Starting phenix.real_space_refine on Fri Mar 6 21:19:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qxf_4668/03_2026/6qxf_4668.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qxf_4668/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6qxf_4668/03_2026/6qxf_4668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qxf_4668/03_2026/6qxf_4668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qxf_4668/03_2026/6qxf_4668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qxf_4668/03_2026/6qxf_4668.map" } 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-dev-5986/lib/python3.9/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: 7.49, per 1000 atoms: 0.22 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: 2.80 Conformation dependent library (CDL) restraints added in 1.5 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: 3.88 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: 7.71 Time building geometry restraints manager: 3.69 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=" N ASN I 62 " pdb=" CA ASN I 62 " ideal model delta sigma weight residual 1.458 1.474 -0.016 1.37e-02 5.33e+03 1.29e+00 bond pdb=" N ASN L 62 " pdb=" CA ASN L 62 " ideal model delta sigma weight residual 1.458 1.474 -0.015 1.37e-02 5.33e+03 1.26e+00 bond pdb=" N ASN R 62 " pdb=" CA ASN R 62 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.37e-02 5.33e+03 1.17e+00 bond pdb=" N ASN O 62 " pdb=" CA ASN O 62 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.37e-02 5.33e+03 1.12e+00 bond pdb=" N LYS I 204 " pdb=" CA LYS I 204 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.23e-02 6.61e+03 8.38e-01 ... (remaining 35415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 47322 1.34 - 2.68: 652 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: 4505 0.045 - 0.091: 747 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: 2.180 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.820 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 0.023 35420 Z= 0.091 Angle : 0.424 6.708 48099 Z= 0.267 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 covalent geometry : bond 0.00165 (35420) covalent geometry : angle 0.42427 (48099) hydrogen bonds : bond 0.09067 ( 1866) hydrogen bonds : angle 8.07375 ( 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 : 0.957 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: 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 160 LYS cc_start: 0.9586 (mttt) cc_final: 0.9281 (tppt) REVERT: E 210 LYS cc_start: 0.9565 (pttt) cc_final: 0.9318 (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: 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: 0.9372 (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: 8 residues processed: 412 average time/residue: 0.2478 time to fit residues: 156.3442 Evaluate side-chains 198 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 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: 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 HIS L 90 GLN L 174 ASN L 211 GLN L 233 ASN ** 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** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 12 HIS ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.064023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.041654 restraints weight = 217616.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042918 restraints weight = 113172.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.043709 restraints weight = 75162.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044208 restraints weight = 57999.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.044486 restraints weight = 49438.655| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 35420 Z= 0.212 Angle : 0.585 7.610 48099 Z= 0.309 Chirality : 0.041 0.209 5560 Planarity : 0.004 0.046 5886 Dihedral : 12.380 58.344 5054 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.24 % Favored : 98.67 % Rotamer: Outliers : 1.04 % Allowed : 6.86 % Favored : 92.10 % 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: 0.77 (0.12), residues: 4048 helix: 1.12 (0.11), residues: 2008 sheet: 0.19 (0.20), residues: 660 loop : -0.06 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 94 TYR 0.018 0.001 TYR E 121 PHE 0.036 0.002 PHE R 246 TRP 0.017 0.001 TRP L 106 HIS 0.006 0.001 HIS M 34 Details of bonding type rmsd covalent geometry : bond 0.00474 (35420) covalent geometry : angle 0.58510 (48099) hydrogen bonds : bond 0.04005 ( 1866) hydrogen bonds : angle 5.14067 ( 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: 40 poor density : 182 time to evaluate : 1.265 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: A 72 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 179 TYR cc_start: 0.7950 (m-80) cc_final: 0.7693 (m-80) REVERT: B 217 TYR cc_start: 0.8251 (t80) cc_final: 0.7808 (t80) REVERT: C 50 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8319 (ptpp) REVERT: C 72 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8615 (p) REVERT: D 109 MET cc_start: 0.7789 (tmm) cc_final: 0.7541 (tmm) REVERT: H 122 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.7825 (p0) REVERT: I 219 MET cc_start: 0.9085 (ppp) cc_final: 0.8512 (ppp) REVERT: J 53 MET cc_start: 0.8441 (tpp) cc_final: 0.8217 (tpp) REVERT: J 127 PHE cc_start: 0.8619 (m-80) cc_final: 0.8323 (m-80) REVERT: J 219 MET cc_start: 0.8416 (ppp) cc_final: 0.8112 (ppp) REVERT: M 53 MET cc_start: 0.8580 (ppp) cc_final: 0.8232 (tmm) REVERT: M 134 MET cc_start: 0.8907 (ttm) cc_final: 0.8493 (mtp) REVERT: M 198 MET cc_start: 0.8083 (mmp) cc_final: 0.7648 (mmm) REVERT: O 163 ASN cc_start: 0.9234 (m-40) cc_final: 0.8749 (t0) REVERT: P 219 MET cc_start: 0.8103 (ppp) cc_final: 0.7695 (ppp) REVERT: R 41 LEU cc_start: 0.9584 (tp) cc_final: 0.9353 (mm) REVERT: R 198 MET cc_start: 0.9053 (tpt) cc_final: 0.8625 (mtp) REVERT: R 219 MET cc_start: 0.8159 (ppp) cc_final: 0.7365 (ppp) REVERT: R 237 ASN cc_start: 0.9411 (m-40) cc_final: 0.9035 (p0) REVERT: S 53 MET cc_start: 0.8545 (tpp) cc_final: 0.8157 (tpp) REVERT: S 134 MET cc_start: 0.9067 (ttt) cc_final: 0.8785 (ppp) REVERT: S 219 MET cc_start: 0.8442 (ppp) cc_final: 0.8146 (ppp) REVERT: S 260 MET cc_start: 0.8298 (ptp) cc_final: 0.7986 (ptp) outliers start: 40 outliers final: 18 residues processed: 216 average time/residue: 0.2321 time to fit residues: 79.5531 Evaluate side-chains 179 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR 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 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 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: chunk 218 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 275 optimal weight: 3.9990 chunk 253 optimal weight: 0.9980 chunk 314 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 chunk 380 optimal weight: 20.0000 chunk 342 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 62 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 = 0.3830 r_free = 0.3830 target = 0.063922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.041467 restraints weight = 217257.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.042734 restraints weight = 112709.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.043526 restraints weight = 74658.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.044012 restraints weight = 57686.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.044284 restraints weight = 49285.316| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35420 Z= 0.138 Angle : 0.499 9.283 48099 Z= 0.264 Chirality : 0.039 0.174 5560 Planarity : 0.003 0.039 5886 Dihedral : 12.445 59.820 5051 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.63 % Favored : 98.27 % Rotamer: Outliers : 1.12 % Allowed : 6.86 % Favored : 92.02 % 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: 1.41 (0.13), residues: 4048 helix: 1.92 (0.11), residues: 2024 sheet: 0.24 (0.20), residues: 660 loop : -0.11 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 55 TYR 0.022 0.001 TYR E 121 PHE 0.024 0.001 PHE R 209 TRP 0.006 0.001 TRP J 4 HIS 0.009 0.001 HIS I 151 Details of bonding type rmsd covalent geometry : bond 0.00305 (35420) covalent geometry : angle 0.49943 (48099) hydrogen bonds : bond 0.03496 ( 1866) hydrogen bonds : angle 4.63965 ( 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 203 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.410 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: A 72 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8629 (p) REVERT: A 179 TYR cc_start: 0.7992 (m-80) cc_final: 0.7702 (m-80) REVERT: B 217 TYR cc_start: 0.8297 (t80) cc_final: 0.7854 (t80) REVERT: C 50 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (ptpp) REVERT: C 72 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8625 (p) REVERT: F 123 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: H 122 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7769 (p0) REVERT: J 32 MET cc_start: 0.8209 (ttp) cc_final: 0.7955 (ttp) REVERT: J 53 MET cc_start: 0.8419 (tpp) cc_final: 0.8155 (tpp) REVERT: J 127 PHE cc_start: 0.8694 (m-80) cc_final: 0.8391 (m-80) REVERT: J 151 HIS cc_start: 0.9108 (OUTLIER) cc_final: 0.8231 (m90) REVERT: J 198 MET cc_start: 0.5603 (mmp) cc_final: 0.5227 (mmp) REVERT: J 219 MET cc_start: 0.8347 (ppp) cc_final: 0.7903 (ppp) REVERT: M 53 MET cc_start: 0.8615 (ppp) cc_final: 0.8208 (tmm) REVERT: M 134 MET cc_start: 0.8924 (ttm) cc_final: 0.8510 (mtp) REVERT: M 198 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7837 (mmp) REVERT: O 163 ASN cc_start: 0.9262 (m-40) cc_final: 0.8789 (t0) REVERT: O 198 MET cc_start: 0.8100 (mtp) cc_final: 0.7865 (mtp) REVERT: P 53 MET cc_start: 0.8475 (tpp) cc_final: 0.8270 (tpp) REVERT: P 219 MET cc_start: 0.8046 (ppp) cc_final: 0.7715 (ppp) REVERT: R 41 LEU cc_start: 0.9583 (tp) cc_final: 0.9366 (mm) REVERT: R 198 MET cc_start: 0.9057 (tpt) cc_final: 0.8645 (mtp) REVERT: R 219 MET cc_start: 0.8196 (ppp) cc_final: 0.7344 (ppp) REVERT: R 237 ASN cc_start: 0.9403 (m-40) cc_final: 0.9032 (p0) REVERT: S 53 MET cc_start: 0.8436 (tpp) cc_final: 0.8172 (tpp) REVERT: S 134 MET cc_start: 0.9078 (ttt) cc_final: 0.8775 (ppp) REVERT: S 219 MET cc_start: 0.8634 (ppp) cc_final: 0.8328 (ppp) REVERT: S 260 MET cc_start: 0.8180 (ptp) cc_final: 0.7850 (ptt) outliers start: 43 outliers final: 16 residues processed: 196 average time/residue: 0.2151 time to fit residues: 68.8065 Evaluate side-chains 169 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 D residue 219 ASN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 123 GLU 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 H residue 159 VAL Chi-restraints excluded: chain I residue 134 MET Chi-restraints excluded: chain J residue 82 TYR Chi-restraints excluded: chain J residue 151 HIS Chi-restraints excluded: chain M residue 82 TYR 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 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: chunk 81 optimal weight: 0.2980 chunk 398 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 260 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 241 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 390 optimal weight: 10.0000 overall best weight: 2.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 ASN J 151 HIS J 211 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 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 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 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 = 0.3815 r_free = 0.3815 target = 0.063284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040802 restraints weight = 216848.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042047 restraints weight = 112035.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.042831 restraints weight = 74224.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043266 restraints weight = 57328.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.043601 restraints weight = 49192.100| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35420 Z= 0.142 Angle : 0.488 9.323 48099 Z= 0.258 Chirality : 0.039 0.170 5560 Planarity : 0.003 0.034 5886 Dihedral : 12.428 60.624 5051 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.56 % Favored : 98.34 % Rotamer: Outliers : 1.07 % Allowed : 7.56 % Favored : 91.37 % 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: 1.76 (0.13), residues: 4048 helix: 2.31 (0.11), residues: 2024 sheet: 0.22 (0.20), residues: 660 loop : -0.02 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 148 TYR 0.013 0.001 TYR C 121 PHE 0.017 0.001 PHE S 24 TRP 0.006 0.001 TRP S 4 HIS 0.010 0.001 HIS O 21 Details of bonding type rmsd covalent geometry : bond 0.00308 (35420) covalent geometry : angle 0.48788 (48099) hydrogen bonds : bond 0.03374 ( 1866) hydrogen bonds : angle 4.35361 ( 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 192 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8673 (p) REVERT: A 109 MET cc_start: 0.8602 (mmp) cc_final: 0.7950 (mmt) REVERT: A 121 TYR cc_start: 0.8312 (p90) cc_final: 0.7640 (p90) REVERT: A 179 TYR cc_start: 0.7986 (m-80) cc_final: 0.7685 (m-80) REVERT: B 217 TYR cc_start: 0.8346 (t80) cc_final: 0.7912 (t80) REVERT: C 1 MET cc_start: 0.6551 (mtp) cc_final: 0.6081 (mtt) REVERT: C 50 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8331 (ptpp) REVERT: C 72 THR cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (p) REVERT: F 123 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: J 53 MET cc_start: 0.8387 (tpp) cc_final: 0.8134 (tpp) REVERT: J 127 PHE cc_start: 0.8704 (m-80) cc_final: 0.8403 (m-80) REVERT: J 219 MET cc_start: 0.8392 (ppp) cc_final: 0.7940 (ppp) REVERT: M 53 MET cc_start: 0.8689 (ppp) cc_final: 0.8319 (tmm) REVERT: M 133 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5218 (tt) REVERT: M 134 MET cc_start: 0.8976 (ttm) cc_final: 0.8468 (mtp) REVERT: M 198 MET cc_start: 0.8306 (mmp) cc_final: 0.7553 (mmt) REVERT: M 260 MET cc_start: 0.8401 (mtp) cc_final: 0.8179 (mtm) REVERT: O 163 ASN cc_start: 0.9255 (m-40) cc_final: 0.8776 (t0) REVERT: P 198 MET cc_start: 0.5278 (mmm) cc_final: 0.4863 (mmm) REVERT: P 219 MET cc_start: 0.8063 (ppp) cc_final: 0.7757 (ppp) REVERT: R 198 MET cc_start: 0.9096 (tpt) cc_final: 0.8763 (mtp) REVERT: R 219 MET cc_start: 0.8161 (ppp) cc_final: 0.7320 (ppp) REVERT: R 237 ASN cc_start: 0.9392 (m-40) cc_final: 0.9034 (p0) REVERT: S 53 MET cc_start: 0.8456 (tpp) cc_final: 0.8144 (tpp) REVERT: S 134 MET cc_start: 0.9114 (ttt) cc_final: 0.8794 (ppp) REVERT: S 219 MET cc_start: 0.8631 (ppp) cc_final: 0.8339 (ppp) REVERT: S 260 MET cc_start: 0.8288 (ptp) cc_final: 0.7910 (ptp) outliers start: 41 outliers final: 21 residues processed: 185 average time/residue: 0.1988 time to fit residues: 61.4796 Evaluate side-chains 171 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 123 GLU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 187 LEU 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 82 TYR Chi-restraints excluded: chain J residue 197 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 328 optimal weight: 4.9990 chunk 364 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 chunk 219 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN D 180 GLN E 71 ASN F 180 GLN H 37 GLN H 180 GLN ** J 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN J 138 HIS J 233 ASN J 236 ASN L 232 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 HIS O 138 HIS ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 ASN S 236 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.060650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.038268 restraints weight = 220184.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.039500 restraints weight = 121142.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040231 restraints weight = 73252.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.040459 restraints weight = 54505.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040550 restraints weight = 53508.796| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 35420 Z= 0.333 Angle : 0.697 10.026 48099 Z= 0.354 Chirality : 0.042 0.159 5560 Planarity : 0.004 0.046 5886 Dihedral : 12.884 61.245 5049 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Rotamer: Outliers : 1.43 % Allowed : 7.95 % Favored : 90.62 % 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: 1.38 (0.13), residues: 4048 helix: 1.92 (0.11), residues: 2080 sheet: -0.02 (0.20), residues: 656 loop : -0.13 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 198 TYR 0.031 0.002 TYR H 121 PHE 0.022 0.002 PHE M 24 TRP 0.013 0.001 TRP S 106 HIS 0.018 0.002 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00736 (35420) covalent geometry : angle 0.69651 (48099) hydrogen bonds : bond 0.04912 ( 1866) hydrogen bonds : angle 4.65967 ( 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 191 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 136 time to evaluate : 1.311 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: 0.9014 (OUTLIER) cc_final: 0.8718 (p) REVERT: A 179 TYR cc_start: 0.8071 (m-80) cc_final: 0.7789 (m-80) REVERT: B 156 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9036 (ptpp) REVERT: B 179 TYR cc_start: 0.8387 (m-80) cc_final: 0.8131 (m-80) REVERT: C 1 MET cc_start: 0.7095 (mtp) cc_final: 0.6737 (mtt) REVERT: C 72 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8742 (p) REVERT: D 12 MET cc_start: 0.8436 (ppp) cc_final: 0.7966 (ppp) REVERT: E 121 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7993 (p90) REVERT: J 45 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8674 (p) REVERT: J 53 MET cc_start: 0.8516 (tpp) cc_final: 0.8196 (tpp) REVERT: J 219 MET cc_start: 0.8440 (ppp) cc_final: 0.7995 (ppp) REVERT: L 219 MET cc_start: 0.8541 (ptm) cc_final: 0.8151 (ptm) REVERT: M 133 ILE cc_start: 0.5626 (OUTLIER) cc_final: 0.5236 (tt) REVERT: M 134 MET cc_start: 0.8964 (ttm) cc_final: 0.8456 (mtp) REVERT: O 53 MET cc_start: 0.8962 (mmm) cc_final: 0.8654 (tpp) REVERT: O 163 ASN cc_start: 0.9307 (m-40) cc_final: 0.8835 (t0) REVERT: O 198 MET cc_start: 0.8134 (mtp) cc_final: 0.7607 (mpp) REVERT: P 146 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8735 (p) REVERT: P 198 MET cc_start: 0.6032 (mmm) cc_final: 0.5505 (mmt) REVERT: P 219 MET cc_start: 0.8342 (ppp) cc_final: 0.8012 (ppp) REVERT: R 198 MET cc_start: 0.9122 (tpt) cc_final: 0.8753 (mtm) REVERT: R 219 MET cc_start: 0.8303 (ppp) cc_final: 0.7323 (ppp) REVERT: R 237 ASN cc_start: 0.9419 (m-40) cc_final: 0.9125 (p0) REVERT: S 53 MET cc_start: 0.8512 (tpp) cc_final: 0.7969 (tpp) REVERT: S 134 MET cc_start: 0.9110 (ttt) cc_final: 0.8799 (ppp) REVERT: S 219 MET cc_start: 0.8750 (ppp) cc_final: 0.8448 (ppp) REVERT: S 260 MET cc_start: 0.8647 (ptp) cc_final: 0.8136 (ptp) outliers start: 55 outliers final: 29 residues processed: 182 average time/residue: 0.2127 time to fit residues: 64.3442 Evaluate side-chains 163 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 127 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 121 TYR 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 F residue 187 LEU Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 159 VAL 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 197 CYS 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 P residue 22 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 146 SER Chi-restraints excluded: chain P residue 197 CYS Chi-restraints excluded: chain S residue 30 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 144 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 183 optimal weight: 30.0000 chunk 284 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 348 optimal weight: 20.0000 chunk 373 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 192 optimal weight: 30.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 233 ASN J 85 HIS J 112 GLN J 233 ASN J 236 ASN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 ASN ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.061286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.038801 restraints weight = 216984.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040184 restraints weight = 117280.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.040837 restraints weight = 69392.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041044 restraints weight = 51902.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.041145 restraints weight = 53488.337| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35420 Z= 0.230 Angle : 0.565 12.758 48099 Z= 0.294 Chirality : 0.040 0.165 5560 Planarity : 0.003 0.039 5886 Dihedral : 13.005 64.113 5043 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.03 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 8.63 % Favored : 90.07 % 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: 2.19 (0.11), residues: 2084 sheet: -0.12 (0.20), residues: 656 loop : -0.01 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 198 TYR 0.018 0.001 TYR B 121 PHE 0.018 0.001 PHE S 24 TRP 0.007 0.001 TRP S 106 HIS 0.012 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00510 (35420) covalent geometry : angle 0.56517 (48099) hydrogen bonds : bond 0.03655 ( 1866) hydrogen bonds : angle 4.38137 ( 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 184 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 1.450 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: 0.9041 (OUTLIER) cc_final: 0.8717 (p) REVERT: A 109 MET cc_start: 0.8733 (mmm) cc_final: 0.7739 (mmt) REVERT: A 121 TYR cc_start: 0.8442 (p90) cc_final: 0.8149 (p90) REVERT: A 179 TYR cc_start: 0.8121 (m-80) cc_final: 0.7828 (m-80) REVERT: B 179 TYR cc_start: 0.8384 (m-80) cc_final: 0.8139 (m-80) REVERT: C 1 MET cc_start: 0.7080 (mtp) cc_final: 0.6766 (mtt) REVERT: C 72 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8724 (p) REVERT: C 109 MET cc_start: 0.9070 (mmp) cc_final: 0.8761 (mmt) REVERT: D 109 MET cc_start: 0.8364 (tmm) cc_final: 0.8000 (tmm) REVERT: F 149 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: J 45 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8633 (p) REVERT: J 53 MET cc_start: 0.8431 (tpp) cc_final: 0.8148 (tpp) REVERT: J 219 MET cc_start: 0.8489 (ppp) cc_final: 0.8059 (ppp) REVERT: L 260 MET cc_start: 0.7019 (tmm) cc_final: 0.6789 (ppp) REVERT: M 133 ILE cc_start: 0.5730 (OUTLIER) cc_final: 0.5338 (tt) REVERT: M 134 MET cc_start: 0.8958 (ttm) cc_final: 0.8414 (mtp) REVERT: O 32 MET cc_start: 0.8267 (tpt) cc_final: 0.7314 (tpt) REVERT: O 53 MET cc_start: 0.8960 (mmm) cc_final: 0.8677 (tpp) REVERT: O 163 ASN cc_start: 0.9353 (m-40) cc_final: 0.8906 (t0) REVERT: O 198 MET cc_start: 0.8178 (mtp) cc_final: 0.7584 (mpp) REVERT: O 219 MET cc_start: 0.8761 (ppp) cc_final: 0.7918 (pmm) REVERT: P 198 MET cc_start: 0.6290 (mmm) cc_final: 0.5887 (mmt) REVERT: P 219 MET cc_start: 0.8417 (ppp) cc_final: 0.8080 (ppp) REVERT: R 198 MET cc_start: 0.9129 (tpt) cc_final: 0.8761 (mtm) REVERT: R 219 MET cc_start: 0.8326 (ppp) cc_final: 0.7425 (ppp) REVERT: R 237 ASN cc_start: 0.9419 (m-40) cc_final: 0.9180 (p0) REVERT: S 53 MET cc_start: 0.8505 (tpp) cc_final: 0.7929 (tpp) REVERT: S 134 MET cc_start: 0.9105 (ttt) cc_final: 0.8804 (ppp) REVERT: S 198 MET cc_start: 0.7813 (mmp) cc_final: 0.7577 (mmp) REVERT: S 219 MET cc_start: 0.8768 (ppp) cc_final: 0.8427 (ppp) REVERT: S 260 MET cc_start: 0.8609 (ptp) cc_final: 0.8338 (ptp) outliers start: 50 outliers final: 27 residues processed: 180 average time/residue: 0.2082 time to fit residues: 62.4033 Evaluate side-chains 157 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 135 VAL 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 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 149 PHE Chi-restraints excluded: chain F residue 156 LYS Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 163 ILE 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 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 197 CYS 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 S residue 50 LEU Chi-restraints excluded: chain S residue 137 TYR 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: chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 348 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 369 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 71 ASN H 180 GLN ** 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** ** S 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.039705 restraints weight = 215843.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.041201 restraints weight = 114881.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041798 restraints weight = 65560.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.041981 restraints weight = 50847.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.042081 restraints weight = 51720.725| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35420 Z= 0.108 Angle : 0.493 14.075 48099 Z= 0.259 Chirality : 0.039 0.160 5560 Planarity : 0.003 0.039 5886 Dihedral : 12.806 65.104 5043 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.17 % Rotamer: Outliers : 0.78 % Allowed : 9.28 % Favored : 89.94 % 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: 1.92 (0.13), residues: 4048 helix: 2.52 (0.11), residues: 2060 sheet: -0.04 (0.21), residues: 656 loop : 0.03 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 84 TYR 0.022 0.001 TYR B 121 PHE 0.032 0.001 PHE R 209 TRP 0.005 0.001 TRP O 106 HIS 0.010 0.001 HIS J 21 Details of bonding type rmsd covalent geometry : bond 0.00237 (35420) covalent geometry : angle 0.49317 (48099) hydrogen bonds : bond 0.03168 ( 1866) hydrogen bonds : angle 4.08095 ( 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 160 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.512 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: A 72 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8774 (p) REVERT: A 109 MET cc_start: 0.8735 (mmm) cc_final: 0.7758 (mmt) REVERT: A 179 TYR cc_start: 0.8024 (m-80) cc_final: 0.7720 (m-80) REVERT: C 72 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8702 (p) REVERT: D 12 MET cc_start: 0.7878 (ppp) cc_final: 0.7548 (ppp) REVERT: D 109 MET cc_start: 0.8359 (tmm) cc_final: 0.7941 (tmm) REVERT: E 121 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.8080 (p90) REVERT: J 45 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8522 (p) REVERT: J 53 MET cc_start: 0.8400 (tpp) cc_final: 0.8118 (tpp) REVERT: J 131 GLN cc_start: 0.9223 (mm-40) cc_final: 0.9009 (mm-40) REVERT: J 198 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6515 (mmp) REVERT: J 219 MET cc_start: 0.8519 (ppp) cc_final: 0.8074 (ppp) REVERT: L 219 MET cc_start: 0.8657 (ptm) cc_final: 0.8197 (ptp) REVERT: L 260 MET cc_start: 0.7101 (tmm) cc_final: 0.6874 (ppp) REVERT: M 133 ILE cc_start: 0.5657 (OUTLIER) cc_final: 0.5247 (tt) REVERT: M 134 MET cc_start: 0.8977 (ttm) cc_final: 0.8501 (mtp) REVERT: O 32 MET cc_start: 0.8273 (tpt) cc_final: 0.7542 (tpt) REVERT: O 53 MET cc_start: 0.8930 (mmm) cc_final: 0.8651 (tpp) REVERT: O 163 ASN cc_start: 0.9311 (m-40) cc_final: 0.8840 (t0) REVERT: O 198 MET cc_start: 0.8249 (mtp) cc_final: 0.7891 (mpp) REVERT: O 219 MET cc_start: 0.8773 (ppp) cc_final: 0.7906 (pmm) REVERT: P 198 MET cc_start: 0.6391 (mmm) cc_final: 0.5578 (mmt) REVERT: P 219 MET cc_start: 0.8441 (ppp) cc_final: 0.8097 (ppp) REVERT: R 198 MET cc_start: 0.9110 (tpt) cc_final: 0.8738 (mtm) REVERT: R 219 MET cc_start: 0.8242 (ppp) cc_final: 0.7406 (ppp) REVERT: R 260 MET cc_start: 0.6982 (ttp) cc_final: 0.6605 (tmm) REVERT: S 53 MET cc_start: 0.8477 (tpp) cc_final: 0.7897 (tpp) REVERT: S 134 MET cc_start: 0.9105 (ttt) cc_final: 0.8793 (ppp) REVERT: S 198 MET cc_start: 0.7739 (mmp) cc_final: 0.7470 (mmp) REVERT: S 219 MET cc_start: 0.8808 (ppp) cc_final: 0.8459 (ppp) REVERT: S 260 MET cc_start: 0.8619 (ptp) cc_final: 0.8327 (ptp) outliers start: 30 outliers final: 17 residues processed: 158 average time/residue: 0.2088 time to fit residues: 55.3918 Evaluate side-chains 147 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 156 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 121 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain J residue 45 THR 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 M residue 133 ILE Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain P residue 30 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 14 optimal weight: 4.9990 chunk 344 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 261 optimal weight: 0.6980 chunk 81 optimal weight: 0.0170 chunk 275 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 273 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.062078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.039671 restraints weight = 214603.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.041064 restraints weight = 113951.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.041705 restraints weight = 68164.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041865 restraints weight = 51041.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041971 restraints weight = 52698.719| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35420 Z= 0.110 Angle : 0.499 15.286 48099 Z= 0.260 Chirality : 0.039 0.158 5560 Planarity : 0.003 0.041 5886 Dihedral : 12.646 65.144 5043 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.95 % Favored : 97.95 % Rotamer: Outliers : 0.83 % Allowed : 9.49 % Favored : 89.68 % 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: 2.02 (0.13), residues: 4048 helix: 2.61 (0.11), residues: 2060 sheet: 0.00 (0.21), residues: 648 loop : 0.07 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 55 TYR 0.027 0.001 TYR B 121 PHE 0.018 0.001 PHE S 24 TRP 0.005 0.001 TRP P 106 HIS 0.009 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00243 (35420) covalent geometry : angle 0.49897 (48099) hydrogen bonds : bond 0.03133 ( 1866) hydrogen bonds : angle 3.99811 ( 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 162 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.110 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: 0.9164 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 179 TYR cc_start: 0.7921 (m-80) cc_final: 0.7618 (m-80) REVERT: C 72 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8791 (p) REVERT: D 12 MET cc_start: 0.7879 (ppp) cc_final: 0.7552 (ppp) REVERT: D 109 MET cc_start: 0.8268 (tmm) cc_final: 0.7905 (tmm) REVERT: E 121 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7976 (p90) REVERT: J 53 MET cc_start: 0.8353 (tpp) cc_final: 0.8080 (tpp) REVERT: J 131 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8987 (mm-40) REVERT: J 219 MET cc_start: 0.8531 (ppp) cc_final: 0.8132 (ppp) REVERT: L 260 MET cc_start: 0.7072 (tmm) cc_final: 0.6827 (ppp) REVERT: M 133 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.5214 (tt) REVERT: M 134 MET cc_start: 0.8993 (ttm) cc_final: 0.8526 (mtp) REVERT: O 32 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7670 (tpt) REVERT: O 163 ASN cc_start: 0.9308 (m-40) cc_final: 0.8821 (t0) REVERT: O 198 MET cc_start: 0.8256 (mtp) cc_final: 0.7930 (mpp) REVERT: O 219 MET cc_start: 0.8753 (ppp) cc_final: 0.7901 (pmm) REVERT: P 53 MET cc_start: 0.8929 (tpt) cc_final: 0.8473 (tpp) REVERT: P 198 MET cc_start: 0.6494 (mmm) cc_final: 0.5736 (mmt) REVERT: P 219 MET cc_start: 0.8424 (ppp) cc_final: 0.8093 (ppp) REVERT: R 198 MET cc_start: 0.9083 (tpt) cc_final: 0.8751 (mtm) REVERT: R 219 MET cc_start: 0.8255 (ppp) cc_final: 0.7426 (ppp) REVERT: R 260 MET cc_start: 0.7062 (ttp) cc_final: 0.6664 (tmm) REVERT: S 53 MET cc_start: 0.8461 (tpp) cc_final: 0.7907 (tpp) REVERT: S 134 MET cc_start: 0.9139 (ttt) cc_final: 0.8820 (ppp) REVERT: S 219 MET cc_start: 0.8801 (ppp) cc_final: 0.8478 (ppp) REVERT: S 260 MET cc_start: 0.8666 (ptp) cc_final: 0.8387 (ptp) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.2101 time to fit residues: 54.9903 Evaluate side-chains 154 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 135 VAL 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 149 PHE Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 121 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain L residue 127 PHE 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 P residue 30 THR Chi-restraints excluded: chain P residue 75 THR 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: chunk 60 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 352 optimal weight: 30.0000 chunk 212 optimal weight: 0.9990 chunk 262 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 366 optimal weight: 30.0000 chunk 385 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 314 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.061997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.039657 restraints weight = 215736.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.041123 restraints weight = 114075.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.041744 restraints weight = 66152.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.041878 restraints weight = 50685.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.041991 restraints weight = 51736.386| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35420 Z= 0.117 Angle : 0.499 15.216 48099 Z= 0.259 Chirality : 0.039 0.155 5560 Planarity : 0.003 0.044 5886 Dihedral : 12.589 65.326 5043 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.97 % Rotamer: Outliers : 0.94 % Allowed : 9.44 % Favored : 89.62 % 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: 2.10 (0.13), residues: 4048 helix: 2.72 (0.11), residues: 2036 sheet: 0.01 (0.21), residues: 648 loop : 0.09 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.028 0.001 TYR B 121 PHE 0.018 0.001 PHE S 24 TRP 0.005 0.001 TRP P 106 HIS 0.009 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00262 (35420) covalent geometry : angle 0.49866 (48099) hydrogen bonds : bond 0.03141 ( 1866) hydrogen bonds : angle 3.98116 ( 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 164 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.267 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: A 72 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 109 MET cc_start: 0.8541 (mmt) cc_final: 0.8043 (mmt) REVERT: A 179 TYR cc_start: 0.8009 (m-80) cc_final: 0.7681 (m-80) REVERT: C 72 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8734 (p) REVERT: D 12 MET cc_start: 0.7912 (ppp) cc_final: 0.7568 (ppp) REVERT: D 109 MET cc_start: 0.8327 (tmm) cc_final: 0.7939 (tmm) REVERT: F 1 MET cc_start: 0.7323 (tpt) cc_final: 0.7115 (tpp) REVERT: F 109 MET cc_start: 0.8533 (ptp) cc_final: 0.8312 (ptp) REVERT: I 32 MET cc_start: 0.8915 (tpt) cc_final: 0.8680 (tpt) REVERT: I 260 MET cc_start: 0.8664 (mmm) cc_final: 0.8406 (mmm) REVERT: J 53 MET cc_start: 0.8394 (tpp) cc_final: 0.8110 (tpp) REVERT: J 131 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8971 (mm-40) REVERT: J 219 MET cc_start: 0.8553 (ppp) cc_final: 0.8150 (ppp) REVERT: L 219 MET cc_start: 0.8663 (ptm) cc_final: 0.8163 (ptp) REVERT: L 260 MET cc_start: 0.7139 (tmm) cc_final: 0.6921 (ppp) REVERT: M 133 ILE cc_start: 0.5668 (OUTLIER) cc_final: 0.5252 (tt) REVERT: M 134 MET cc_start: 0.8982 (ttm) cc_final: 0.8514 (mtp) REVERT: O 32 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7747 (tpt) REVERT: O 53 MET cc_start: 0.8824 (tmm) cc_final: 0.8295 (tmm) REVERT: O 163 ASN cc_start: 0.9291 (m-40) cc_final: 0.8736 (t0) REVERT: O 198 MET cc_start: 0.8283 (mtp) cc_final: 0.7887 (mpp) REVERT: P 53 MET cc_start: 0.8929 (tpt) cc_final: 0.8396 (tpp) REVERT: P 198 MET cc_start: 0.6480 (mmm) cc_final: 0.5586 (mmp) REVERT: P 219 MET cc_start: 0.8468 (ppp) cc_final: 0.8135 (ppp) REVERT: R 198 MET cc_start: 0.9093 (tpt) cc_final: 0.8743 (mtm) REVERT: R 219 MET cc_start: 0.8266 (ppp) cc_final: 0.7414 (ppp) REVERT: R 260 MET cc_start: 0.7060 (ttp) cc_final: 0.6683 (tmm) REVERT: S 53 MET cc_start: 0.8501 (tpp) cc_final: 0.7925 (tpp) REVERT: S 134 MET cc_start: 0.9159 (ttt) cc_final: 0.8828 (ppp) REVERT: S 219 MET cc_start: 0.8830 (ppp) cc_final: 0.8509 (ppp) REVERT: S 260 MET cc_start: 0.8676 (ptp) cc_final: 0.8461 (ptt) outliers start: 36 outliers final: 26 residues processed: 158 average time/residue: 0.2018 time to fit residues: 53.2771 Evaluate side-chains 154 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL 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 149 PHE Chi-restraints excluded: chain D residue 156 LYS 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 159 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain M residue 82 TYR 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 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: chunk 348 optimal weight: 20.0000 chunk 366 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 262 optimal weight: 9.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN ** L 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.061762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039443 restraints weight = 217143.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040928 restraints weight = 115675.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.041569 restraints weight = 65981.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.041722 restraints weight = 50682.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041830 restraints weight = 51385.303| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35420 Z= 0.135 Angle : 0.518 18.029 48099 Z= 0.267 Chirality : 0.039 0.186 5560 Planarity : 0.003 0.044 5886 Dihedral : 12.570 65.724 5043 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 0.83 % Allowed : 9.59 % Favored : 89.57 % 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: 2.08 (0.13), residues: 4048 helix: 2.74 (0.11), residues: 2036 sheet: -0.03 (0.21), residues: 656 loop : 0.05 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 198 TYR 0.027 0.001 TYR B 121 PHE 0.018 0.001 PHE S 24 TRP 0.004 0.001 TRP P 106 HIS 0.009 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00302 (35420) covalent geometry : angle 0.51771 (48099) hydrogen bonds : bond 0.03211 ( 1866) hydrogen bonds : angle 4.00792 ( 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 158 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.914 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: 0.9167 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 109 MET cc_start: 0.8460 (mmt) cc_final: 0.8221 (mmt) REVERT: A 179 TYR cc_start: 0.7919 (m-80) cc_final: 0.7613 (m-80) REVERT: D 12 MET cc_start: 0.7917 (ppp) cc_final: 0.7573 (ppp) REVERT: D 109 MET cc_start: 0.8255 (tmm) cc_final: 0.7920 (tmm) REVERT: F 109 MET cc_start: 0.8482 (ptp) cc_final: 0.8267 (ptp) REVERT: I 260 MET cc_start: 0.8680 (mmm) cc_final: 0.8474 (mmm) REVERT: J 53 MET cc_start: 0.8380 (tpp) cc_final: 0.8107 (tpp) REVERT: J 131 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8954 (mm-40) REVERT: J 219 MET cc_start: 0.8538 (ppp) cc_final: 0.8131 (ppp) REVERT: L 219 MET cc_start: 0.8704 (ptm) cc_final: 0.8232 (ptp) REVERT: L 260 MET cc_start: 0.7077 (tmm) cc_final: 0.6842 (ppp) REVERT: M 133 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5327 (tt) REVERT: M 134 MET cc_start: 0.9022 (ttm) cc_final: 0.8542 (mtp) REVERT: M 198 MET cc_start: 0.8570 (mmp) cc_final: 0.8226 (mmp) REVERT: O 32 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7685 (tpt) REVERT: O 53 MET cc_start: 0.8816 (tmm) cc_final: 0.8251 (tmm) REVERT: O 163 ASN cc_start: 0.9284 (m-40) cc_final: 0.8724 (t0) REVERT: O 198 MET cc_start: 0.8332 (mtp) cc_final: 0.7918 (mpp) REVERT: O 219 MET cc_start: 0.8505 (ppp) cc_final: 0.7637 (pmm) REVERT: P 53 MET cc_start: 0.8904 (tpt) cc_final: 0.8434 (tpp) REVERT: P 198 MET cc_start: 0.6487 (mmm) cc_final: 0.5681 (mmp) REVERT: P 219 MET cc_start: 0.8451 (ppp) cc_final: 0.8134 (ppp) REVERT: R 198 MET cc_start: 0.9071 (tpt) cc_final: 0.8756 (mtm) REVERT: R 219 MET cc_start: 0.8295 (ppp) cc_final: 0.7417 (ppp) REVERT: R 260 MET cc_start: 0.7063 (ttp) cc_final: 0.6690 (tmm) REVERT: S 53 MET cc_start: 0.8512 (tpp) cc_final: 0.7909 (tpp) REVERT: S 134 MET cc_start: 0.9174 (ttt) cc_final: 0.8829 (ppp) REVERT: S 198 MET cc_start: 0.7798 (mmp) cc_final: 0.7538 (mmp) REVERT: S 219 MET cc_start: 0.8815 (ppp) cc_final: 0.8517 (ppp) outliers start: 32 outliers final: 26 residues processed: 153 average time/residue: 0.1969 time to fit residues: 51.2872 Evaluate side-chains 152 residues out of total 3836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 149 PHE Chi-restraints excluded: chain D residue 156 LYS 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 159 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain G residue 121 TYR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 149 PHE Chi-restraints excluded: chain J residue 197 CYS Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain M residue 82 TYR 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 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: chunk 82 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 284 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 138 HIS ** 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 = 0.3775 r_free = 0.3775 target = 0.061454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039168 restraints weight = 217139.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040649 restraints weight = 115595.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.041271 restraints weight = 66156.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041412 restraints weight = 51224.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.041519 restraints weight = 51604.893| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35420 Z= 0.156 Angle : 0.536 15.403 48099 Z= 0.275 Chirality : 0.039 0.230 5560 Planarity : 0.003 0.045 5886 Dihedral : 12.584 66.442 5042 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 0.89 % Allowed : 9.57 % Favored : 89.55 % 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: 2.10 (0.13), residues: 4048 helix: 2.73 (0.11), residues: 2036 sheet: 0.04 (0.21), residues: 644 loop : 0.04 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.028 0.001 TYR B 121 PHE 0.019 0.001 PHE S 24 TRP 0.005 0.001 TRP S 106 HIS 0.008 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00348 (35420) covalent geometry : angle 0.53558 (48099) hydrogen bonds : bond 0.03314 ( 1866) hydrogen bonds : angle 4.03309 ( 5404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5838.83 seconds wall clock time: 101 minutes 45.94 seconds (6105.94 seconds total)