O 198 MET cc_start: 0.7796 (mtp) cc_final: 0.7154 (mpp) REVERT: O 219 MET cc_start: 0.8731 (ppp) cc_final: 0.7847 (pmm) REVERT: P 146 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8743 (p) REVERT: P 198 MET cc_start: 0.5527 (mmm) cc_final: 0.5109 (mmt) REVERT: P 219 MET cc_start: 0.8264 (ppp) cc_final: 0.7943 (ppp) REVERT: R 41 LEU cc_start: 0.9589 (tp) cc_final: 0.9376 (mm) REVERT: R 198 MET cc_start: 0.9123 (tpt) cc_final: 0.8776 (mtp) REVERT: R 219 MET cc_start: 0.8266 (ppp) cc_final: 0.7391 (ppp) REVERT: R 237 ASN cc_start: 0.9408 (m-40) cc_final: 0.9128 (p0) REVERT: S 53 MET cc_start: 0.8544 (tpp) cc_final: 0.8202 (tpp) REVERT: S 134 MET cc_start: 0.9122 (ttt) cc_final: 0.8842 (ppp) REVERT: S 219 MET cc_start: 0.8753 (ppp) cc_final: 0.8411 (ppp) REVERT: S 260 MET cc_start: 0.8667 (ptp) cc_final: 0.8420 (ptp) outliers start: 52 outliers final: 28 residues processed: 184 average time/residue: 0.1934 time to fit residues: 60.0802 Evaluate side-chains 168 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 146 SER Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [89, 11, 348, 143, 369, 33, 314, 96, 133, 210, 106] chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 369 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 314 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 71 ASN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.061700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.039112 restraints weight = 217049.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.040306 restraints weight = 112287.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041062 restraints weight = 74556.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.041531 restraints weight = 57688.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041802 restraints weight = 49345.002| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35420 Z= 0.165 Angle : 0.526 13.078 48099 Z= 0.272 Chirality : 0.039 0.305 5560 Planarity : 0.003 0.035 5886 Dihedral : 12.847 61.253 5043 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.90 % Favored : 98.00 % Rotamer: Outliers : 1.07 % Allowed : 8.34 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.13), residues: 4048 helix: 2.49 (0.11), residues: 2052 sheet: 0.08 (0.21), residues: 656 loop : -0.03 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 55 TYR 0.038 0.001 TYR D 121 PHE 0.019 0.001 PHE S 24 TRP 0.007 0.001 TRP S 106 HIS 0.008 0.001 HIS O 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (35420) covalent geometry : angle 0.52565 / 0.27 (48099) hydrogen bonds : bond 0.03446 / 2.26 ( 1866) hydrogen bonds : angle 4.23010 / 2.92 ( 5404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8779 (p) REVERT: A 109 MET cc_start: 0.8768 (mmm) cc_final: 0.8015 (mmt) REVERT: A 179 TYR cc_start: 0.8056 (m-80) cc_final: 0.7767 (m-80) REVERT: C 1 MET cc_start: 0.6855 (mtp) cc_final: 0.6499 (mtt) REVERT: C 72 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8710 (p) REVERT: C 109 MET cc_start: 0.9137 (mmp) cc_final: 0.8855 (mmt) REVERT: J 219 MET cc_start: 0.8457 (ppp) cc_final: 0.8002 (ppp) REVERT: L 198 MET cc_start: 0.8707 (mmt) cc_final: 0.8502 (mtm) REVERT: L 219 MET cc_start: 0.8392 (ptm) cc_final: 0.7926 (ptp) REVERT: M 53 MET cc_start: 0.8836 (ppp) cc_final: 0.8333 (tmm) REVERT: M 133 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5148 (tt) REVERT: M 134 MET cc_start: 0.9011 (ttm) cc_final: 0.8475 (mtp) REVERT: M 198 MET cc_start: 0.8326 (mmt) cc_final: 0.7908 (mmp) REVERT: O 32 MET cc_start: 0.8238 (tpt) cc_final: 0.7364 (tpt) REVERT: O 53 MET cc_start: 0.8859 (mmm) cc_final: 0.8409 (tmm) REVERT: O 163 ASN cc_start: 0.9288 (m-40) cc_final: 0.8817 (t0) REVERT: O 198 MET cc_start: 0.7874 (mtp) cc_final: 0.7199 (mpp) REVERT: O 219 MET cc_start: 0.8739 (ppp) cc_final: 0.7821 (pmm) REVERT: P 53 MET cc_start: 0.8601 (tpp) cc_final: 0.8292 (tpt) REVERT: P 198 MET cc_start: 0.5606 (mmm) cc_final: 0.5229 (mmt) REVERT: P 219 MET cc_start: 0.8369 (ppp) cc_final: 0.8045 (ppp) REVERT: R 41 LEU cc_start: 0.9571 (tp) cc_final: 0.9360 (mm) REVERT: R 198 MET cc_start: 0.9070 (tpt) cc_final: 0.8772 (mtp) REVERT: R 219 MET cc_start: 0.8239 (ppp) cc_final: 0.7388 (ppp) REVERT: R 237 ASN cc_start: 0.9399 (m-40) cc_final: 0.9107 (p0) REVERT: R 260 MET cc_start: 0.6814 (ttp) cc_final: 0.6445 (tmm) REVERT: S 53 MET cc_start: 0.8490 (tpp) cc_final: 0.8133 (tpp) REVERT: S 134 MET cc_start: 0.9141 (ttt) cc_final: 0.8805 (ppp) REVERT: S 219 MET cc_start: 0.8712 (ppp) cc_final: 0.8391 (ppp) REVERT: S 260 MET cc_start: 0.8597 (ptp) cc_final: 0.8339 (ptp) outliers start: 41 outliers final: 24 residues processed: 174 average time/residue: 0.1865 time to fit residues: 55.2181 Evaluate side-chains 159 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [14, 344, 321, 261, 81, 275, 222, 273, 249, 40, 46] chunk 14 optimal weight: 0.9980 chunk 344 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.061908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039466 restraints weight = 216834.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040927 restraints weight = 117405.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041513 restraints weight = 68088.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041702 restraints weight = 52595.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041799 restraints weight = 53235.285| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35420 Z= 0.149 Angle : 0.516 13.378 48099 Z= 0.266 Chirality : 0.039 0.157 5560 Planarity : 0.003 0.036 5886 Dihedral : 12.793 61.813 5043 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.90 % Rotamer: Outliers : 1.02 % Allowed : 8.45 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.13), residues: 4048 helix: 2.55 (0.11), residues: 2060 sheet: 0.07 (0.21), residues: 656 loop : 0.01 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 162 TYR 0.025 0.001 TYR F 121 PHE 0.020 0.001 PHE S 24 TRP 0.006 0.001 TRP S 106 HIS 0.016 0.001 HIS I 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (35420) covalent geometry : angle 0.51595 / 0.27 (48099) hydrogen bonds : bond 0.03351 / 2.20 ( 1866) hydrogen bonds : angle 4.13383 / 2.84 ( 5404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8761 (p) REVERT: A 179 TYR cc_start: 0.8107 (m-80) cc_final: 0.7791 (m-80) REVERT: C 1 MET cc_start: 0.6805 (mtp) cc_final: 0.6536 (mtt) REVERT: C 72 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8700 (p) REVERT: C 109 MET cc_start: 0.9149 (mmp) cc_final: 0.8890 (mmt) REVERT: D 109 MET cc_start: 0.9339 (mmp) cc_final: 0.9023 (mmp) REVERT: J 219 MET cc_start: 0.8533 (ppp) cc_final: 0.8112 (ppp) REVERT: L 219 MET cc_start: 0.8465 (ptm) cc_final: 0.7993 (ptp) REVERT: M 53 MET cc_start: 0.8849 (ppp) cc_final: 0.8345 (tmm) REVERT: M 133 ILE cc_start: 0.5639 (OUTLIER) cc_final: 0.5217 (tt) REVERT: M 134 MET cc_start: 0.8951 (ttm) cc_final: 0.8463 (mtp) REVERT: M 198 MET cc_start: 0.8356 (mmt) cc_final: 0.7628 (mmp) REVERT: O 32 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7474 (tpt) REVERT: O 53 MET cc_start: 0.8868 (mmm) cc_final: 0.8352 (tmm) REVERT: O 163 ASN cc_start: 0.9295 (m-40) cc_final: 0.8810 (t0) REVERT: O 198 MET cc_start: 0.7885 (mtp) cc_final: 0.7482 (mpp) REVERT: O 219 MET cc_start: 0.8771 (ppp) cc_final: 0.7877 (pmm) REVERT: P 198 MET cc_start: 0.5665 (mmm) cc_final: 0.5307 (mmt) REVERT: P 219 MET cc_start: 0.8426 (ppp) cc_final: 0.8113 (ppp) REVERT: R 41 LEU cc_start: 0.9592 (tp) cc_final: 0.9373 (mm) REVERT: R 198 MET cc_start: 0.9100 (tpt) cc_final: 0.8717 (mtm) REVERT: R 219 MET cc_start: 0.8223 (ppp) cc_final: 0.7420 (ppp) REVERT: R 237 ASN cc_start: 0.9432 (m-40) cc_final: 0.9151 (p0) REVERT: S 53 MET cc_start: 0.8485 (tpp) cc_final: 0.8123 (tpp) REVERT: S 134 MET cc_start: 0.9122 (ttt) cc_final: 0.8816 (ppp) REVERT: S 219 MET cc_start: 0.8763 (ppp) cc_final: 0.8422 (ppp) REVERT: S 260 MET cc_start: 0.8710 (ptp) cc_final: 0.8489 (ptp) outliers start: 39 outliers final: 30 residues processed: 170 average time/residue: 0.1810 time to fit residues: 52.2964 Evaluate side-chains 164 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [60, 136, 11, 352, 212, 262, 353, 366, 385, 163, 314] chunk 60 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 352 optimal weight: 50.0000 chunk 212 optimal weight: 0.0670 chunk 262 optimal weight: 6.9990 chunk 353 optimal weight: 0.8980 chunk 366 optimal weight: 30.0000 chunk 385 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 314 optimal weight: 7.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 GLN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.062191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.039800 restraints weight = 215717.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041221 restraints weight = 118189.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041886 restraints weight = 68679.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042029 restraints weight = 51408.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042142 restraints weight = 53820.334| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35420 Z= 0.107 Angle : 0.513 14.660 48099 Z= 0.264 Chirality : 0.039 0.178 5560 Planarity : 0.003 0.034 5886 Dihedral : 12.724 61.830 5043 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.88 % Favored : 98.02 % Rotamer: Outliers : 0.94 % Allowed : 8.84 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.13), residues: 4048 helix: 2.59 (0.11), residues: 2060 sheet: 0.12 (0.21), residues: 648 loop : 0.04 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 84 TYR 0.032 0.001 TYR B 121 PHE 0.019 0.001 PHE S 24 TRP 0.004 0.001 TRP P 106 HIS 0.010 0.001 HIS I 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (35420) covalent geometry : angle 0.51253 / 0.26 (48099) hydrogen bonds : bond 0.03184 / 2.10 ( 1866) hydrogen bonds : angle 4.04182 / 2.78 ( 5404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 109 MET cc_start: 0.8664 (mmt) cc_final: 0.8296 (mmt) REVERT: A 179 TYR cc_start: 0.8112 (m-80) cc_final: 0.7789 (m-80) REVERT: A 210 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9222 (ptpp) REVERT: C 1 MET cc_start: 0.6716 (mtp) cc_final: 0.6467 (mtt) REVERT: C 72 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 109 MET cc_start: 0.9135 (mmp) cc_final: 0.8865 (mmt) REVERT: D 109 MET cc_start: 0.9335 (mmp) cc_final: 0.9058 (mmp) REVERT: D 162 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.8362 (tpp80) REVERT: G 109 MET cc_start: 0.8661 (mmp) cc_final: 0.8449 (mmp) REVERT: I 32 MET cc_start: 0.8409 (tpt) cc_final: 0.7965 (tmm) REVERT: J 219 MET cc_start: 0.8512 (ppp) cc_final: 0.8091 (ppp) REVERT: L 219 MET cc_start: 0.8460 (ptm) cc_final: 0.7992 (ptp) REVERT: M 53 MET cc_start: 0.8855 (ppp) cc_final: 0.8304 (tmm) REVERT: M 133 ILE cc_start: 0.5627 (OUTLIER) cc_final: 0.5206 (tt) REVERT: M 134 MET cc_start: 0.8934 (ttm) cc_final: 0.8459 (mtp) REVERT: M 198 MET cc_start: 0.8366 (mmt) cc_final: 0.7709 (mmp) REVERT: O 32 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7658 (tpt) REVERT: O 53 MET cc_start: 0.8857 (mmm) cc_final: 0.8352 (tmm) REVERT: O 163 ASN cc_start: 0.9298 (m-40) cc_final: 0.8824 (t0) REVERT: O 198 MET cc_start: 0.8061 (mtp) cc_final: 0.7733 (mpp) REVERT: O 219 MET cc_start: 0.8740 (ppp) cc_final: 0.7818 (pmm) REVERT: P 198 MET cc_start: 0.5676 (mmm) cc_final: 0.5333 (mmt) REVERT: P 219 MET cc_start: 0.8450 (ppp) cc_final: 0.8131 (ppp) REVERT: R 41 LEU cc_start: 0.9587 (tp) cc_final: 0.9372 (mm) REVERT: R 198 MET cc_start: 0.9104 (tpt) cc_final: 0.8701 (mtm) REVERT: R 219 MET cc_start: 0.8201 (ppp) cc_final: 0.7425 (ppp) REVERT: R 237 ASN cc_start: 0.9435 (m-40) cc_final: 0.9171 (p0) REVERT: R 260 MET cc_start: 0.7065 (ttp) cc_final: 0.6596 (tmm) REVERT: S 53 MET cc_start: 0.8458 (tpp) cc_final: 0.8095 (tpp) REVERT: S 134 MET cc_start: 0.9119 (ttt) cc_final: 0.8814 (ppp) REVERT: S 219 MET cc_start: 0.8789 (ppp) cc_final: 0.8438 (ppp) REVERT: S 260 MET cc_start: 0.8687 (ptp) cc_final: 0.8453 (ptp) outliers start: 36 outliers final: 26 residues processed: 168 average time/residue: 0.1902 time to fit residues: 53.8978 Evaluate side-chains 161 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 82 TYR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 177 LEU Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [348, 366, 344, 315, 203, 178, 155, 195, 150, 18, 262] chunk 348 optimal weight: 5.9990 chunk 366 optimal weight: 20.0000 chunk 344 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 178 optimal weight: 30.0000 chunk 155 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 GLN F 180 GLN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.061139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038725 restraints weight = 218402.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040102 restraints weight = 120359.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040728 restraints weight = 70837.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040935 restraints weight = 52903.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041020 restraints weight = 54921.549| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35420 Z= 0.214 Angle : 0.594 14.007 48099 Z= 0.300 Chirality : 0.040 0.212 5560 Planarity : 0.003 0.037 5886 Dihedral : 12.754 61.866 5043 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer: Outliers : 0.91 % Allowed : 8.97 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.13), residues: 4048 helix: 2.63 (0.11), residues: 2036 sheet: -0.02 (0.21), residues: 648 loop : 0.06 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 72 TYR 0.032 0.001 TYR F 121 PHE 0.021 0.001 PHE M 24 TRP 0.008 0.001 TRP S 106 HIS 0.009 0.001 HIS I 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (35420) covalent geometry : angle 0.59394 / 0.30 (48099) hydrogen bonds : bond 0.03748 / 2.45 ( 1866) hydrogen bonds : angle 4.22479 / 2.91 ( 5404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8096 Ramachandran restraints generated. 4048 Oldfield, 0 Emsley, 4048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 109 MET cc_start: 0.8557 (mmt) cc_final: 0.8129 (mmt) REVERT: A 179 TYR cc_start: 0.8101 (m-80) cc_final: 0.7778 (m-80) REVERT: C 1 MET cc_start: 0.6889 (mtp) cc_final: 0.6648 (mtt) REVERT: C 72 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 109 MET cc_start: 0.9166 (mmp) cc_final: 0.8907 (mmt) REVERT: D 109 MET cc_start: 0.9332 (mmp) cc_final: 0.9038 (mmp) REVERT: J 219 MET cc_start: 0.8555 (ppp) cc_final: 0.8136 (ppp) REVERT: L 219 MET cc_start: 0.8502 (ptm) cc_final: 0.8031 (ptp) REVERT: M 53 MET cc_start: 0.8890 (ppp) cc_final: 0.8636 (ppp) REVERT: M 133 ILE cc_start: 0.5715 (OUTLIER) cc_final: 0.5304 (tt) REVERT: M 134 MET cc_start: 0.8976 (ttm) cc_final: 0.8505 (mtp) REVERT: M 198 MET cc_start: 0.8490 (mmt) cc_final: 0.7858 (mmp) REVERT: O 32 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7592 (tpt) REVERT: O 53 MET cc_start: 0.8895 (mmm) cc_final: 0.8615 (tpp) REVERT: O 163 ASN cc_start: 0.9311 (m-40) cc_final: 0.8829 (t0) REVERT: O 198 MET cc_start: 0.8126 (mtp) cc_final: 0.7468 (mpp) REVERT: P 53 MET cc_start: 0.8960 (tpt) cc_final: 0.8549 (tpp) REVERT: P 198 MET cc_start: 0.5851 (mmm) cc_final: 0.5573 (mmm) REVERT: P 219 MET cc_start: 0.8501 (ppp) cc_final: 0.8182 (ppp) REVERT: R 41 LEU cc_start: 0.9588 (tp) cc_final: 0.9387 (mm) REVERT: R 198 MET cc_start: 0.9124 (tpt) cc_final: 0.8726 (mtm) REVERT: R 219 MET cc_start: 0.8284 (ppp) cc_final: 0.7434 (ppp) REVERT: R 237 ASN cc_start: 0.9418 (m-40) cc_final: 0.9163 (p0) REVERT: S 53 MET cc_start: 0.8550 (tpp) cc_final: 0.7993 (tpp) REVERT: S 134 MET cc_start: 0.9124 (ttt) cc_final: 0.8810 (ppp) REVERT: S 219 MET cc_start: 0.8817 (ppp) cc_final: 0.8483 (ppp) REVERT: S 260 MET cc_start: 0.8746 (ptp) cc_final: 0.8533 (ptp) outliers start: 35 outliers final: 27 residues processed: 163 average time/residue: 0.1898 time to fit residues: 52.6720 Evaluate side-chains 158 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 HIS Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR Chi-restraints excluded: chain S residue 235 HIS Chi-restraints excluded: chain T residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: [82, 208, 284, 257, 38, 71, 135, 174, 66, 372, 146] chunk 82 optimal weight: 0.7980 chunk 208 optimal weight: 8.9990 chunk 284 optimal weight: 9.9990 chunk 257 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 372 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 180 GLN F 180 GLN I 279 GLN ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 HIS J 112 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.062086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.039714 restraints weight = 215824.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041210 restraints weight = 115932.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041779 restraints weight = 67203.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042004 restraints weight = 51460.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042088 restraints weight = 52669.400| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 35420 Z= 0.101 Angle : 0.528 15.529 48099 Z= 0.271 Chirality : 0.040 0.205 5560 Planarity : 0.003 0.043 5886 Dihedral : 12.722 61.762 5041 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.90 % Favored : 98.00 % Rotamer: Outliers : 0.81 % Allowed : 9.18 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.13), residues: 4048 helix: 2.70 (0.11), residues: 2032 sheet: 0.04 (0.21), residues: 648 loop : 0.03 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 55 TYR 0.030 0.001 TYR F 121 PHE 0.019 0.001 PHE M 24 TRP 0.004 0.001 TRP L 106 HIS 0.009 0.001 HIS I 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (35420) covalent geometry : angle 0.52818 / 0.27 (48099) hydrogen bonds : bond 0.03189 / 2.11 ( 1866) hydrogen bonds : angle 4.03255 / 2.77 ( 5404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5653.24 seconds wall clock time: 98 minutes 33.21 seconds (5913.21 seconds total)