Starting phenix.real_space_refine on Thu Mar 5 16:55:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vny_32047/03_2026/7vny_32047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vny_32047/03_2026/7vny_32047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vny_32047/03_2026/7vny_32047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vny_32047/03_2026/7vny_32047.map" model { file = "/net/cci-nas-00/data/ceres_data/7vny_32047/03_2026/7vny_32047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vny_32047/03_2026/7vny_32047.cif" } resolution = 2.79 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= 0.015 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 13 5.49 5 Mg 32 5.21 5 S 90 5.16 5 C 15852 2.51 5 N 3120 2.21 5 O 3364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s 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: 22472 Number of models: 1 Model: "" Number of chains: 64 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1875 Classifications: {'peptide': 247} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 223} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "3" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "1" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 447 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "2" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 316 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Y" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 368 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "L" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 409 Unusual residues: {'BCL': 3, 'BPB': 1, 'PC1': 2, 'U10': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-7': 1} Unresolved non-hydrogen planarities: 36 Chain: "M" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'BCL': 1, 'BPB': 1, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'CDL': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'PC1:plan-1': 1, 'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 209 Unusual residues: {'BCL': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'SPO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "1" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 117 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'U10': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 5.38, per 1000 atoms: 0.24 Number of scatterers: 22472 At special positions: 0 Unit cell: (138.86, 132.5, 112.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 90 16.00 P 13 15.00 Mg 32 11.99 O 3364 8.00 N 3120 7.00 C 15852 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=31, symmetry=0 Number of additional bonds: simple=31, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 718.1 milliseconds 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 8 sheets defined 73.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 79 through 82 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.687A pdb=" N PHE L 119 " --> pdb=" O TYR L 115 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.672A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 164 removed outlier: 3.543A pdb=" N ASP L 155 " --> pdb=" O TRP L 151 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 220 Processing helix chain 'L' and resid 225 through 250 Processing helix chain 'L' and resid 258 through 263 Processing helix chain 'L' and resid 263 through 268 removed outlier: 4.123A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 29 Processing helix chain 'M' and resid 36 through 43 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.671A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.503A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 193 removed outlier: 3.910A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 227 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 233 through 240 removed outlier: 3.614A pdb=" N ALA M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 3.715A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'H' and resid 11 through 36 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 210 through 216 Processing helix chain 'H' and resid 226 through 244 removed outlier: 4.169A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'I' and resid 3 through 10 Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 51 removed outlier: 3.503A pdb=" N ALA I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 removed outlier: 3.829A pdb=" N ILE K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 10 Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 51 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 52 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 10 removed outlier: 3.627A pdb=" N LYS S 6 " --> pdb=" O LYS S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 10 removed outlier: 3.626A pdb=" N LYS U 6 " --> pdb=" O LYS U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 38 Processing helix chain 'U' and resid 42 through 52 Processing helix chain 'V' and resid 13 through 46 removed outlier: 3.626A pdb=" N GLU V 19 " --> pdb=" O GLU V 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 10 removed outlier: 3.516A pdb=" N TRP W 8 " --> pdb=" O TYR W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'C' and resid 13 through 46 Processing helix chain '3' and resid 5 through 11 Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 51 Processing helix chain 'Z' and resid 13 through 46 Processing helix chain '1' and resid 6 through 11 Processing helix chain '1' and resid 12 through 38 Processing helix chain '1' and resid 42 through 52 Processing helix chain '2' and resid 13 through 46 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 37 Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 10 Processing helix chain '9' and resid 12 through 38 removed outlier: 3.551A pdb=" N THR 9 38 " --> pdb=" O ILE 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 51 Processing helix chain '0' and resid 13 through 46 Processing helix chain 'X' and resid 17 through 55 Processing helix chain 'Y' and resid 5 through 29 Processing helix chain 'Y' and resid 31 through 48 removed outlier: 3.821A pdb=" N GLY Y 35 " --> pdb=" O HIS Y 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 4.179A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'M' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.357A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.663A pdb=" N VAL H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.560A pdb=" N VAL H 153 " --> pdb=" O ALA H 161 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3717 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 5603 1.34 - 1.55: 16521 1.55 - 1.76: 901 1.76 - 1.96: 175 1.96 - 2.17: 128 Bond restraints: 23328 Sorted by residual: bond pdb=" C3C BPB L 303 " pdb=" CAC BPB L 303 " ideal model delta sigma weight residual 1.334 1.557 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3C BPB M 403 " pdb=" CAC BPB M 403 " ideal model delta sigma weight residual 1.334 1.547 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C16 SPO T 102 " pdb=" C17 SPO T 102 " ideal model delta sigma weight residual 1.444 1.650 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C23 SPO E 102 " pdb=" C25 SPO E 102 " ideal model delta sigma weight residual 1.448 1.652 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C16 SPO 3 104 " pdb=" C17 SPO 3 104 " ideal model delta sigma weight residual 1.444 1.647 -0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 23323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.72: 31531 16.72 - 33.44: 360 33.44 - 50.16: 109 50.16 - 66.88: 5 66.88 - 83.60: 1 Bond angle restraints: 32006 Sorted by residual: angle pdb=" C29 SPO V 101 " pdb=" C28 SPO V 101 " pdb=" C30 SPO V 101 " ideal model delta sigma weight residual 115.38 31.78 83.60 3.00e+00 1.11e-01 7.77e+02 angle pdb=" C34 SPO J 103 " pdb=" C33 SPO J 103 " pdb=" C35 SPO J 103 " ideal model delta sigma weight residual 115.46 60.59 54.87 3.00e+00 1.11e-01 3.34e+02 angle pdb=" C34 SPO 3 104 " pdb=" C33 SPO 3 104 " pdb=" C35 SPO 3 104 " ideal model delta sigma weight residual 115.46 61.87 53.59 3.00e+00 1.11e-01 3.19e+02 angle pdb=" C32 SPO U 104 " pdb=" C33 SPO U 104 " pdb=" C35 SPO U 104 " ideal model delta sigma weight residual 120.11 172.75 -52.64 3.00e+00 1.11e-01 3.08e+02 angle pdb=" C32 SPO M 405 " pdb=" C33 SPO M 405 " pdb=" C35 SPO M 405 " ideal model delta sigma weight residual 120.11 172.09 -51.98 3.00e+00 1.11e-01 3.00e+02 ... (remaining 32001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 11898 35.92 - 71.85: 548 71.85 - 107.77: 64 107.77 - 143.69: 6 143.69 - 179.61: 2 Dihedral angle restraints: 12518 sinusoidal: 5917 harmonic: 6601 Sorted by residual: dihedral pdb=" C1 BCL L 307 " pdb=" C2 BCL L 307 " pdb=" C3 BCL L 307 " pdb=" C5 BCL L 307 " ideal model delta sinusoidal sigma weight residual 180.00 0.39 179.61 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C6 U10 L 305 " pdb=" C7 U10 L 305 " pdb=" C8 U10 L 305 " pdb=" C9 U10 L 305 " ideal model delta sinusoidal sigma weight residual 101.51 -128.74 -129.75 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" C3M U10 M 404 " pdb=" C3 U10 M 404 " pdb=" O3 U10 M 404 " pdb=" C4 U10 M 404 " ideal model delta sinusoidal sigma weight residual 244.38 125.42 118.96 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 12515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2339 0.048 - 0.095: 660 0.095 - 0.143: 95 0.143 - 0.191: 8 0.191 - 0.238: 3 Chirality restraints: 3105 Sorted by residual: chirality pdb=" CA PRO H 78 " pdb=" N PRO H 78 " pdb=" C PRO H 78 " pdb=" CB PRO H 78 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2C BPB M 403 " pdb=" C1C BPB M 403 " pdb=" C3C BPB M 403 " pdb=" CMC BPB M 403 " both_signs ideal model delta sigma weight residual False -2.78 -2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PHE L 216 " pdb=" N PHE L 216 " pdb=" C PHE L 216 " pdb=" CB PHE L 216 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 3102 not shown) Planarity restraints: 3909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2C BPB L 303 " -0.329 2.00e-02 2.50e+03 5.00e-01 3.13e+03 pdb=" C3C BPB L 303 " 0.497 2.00e-02 2.50e+03 pdb=" C4C BPB L 303 " -0.262 2.00e-02 2.50e+03 pdb=" CAC BPB L 303 " 0.688 2.00e-02 2.50e+03 pdb=" CBC BPB L 303 " -0.595 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2C BPB M 403 " 0.022 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" C3C BPB M 403 " 0.326 2.00e-02 2.50e+03 pdb=" C4C BPB M 403 " -0.134 2.00e-02 2.50e+03 pdb=" CAC BPB M 403 " -0.395 2.00e-02 2.50e+03 pdb=" CBC BPB M 403 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 77 " 0.109 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO H 78 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO H 78 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO H 78 " 0.077 5.00e-02 4.00e+02 ... (remaining 3906 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 312 2.61 - 3.19: 17526 3.19 - 3.76: 35542 3.76 - 4.33: 52985 4.33 - 4.90: 85708 Nonbonded interactions: 192073 Sorted by model distance: nonbonded pdb=" OG1 THR O 38 " pdb=" O SER O 40 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR W 38 " pdb=" O SER W 40 " model vdw 2.116 3.040 nonbonded pdb=" OG SER H 80 " pdb=" OD1 ASP H 82 " model vdw 2.124 3.040 nonbonded pdb=" NZ LYS S 6 " pdb=" OE1 GLU V 19 " model vdw 2.132 3.120 nonbonded pdb=" O SER 3 40 " pdb=" NH1 ARG Z 46 " model vdw 2.152 3.120 ... (remaining 192068 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 '0' and resid 8 through 49) selection = (chain '8' and resid 8 through 49) selection = (chain 'B' and resid 8 through 49) selection = (chain 'C' and resid 8 through 49) selection = (chain 'E' and resid 8 through 49) selection = (chain 'G' and resid 8 through 49) selection = (chain 'J' and resid 8 through 49) selection = (chain 'N' and resid 8 through 49) selection = (chain 'P' and resid 8 through 49) selection = (chain 'R' and resid 8 through 49) selection = (chain 'T' and resid 8 through 49) selection = (chain 'V' and resid 8 through 49) selection = chain 'Z' } ncs_group { reference = (chain '1' and resid 2 through 54) selection = (chain '3' and resid 2 through 54) selection = (chain '9' and resid 2 through 54) selection = (chain 'A' and resid 2 through 54) selection = (chain 'D' and resid 2 through 54) selection = (chain 'F' and resid 2 through 54) selection = (chain 'I' and resid 2 through 54) selection = (chain 'K' and resid 2 through 54) selection = (chain 'O' and resid 2 through 54) selection = (chain 'Q' and resid 2 through 54) selection = (chain 'S' and resid 2 through 54) selection = (chain 'U' and resid 2 through 54) selection = (chain 'W' and resid 2 through 54) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.550 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 0.021 0.348 23359 Z= 1.260 Angle : 3.948 83.604 32006 Z= 1.342 Chirality : 0.043 0.238 3105 Planarity : 0.012 0.500 3909 Dihedral : 19.174 179.613 8276 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.68 % Allowed : 8.52 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.66 (0.17), residues: 2217 helix: 1.88 (0.12), residues: 1503 sheet: -0.85 (0.75), residues: 44 loop : -0.53 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 136 TYR 0.026 0.002 TYR M 198 PHE 0.090 0.002 PHE M 216 TRP 0.090 0.002 TRP L 272 HIS 0.014 0.002 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.01966 (23328) covalent geometry : angle 3.94791 (32006) hydrogen bonds : bond 0.12287 ( 1310) hydrogen bonds : angle 4.37735 ( 3717) Misc. bond : bond 0.21857 ( 31) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 304 time to evaluate : 0.772 Fit side-chains REVERT: M 168 MET cc_start: 0.8516 (mmm) cc_final: 0.7795 (mmm) REVERT: M 261 THR cc_start: 0.8395 (m) cc_final: 0.8081 (p) REVERT: H 130 LYS cc_start: 0.7905 (tttt) cc_final: 0.7657 (tttm) REVERT: B 19 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6059 (tm-30) REVERT: B 40 LEU cc_start: 0.8107 (mt) cc_final: 0.7760 (tt) REVERT: D 1 MET cc_start: 0.5152 (mtp) cc_final: 0.4936 (mtp) REVERT: F 3 LYS cc_start: 0.7589 (mttp) cc_final: 0.7298 (mtmm) REVERT: I 10 ILE cc_start: 0.7574 (pt) cc_final: 0.7325 (pp) REVERT: J 24 TYR cc_start: 0.8297 (t80) cc_final: 0.8040 (t80) REVERT: O 5 TYR cc_start: 0.7297 (p90) cc_final: 0.6871 (p90) REVERT: U 9 MET cc_start: 0.7312 (mtm) cc_final: 0.6723 (mtm) REVERT: U 15 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6767 (mtp85) REVERT: U 46 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7472 (pp) REVERT: U 51 TYR cc_start: 0.8052 (m-80) cc_final: 0.7832 (m-80) REVERT: W 6 LYS cc_start: 0.6967 (mttm) cc_final: 0.6349 (ttmm) REVERT: W 15 ARG cc_start: 0.6321 (mmm-85) cc_final: 0.5703 (mmt180) REVERT: Z 25 MET cc_start: 0.7913 (mmp) cc_final: 0.7652 (mmm) REVERT: 8 22 SER cc_start: 0.7615 (t) cc_final: 0.7241 (m) REVERT: 8 25 MET cc_start: 0.8123 (mmp) cc_final: 0.7811 (mmm) REVERT: Y 6 GLU cc_start: 0.5518 (tp30) cc_final: 0.5213 (tm-30) outliers start: 13 outliers final: 5 residues processed: 311 average time/residue: 0.6451 time to fit residues: 228.2258 Evaluate side-chains 282 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 275 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain U residue 46 ILE Chi-restraints excluded: chain 3 residue 39 PRO Chi-restraints excluded: chain 0 residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 4 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN C 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.096552 restraints weight = 24247.443| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.18 r_work: 0.2697 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23359 Z= 0.201 Angle : 1.133 41.492 32006 Z= 0.422 Chirality : 0.041 0.147 3105 Planarity : 0.006 0.076 3909 Dihedral : 18.016 179.830 4281 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 9.21 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.95 (0.17), residues: 2217 helix: 2.11 (0.12), residues: 1505 sheet: -0.89 (0.73), residues: 46 loop : -0.43 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 136 TYR 0.020 0.002 TYR M 198 PHE 0.050 0.002 PHE M 216 TRP 0.040 0.002 TRP L 272 HIS 0.011 0.002 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.00482 (23328) covalent geometry : angle 1.13274 (32006) hydrogen bonds : bond 0.06524 ( 1310) hydrogen bonds : angle 3.86233 ( 3717) Misc. bond : bond 0.00239 ( 31) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 0.692 Fit side-chains REVERT: L 271 TRP cc_start: 0.8497 (p90) cc_final: 0.8290 (p90) REVERT: M 168 MET cc_start: 0.8933 (mmm) cc_final: 0.8453 (mmm) REVERT: M 232 GLU cc_start: 0.7950 (pm20) cc_final: 0.7706 (pm20) REVERT: H 177 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7401 (mtp180) REVERT: B 12 LEU cc_start: 0.8323 (mt) cc_final: 0.8078 (mt) REVERT: B 19 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: D 9 MET cc_start: 0.8298 (mtm) cc_final: 0.8086 (mtm) REVERT: E 46 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7178 (ttm170) REVERT: F 3 LYS cc_start: 0.8023 (mttp) cc_final: 0.7741 (mtmm) REVERT: I 5 TYR cc_start: 0.8232 (p90) cc_final: 0.7963 (p90) REVERT: I 11 PHE cc_start: 0.8308 (m-80) cc_final: 0.8082 (m-10) REVERT: J 23 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8291 (t) REVERT: N 24 TYR cc_start: 0.8497 (t80) cc_final: 0.8211 (t80) REVERT: O 5 TYR cc_start: 0.8167 (p90) cc_final: 0.7643 (p90) REVERT: O 10 ILE cc_start: 0.8366 (mt) cc_final: 0.8034 (mm) REVERT: O 20 GLN cc_start: 0.8405 (tt0) cc_final: 0.7949 (tt0) REVERT: O 52 ASN cc_start: 0.7335 (m-40) cc_final: 0.7098 (m-40) REVERT: S 15 ARG cc_start: 0.7579 (mtp85) cc_final: 0.6859 (mtp-110) REVERT: T 25 MET cc_start: 0.8795 (mmm) cc_final: 0.8566 (mmp) REVERT: U 9 MET cc_start: 0.7792 (mtm) cc_final: 0.7334 (mtm) REVERT: U 15 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7942 (mtp85) REVERT: W 5 TYR cc_start: 0.8053 (p90) cc_final: 0.7599 (p90) REVERT: W 6 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7254 (ttmm) REVERT: W 15 ARG cc_start: 0.7499 (mmm-85) cc_final: 0.7208 (mmt180) REVERT: W 26 LEU cc_start: 0.9014 (mt) cc_final: 0.8775 (mt) REVERT: 3 38 THR cc_start: 0.7911 (p) cc_final: 0.7656 (t) REVERT: 1 38 THR cc_start: 0.6776 (m) cc_final: 0.6232 (p) REVERT: 1 47 SER cc_start: 0.8283 (t) cc_final: 0.7896 (p) REVERT: 2 37 VAL cc_start: 0.7259 (p) cc_final: 0.7022 (m) REVERT: 8 22 SER cc_start: 0.8495 (t) cc_final: 0.8208 (m) REVERT: X 27 MET cc_start: 0.7322 (mtt) cc_final: 0.7017 (mtt) REVERT: Y 6 GLU cc_start: 0.6252 (tp30) cc_final: 0.6018 (tm-30) outliers start: 43 outliers final: 22 residues processed: 319 average time/residue: 0.6257 time to fit residues: 227.2995 Evaluate side-chains 308 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 20 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN D 20 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098488 restraints weight = 24174.535| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.14 r_work: 0.2731 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23359 Z= 0.158 Angle : 1.014 42.476 32006 Z= 0.378 Chirality : 0.038 0.131 3105 Planarity : 0.005 0.063 3909 Dihedral : 17.256 179.699 4271 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.52 % Allowed : 10.47 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.28 (0.17), residues: 2217 helix: 2.38 (0.12), residues: 1502 sheet: -1.07 (0.86), residues: 36 loop : -0.35 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 15 TYR 0.015 0.002 TYR M 198 PHE 0.028 0.002 PHE M 216 TRP 0.023 0.002 TRP L 272 HIS 0.008 0.001 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.00368 (23328) covalent geometry : angle 1.01413 (32006) hydrogen bonds : bond 0.05826 ( 1310) hydrogen bonds : angle 3.70345 ( 3717) Misc. bond : bond 0.00196 ( 31) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 0.775 Fit side-chains REVERT: L 216 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: M 168 MET cc_start: 0.8911 (mmm) cc_final: 0.8390 (mmm) REVERT: M 232 GLU cc_start: 0.7903 (pm20) cc_final: 0.7672 (pm20) REVERT: M 233 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: H 1 MET cc_start: 0.7389 (tpp) cc_final: 0.7181 (tpp) REVERT: H 177 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7620 (mtp-110) REVERT: A 30 MET cc_start: 0.8685 (ttt) cc_final: 0.8454 (ttp) REVERT: B 12 LEU cc_start: 0.8251 (mt) cc_final: 0.7996 (mt) REVERT: B 19 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: D 9 MET cc_start: 0.8125 (mtm) cc_final: 0.7923 (mtm) REVERT: E 46 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7251 (ttm170) REVERT: F 3 LYS cc_start: 0.8021 (mttp) cc_final: 0.7736 (mtmm) REVERT: I 5 TYR cc_start: 0.8267 (p90) cc_final: 0.7875 (p90) REVERT: I 10 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8102 (pp) REVERT: I 11 PHE cc_start: 0.8238 (m-80) cc_final: 0.7916 (m-10) REVERT: I 15 ARG cc_start: 0.7016 (mtm110) cc_final: 0.6356 (mmt90) REVERT: J 23 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8302 (t) REVERT: N 24 TYR cc_start: 0.8500 (t80) cc_final: 0.8225 (t80) REVERT: O 5 TYR cc_start: 0.8209 (p90) cc_final: 0.7666 (p90) REVERT: O 10 ILE cc_start: 0.8380 (mt) cc_final: 0.8040 (mm) REVERT: O 20 GLN cc_start: 0.8280 (tt0) cc_final: 0.7957 (tt0) REVERT: O 52 ASN cc_start: 0.7329 (m-40) cc_final: 0.7082 (m-40) REVERT: R 18 GLN cc_start: 0.8086 (mt0) cc_final: 0.7259 (mt0) REVERT: S 1 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.4846 (ptp) REVERT: S 3 LYS cc_start: 0.8107 (tppt) cc_final: 0.7478 (mmmm) REVERT: U 9 MET cc_start: 0.7774 (mtm) cc_final: 0.7297 (mtm) REVERT: U 15 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7851 (mtp85) REVERT: W 6 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7255 (ttmm) REVERT: W 9 MET cc_start: 0.7829 (mmt) cc_final: 0.7370 (mtp) REVERT: W 26 LEU cc_start: 0.8955 (mt) cc_final: 0.8702 (mt) REVERT: 1 38 THR cc_start: 0.6810 (m) cc_final: 0.6273 (p) REVERT: 1 47 SER cc_start: 0.8260 (t) cc_final: 0.7897 (p) REVERT: 8 22 SER cc_start: 0.8476 (t) cc_final: 0.8177 (m) REVERT: 8 36 ILE cc_start: 0.8307 (mt) cc_final: 0.7899 (mt) REVERT: X 27 MET cc_start: 0.7298 (mtt) cc_final: 0.7033 (mtt) REVERT: Y 6 GLU cc_start: 0.6201 (tp30) cc_final: 0.5980 (tm-30) outliers start: 48 outliers final: 22 residues processed: 322 average time/residue: 0.6364 time to fit residues: 233.3718 Evaluate side-chains 309 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 281 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 7 residue 30 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 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 = 0.3267 r_free = 0.3267 target = 0.122044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.096828 restraints weight = 24106.123| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.14 r_work: 0.2708 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23359 Z= 0.187 Angle : 1.050 42.387 32006 Z= 0.394 Chirality : 0.040 0.136 3105 Planarity : 0.005 0.064 3909 Dihedral : 17.244 179.750 4271 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.95 % Allowed : 11.26 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.16 (0.17), residues: 2217 helix: 2.27 (0.12), residues: 1508 sheet: -1.08 (0.85), residues: 36 loop : -0.36 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 136 TYR 0.018 0.002 TYR M 198 PHE 0.020 0.002 PHE L 216 TRP 0.016 0.002 TRP M 157 HIS 0.009 0.002 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.00448 (23328) covalent geometry : angle 1.04955 (32006) hydrogen bonds : bond 0.06264 ( 1310) hydrogen bonds : angle 3.78537 ( 3717) Misc. bond : bond 0.00241 ( 31) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.691 Fit side-chains REVERT: L 216 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: M 168 MET cc_start: 0.8944 (mmm) cc_final: 0.8382 (mmm) REVERT: H 177 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7797 (mtp-110) REVERT: B 12 LEU cc_start: 0.8292 (mt) cc_final: 0.8046 (mt) REVERT: B 19 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: D 9 MET cc_start: 0.8060 (mtm) cc_final: 0.7852 (mtm) REVERT: E 46 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7274 (ttm170) REVERT: F 3 LYS cc_start: 0.7953 (mttp) cc_final: 0.7694 (mtmm) REVERT: F 9 MET cc_start: 0.8200 (mtp) cc_final: 0.7725 (mpp) REVERT: I 5 TYR cc_start: 0.8282 (p90) cc_final: 0.7948 (p90) REVERT: I 11 PHE cc_start: 0.8257 (m-80) cc_final: 0.7918 (m-10) REVERT: I 15 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6373 (mmt90) REVERT: J 23 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8295 (t) REVERT: N 24 TYR cc_start: 0.8525 (t80) cc_final: 0.8283 (t80) REVERT: O 5 TYR cc_start: 0.8243 (p90) cc_final: 0.7745 (p90) REVERT: O 10 ILE cc_start: 0.8335 (mt) cc_final: 0.8007 (mm) REVERT: O 20 GLN cc_start: 0.8332 (tt0) cc_final: 0.7941 (tt0) REVERT: O 52 ASN cc_start: 0.7215 (m-40) cc_final: 0.6949 (m-40) REVERT: P 40 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8052 (mm) REVERT: R 18 GLN cc_start: 0.8121 (mt0) cc_final: 0.7281 (mt0) REVERT: S 1 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5136 (ptp) REVERT: S 15 ARG cc_start: 0.7567 (mtp85) cc_final: 0.6935 (mtp-110) REVERT: U 9 MET cc_start: 0.7748 (mtm) cc_final: 0.7272 (mtm) REVERT: U 15 ARG cc_start: 0.8119 (mtp180) cc_final: 0.7844 (mtp85) REVERT: U 45 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7353 (mm-30) REVERT: W 6 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7257 (ttmm) REVERT: W 9 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7521 (mtp) REVERT: W 26 LEU cc_start: 0.8961 (mt) cc_final: 0.8755 (mt) REVERT: W 37 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.7998 (m) REVERT: 1 38 THR cc_start: 0.6762 (m) cc_final: 0.6248 (p) REVERT: 1 47 SER cc_start: 0.8298 (t) cc_final: 0.7907 (p) REVERT: 8 22 SER cc_start: 0.8461 (t) cc_final: 0.8185 (m) REVERT: 8 36 ILE cc_start: 0.8320 (mt) cc_final: 0.7904 (mt) REVERT: 0 9 TYR cc_start: 0.8499 (m-10) cc_final: 0.8223 (m-10) REVERT: X 27 MET cc_start: 0.7364 (mtt) cc_final: 0.7076 (mtt) REVERT: Y 6 GLU cc_start: 0.6248 (tp30) cc_final: 0.5978 (tm-30) outliers start: 56 outliers final: 25 residues processed: 316 average time/residue: 0.6338 time to fit residues: 228.1091 Evaluate side-chains 310 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 6 LYS Chi-restraints excluded: chain W residue 9 MET Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 2 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN Q 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.120629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.095430 restraints weight = 24066.951| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.14 r_work: 0.2688 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 23359 Z= 0.240 Angle : 1.114 42.856 32006 Z= 0.423 Chirality : 0.044 0.160 3105 Planarity : 0.005 0.074 3909 Dihedral : 17.672 179.582 4271 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.21 % Allowed : 12.15 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.81 (0.17), residues: 2217 helix: 2.01 (0.12), residues: 1506 sheet: -1.11 (0.84), residues: 36 loop : -0.52 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 136 TYR 0.022 0.002 TYR D 51 PHE 0.020 0.002 PHE L 216 TRP 0.018 0.002 TRP M 157 HIS 0.011 0.002 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00588 (23328) covalent geometry : angle 1.11405 (32006) hydrogen bonds : bond 0.06867 ( 1310) hydrogen bonds : angle 3.92348 ( 3717) Misc. bond : bond 0.00294 ( 31) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 0.760 Fit side-chains REVERT: L 216 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: H 60 LYS cc_start: 0.7162 (mptp) cc_final: 0.6906 (mttt) REVERT: H 106 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7289 (tttp) REVERT: H 177 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7508 (mtp180) REVERT: B 12 LEU cc_start: 0.8347 (mt) cc_final: 0.8108 (mt) REVERT: B 19 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: B 30 LEU cc_start: 0.8412 (tp) cc_final: 0.8186 (tp) REVERT: F 9 MET cc_start: 0.8197 (mtp) cc_final: 0.7772 (mpp) REVERT: I 5 TYR cc_start: 0.8239 (p90) cc_final: 0.7848 (p90) REVERT: I 11 PHE cc_start: 0.8286 (m-80) cc_final: 0.7967 (m-10) REVERT: I 15 ARG cc_start: 0.7015 (mtm110) cc_final: 0.6347 (mmt90) REVERT: J 23 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8325 (t) REVERT: K 14 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6675 (ttm-80) REVERT: N 24 TYR cc_start: 0.8528 (t80) cc_final: 0.8301 (t80) REVERT: O 1 MET cc_start: 0.5616 (mmt) cc_final: 0.5382 (tpt) REVERT: O 5 TYR cc_start: 0.8266 (p90) cc_final: 0.7711 (p90) REVERT: O 9 MET cc_start: 0.8013 (mtp) cc_final: 0.7770 (mtp) REVERT: O 10 ILE cc_start: 0.8338 (mt) cc_final: 0.8017 (mm) REVERT: O 20 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: O 52 ASN cc_start: 0.7267 (m-40) cc_final: 0.6978 (m-40) REVERT: R 18 GLN cc_start: 0.8128 (mt0) cc_final: 0.7299 (mt0) REVERT: S 1 MET cc_start: 0.5942 (OUTLIER) cc_final: 0.5125 (ptp) REVERT: S 15 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7121 (mtp-110) REVERT: U 45 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7523 (mm-30) REVERT: W 9 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7498 (mtp) REVERT: W 37 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8027 (m) REVERT: 1 47 SER cc_start: 0.8302 (t) cc_final: 0.7911 (p) REVERT: 2 22 SER cc_start: 0.7212 (p) cc_final: 0.6903 (t) REVERT: 8 22 SER cc_start: 0.8344 (t) cc_final: 0.8089 (m) REVERT: 0 9 TYR cc_start: 0.8575 (m-10) cc_final: 0.8322 (m-10) REVERT: 0 18 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: X 27 MET cc_start: 0.7602 (mtt) cc_final: 0.6251 (mtt) REVERT: Y 6 GLU cc_start: 0.6243 (tp30) cc_final: 0.5983 (tm-30) outliers start: 61 outliers final: 36 residues processed: 312 average time/residue: 0.6315 time to fit residues: 224.5210 Evaluate side-chains 318 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 9 MET Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 36 ILE Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 19 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN ** C 16 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 = 0.3271 r_free = 0.3271 target = 0.122453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097283 restraints weight = 24084.497| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.15 r_work: 0.2709 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23359 Z= 0.172 Angle : 1.022 42.552 32006 Z= 0.385 Chirality : 0.039 0.136 3105 Planarity : 0.005 0.063 3909 Dihedral : 17.235 179.607 4271 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.10 % Allowed : 12.73 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.11 (0.17), residues: 2217 helix: 2.27 (0.12), residues: 1506 sheet: -1.12 (0.84), residues: 36 loop : -0.47 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 15 TYR 0.014 0.002 TYR M 198 PHE 0.018 0.002 PHE L 216 TRP 0.017 0.002 TRP M 157 HIS 0.007 0.001 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.00406 (23328) covalent geometry : angle 1.02247 (32006) hydrogen bonds : bond 0.06055 ( 1310) hydrogen bonds : angle 3.76022 ( 3717) Misc. bond : bond 0.00223 ( 31) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 0.606 Fit side-chains REVERT: L 216 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: L 258 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6598 (mm-40) REVERT: M 168 MET cc_start: 0.8936 (mmm) cc_final: 0.8408 (mmm) REVERT: H 60 LYS cc_start: 0.7173 (mptp) cc_final: 0.6925 (mttt) REVERT: H 106 LYS cc_start: 0.7687 (mmtt) cc_final: 0.7293 (tttp) REVERT: H 177 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7532 (mtp180) REVERT: B 12 LEU cc_start: 0.8265 (mt) cc_final: 0.8024 (mt) REVERT: B 19 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: B 30 LEU cc_start: 0.8481 (tp) cc_final: 0.8263 (tp) REVERT: E 46 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7277 (ttm170) REVERT: F 3 LYS cc_start: 0.7914 (mttp) cc_final: 0.7658 (mttm) REVERT: F 9 MET cc_start: 0.8167 (mtp) cc_final: 0.7684 (mpp) REVERT: I 5 TYR cc_start: 0.8305 (p90) cc_final: 0.7850 (p90) REVERT: I 11 PHE cc_start: 0.8244 (m-80) cc_final: 0.7988 (m-10) REVERT: I 15 ARG cc_start: 0.7020 (mtm110) cc_final: 0.6368 (mmt90) REVERT: J 23 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8335 (t) REVERT: N 24 TYR cc_start: 0.8512 (t80) cc_final: 0.8259 (t80) REVERT: O 1 MET cc_start: 0.5689 (mmt) cc_final: 0.5435 (tpt) REVERT: O 5 TYR cc_start: 0.8340 (p90) cc_final: 0.7751 (p90) REVERT: O 9 MET cc_start: 0.8072 (mtp) cc_final: 0.7824 (mtp) REVERT: O 10 ILE cc_start: 0.8332 (mt) cc_final: 0.8012 (mm) REVERT: O 52 ASN cc_start: 0.7242 (m-40) cc_final: 0.6958 (m-40) REVERT: P 13 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.5986 (t) REVERT: R 18 GLN cc_start: 0.8246 (mt0) cc_final: 0.7387 (mt0) REVERT: S 1 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5070 (ptp) REVERT: U 1 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.5239 (mpp) REVERT: U 9 MET cc_start: 0.7723 (mtm) cc_final: 0.7214 (mtm) REVERT: U 45 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7536 (mm-30) REVERT: W 37 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8019 (m) REVERT: 1 47 SER cc_start: 0.8311 (t) cc_final: 0.7923 (p) REVERT: 8 22 SER cc_start: 0.8452 (t) cc_final: 0.8177 (m) REVERT: 0 9 TYR cc_start: 0.8562 (m-10) cc_final: 0.8329 (m-10) REVERT: X 27 MET cc_start: 0.7596 (mtt) cc_final: 0.6277 (mtt) REVERT: Y 6 GLU cc_start: 0.6229 (tp30) cc_final: 0.5950 (tm-30) outliers start: 59 outliers final: 33 residues processed: 314 average time/residue: 0.6253 time to fit residues: 223.9716 Evaluate side-chains 317 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 258 GLN Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 60 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN S 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 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 = 0.3250 r_free = 0.3250 target = 0.120792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.095578 restraints weight = 24302.994| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.14 r_work: 0.2689 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 23359 Z= 0.227 Angle : 1.098 42.821 32006 Z= 0.417 Chirality : 0.043 0.178 3105 Planarity : 0.005 0.070 3909 Dihedral : 17.452 179.795 4271 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.52 % Allowed : 12.84 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 1.82 (0.17), residues: 2217 helix: 2.04 (0.12), residues: 1506 sheet: -1.18 (0.82), residues: 36 loop : -0.54 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 15 TYR 0.019 0.002 TYR U 5 PHE 0.020 0.002 PHE L 216 TRP 0.017 0.002 TRP M 157 HIS 0.009 0.002 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.00553 (23328) covalent geometry : angle 1.09774 (32006) hydrogen bonds : bond 0.06741 ( 1310) hydrogen bonds : angle 3.90045 ( 3717) Misc. bond : bond 0.00290 ( 31) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 280 time to evaluate : 0.739 Fit side-chains REVERT: L 216 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8279 (m-80) REVERT: H 60 LYS cc_start: 0.7171 (mptp) cc_final: 0.6913 (mttt) REVERT: H 106 LYS cc_start: 0.7693 (mmtt) cc_final: 0.7284 (tttp) REVERT: H 177 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7576 (mtp180) REVERT: B 12 LEU cc_start: 0.8329 (mt) cc_final: 0.8103 (mt) REVERT: B 19 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: F 9 MET cc_start: 0.8212 (mtp) cc_final: 0.7759 (mpp) REVERT: I 5 TYR cc_start: 0.8313 (p90) cc_final: 0.7893 (p90) REVERT: I 11 PHE cc_start: 0.8364 (m-80) cc_final: 0.8136 (m-10) REVERT: I 15 ARG cc_start: 0.7036 (mtm110) cc_final: 0.6010 (mtt-85) REVERT: J 23 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8334 (t) REVERT: N 24 TYR cc_start: 0.8528 (t80) cc_final: 0.8278 (t80) REVERT: O 1 MET cc_start: 0.5460 (mmt) cc_final: 0.5247 (tpt) REVERT: O 5 TYR cc_start: 0.8356 (p90) cc_final: 0.8131 (p90) REVERT: O 9 MET cc_start: 0.8053 (mtp) cc_final: 0.7821 (mtp) REVERT: O 10 ILE cc_start: 0.8325 (mt) cc_final: 0.8003 (mm) REVERT: O 52 ASN cc_start: 0.7261 (m-40) cc_final: 0.6972 (m-40) REVERT: P 13 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.6165 (t) REVERT: R 18 GLN cc_start: 0.8249 (mt0) cc_final: 0.7390 (mt0) REVERT: S 1 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5149 (ptp) REVERT: U 45 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7582 (mm-30) REVERT: 3 1 MET cc_start: 0.2894 (mtm) cc_final: 0.2342 (mtt) REVERT: 1 47 SER cc_start: 0.8317 (t) cc_final: 0.7939 (p) REVERT: 2 22 SER cc_start: 0.7208 (p) cc_final: 0.6880 (t) REVERT: 8 14 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: 8 22 SER cc_start: 0.8426 (t) cc_final: 0.8163 (m) REVERT: 0 18 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: X 27 MET cc_start: 0.7604 (mtt) cc_final: 0.6247 (mtt) REVERT: Y 6 GLU cc_start: 0.6244 (tp30) cc_final: 0.5993 (tm-30) outliers start: 67 outliers final: 41 residues processed: 316 average time/residue: 0.6228 time to fit residues: 224.4431 Evaluate side-chains 327 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 40 LEU Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain 3 residue 9 MET Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 36 ILE Chi-restraints excluded: chain 0 residue 18 GLN Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.101448 restraints weight = 24034.972| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.17 r_work: 0.2784 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23359 Z= 0.118 Angle : 0.940 42.298 32006 Z= 0.352 Chirality : 0.036 0.142 3105 Planarity : 0.004 0.051 3909 Dihedral : 16.421 179.605 4271 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.21 % Allowed : 14.15 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.61 (0.17), residues: 2217 helix: 2.67 (0.12), residues: 1506 sheet: -1.00 (0.86), residues: 36 loop : -0.32 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 15 TYR 0.020 0.001 TYR U 5 PHE 0.017 0.001 PHE M 162 TRP 0.018 0.001 TRP N 29 HIS 0.005 0.001 HIS L 230 Details of bonding type rmsd covalent geometry : bond 0.00254 (23328) covalent geometry : angle 0.94014 (32006) hydrogen bonds : bond 0.05017 ( 1310) hydrogen bonds : angle 3.54227 ( 3717) Misc. bond : bond 0.00133 ( 31) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 0.883 Fit side-chains REVERT: L 216 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: M 168 MET cc_start: 0.8861 (mmm) cc_final: 0.8364 (mmm) REVERT: H 60 LYS cc_start: 0.7183 (mptp) cc_final: 0.6892 (mttt) REVERT: H 106 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7276 (tttp) REVERT: H 177 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7530 (mtp180) REVERT: B 19 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: D 9 MET cc_start: 0.7939 (mtm) cc_final: 0.7691 (mtm) REVERT: E 46 ARG cc_start: 0.7482 (mtt180) cc_final: 0.7250 (ttm170) REVERT: F 3 LYS cc_start: 0.7967 (mttp) cc_final: 0.7718 (mttm) REVERT: I 5 TYR cc_start: 0.8302 (p90) cc_final: 0.7864 (p90) REVERT: I 15 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6047 (mtt-85) REVERT: K 6 LYS cc_start: 0.7835 (mttm) cc_final: 0.7449 (mttp) REVERT: N 24 TYR cc_start: 0.8515 (t80) cc_final: 0.8231 (t80) REVERT: O 1 MET cc_start: 0.5334 (mmt) cc_final: 0.5067 (tpt) REVERT: O 5 TYR cc_start: 0.8227 (p90) cc_final: 0.7989 (p90) REVERT: O 9 MET cc_start: 0.7973 (mtp) cc_final: 0.7744 (mtp) REVERT: O 10 ILE cc_start: 0.8244 (mt) cc_final: 0.7925 (mm) REVERT: O 52 ASN cc_start: 0.7237 (m-40) cc_final: 0.6955 (m-40) REVERT: P 13 THR cc_start: 0.6312 (OUTLIER) cc_final: 0.5978 (t) REVERT: Q 1 MET cc_start: 0.1719 (mpt) cc_final: -0.1180 (pp-130) REVERT: R 18 GLN cc_start: 0.8135 (mt0) cc_final: 0.7347 (mt0) REVERT: R 25 MET cc_start: 0.8789 (mmm) cc_final: 0.8580 (mmm) REVERT: S 1 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.4926 (ptp) REVERT: U 9 MET cc_start: 0.7755 (mtm) cc_final: 0.7240 (mtm) REVERT: U 45 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7537 (mm-30) REVERT: 3 1 MET cc_start: 0.2504 (mtm) cc_final: 0.1979 (mtt) REVERT: 1 38 THR cc_start: 0.6649 (m) cc_final: 0.6111 (p) REVERT: 1 47 SER cc_start: 0.8331 (t) cc_final: 0.7958 (p) REVERT: 2 36 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6697 (mm) REVERT: 8 14 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: 8 22 SER cc_start: 0.8387 (t) cc_final: 0.8083 (m) REVERT: 8 36 ILE cc_start: 0.8292 (mt) cc_final: 0.7914 (mt) REVERT: 8 37 VAL cc_start: 0.8152 (p) cc_final: 0.7741 (m) REVERT: 8 43 TYR cc_start: 0.8341 (t80) cc_final: 0.8063 (t80) REVERT: 0 19 GLU cc_start: 0.7434 (tp30) cc_final: 0.7047 (mm-30) REVERT: X 27 MET cc_start: 0.7349 (mtt) cc_final: 0.7085 (mtt) REVERT: Y 6 GLU cc_start: 0.6108 (tp30) cc_final: 0.5825 (tm-30) outliers start: 42 outliers final: 15 residues processed: 324 average time/residue: 0.6036 time to fit residues: 223.9459 Evaluate side-chains 306 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 285 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 8 residue 14 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.123749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098566 restraints weight = 23788.562| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.14 r_work: 0.2740 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23359 Z= 0.147 Angle : 0.976 42.492 32006 Z= 0.368 Chirality : 0.038 0.135 3105 Planarity : 0.004 0.056 3909 Dihedral : 16.432 179.666 4271 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.00 % Allowed : 14.57 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.52 (0.17), residues: 2217 helix: 2.59 (0.12), residues: 1507 sheet: -1.03 (0.86), residues: 36 loop : -0.34 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 15 TYR 0.026 0.001 TYR U 5 PHE 0.017 0.001 PHE L 216 TRP 0.018 0.002 TRP N 29 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00339 (23328) covalent geometry : angle 0.97603 (32006) hydrogen bonds : bond 0.05531 ( 1310) hydrogen bonds : angle 3.63044 ( 3717) Misc. bond : bond 0.00197 ( 31) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.618 Fit side-chains REVERT: L 216 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: M 168 MET cc_start: 0.8890 (mmm) cc_final: 0.8338 (mmm) REVERT: H 60 LYS cc_start: 0.7184 (mptp) cc_final: 0.6890 (mttt) REVERT: H 106 LYS cc_start: 0.7683 (mmtt) cc_final: 0.7343 (tttp) REVERT: H 177 ARG cc_start: 0.7983 (mtt-85) cc_final: 0.7450 (mtp180) REVERT: B 19 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: E 46 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7303 (ttm170) REVERT: F 3 LYS cc_start: 0.7959 (mttp) cc_final: 0.7714 (mttm) REVERT: I 5 TYR cc_start: 0.8324 (p90) cc_final: 0.7884 (p90) REVERT: I 15 ARG cc_start: 0.6953 (mtm110) cc_final: 0.6052 (mtt-85) REVERT: N 24 TYR cc_start: 0.8523 (t80) cc_final: 0.8286 (t80) REVERT: O 5 TYR cc_start: 0.8279 (p90) cc_final: 0.8044 (p90) REVERT: O 9 MET cc_start: 0.8103 (mtp) cc_final: 0.7872 (mtp) REVERT: O 10 ILE cc_start: 0.8236 (mt) cc_final: 0.7881 (mm) REVERT: O 52 ASN cc_start: 0.7260 (m-40) cc_final: 0.6967 (m-40) REVERT: P 13 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.6066 (t) REVERT: Q 1 MET cc_start: 0.1727 (mpt) cc_final: -0.1028 (pp-130) REVERT: R 18 GLN cc_start: 0.8140 (mt0) cc_final: 0.7333 (mt0) REVERT: S 1 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.4873 (ptp) REVERT: U 1 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5299 (mpp) REVERT: U 9 MET cc_start: 0.7683 (mtm) cc_final: 0.7248 (mtm) REVERT: U 45 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7537 (mm-30) REVERT: W 30 MET cc_start: 0.8832 (ttp) cc_final: 0.8623 (ttt) REVERT: 3 1 MET cc_start: 0.2649 (mtm) cc_final: 0.2082 (mtt) REVERT: 1 38 THR cc_start: 0.6654 (m) cc_final: 0.6126 (p) REVERT: 1 47 SER cc_start: 0.8236 (t) cc_final: 0.7892 (p) REVERT: 2 36 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6736 (mm) REVERT: 8 14 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: 8 22 SER cc_start: 0.8418 (t) cc_final: 0.8129 (m) REVERT: 8 36 ILE cc_start: 0.8291 (mt) cc_final: 0.7880 (mt) REVERT: X 27 MET cc_start: 0.7372 (mtt) cc_final: 0.7124 (mtt) REVERT: Y 6 GLU cc_start: 0.6256 (tp30) cc_final: 0.5985 (tm-30) outliers start: 38 outliers final: 21 residues processed: 303 average time/residue: 0.6221 time to fit residues: 214.9733 Evaluate side-chains 307 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 2 residue 36 ILE Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 8 residue 14 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 131 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.125748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100662 restraints weight = 23713.431| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.15 r_work: 0.2770 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23359 Z= 0.124 Angle : 0.939 42.303 32006 Z= 0.352 Chirality : 0.037 0.134 3105 Planarity : 0.004 0.049 3909 Dihedral : 16.091 179.576 4271 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.53 % Allowed : 15.10 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.70 (0.17), residues: 2217 helix: 2.73 (0.12), residues: 1506 sheet: -0.95 (0.87), residues: 36 loop : -0.29 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 15 TYR 0.028 0.001 TYR U 5 PHE 0.015 0.001 PHE L 216 TRP 0.023 0.001 TRP N 29 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00276 (23328) covalent geometry : angle 0.93881 (32006) hydrogen bonds : bond 0.05108 ( 1310) hydrogen bonds : angle 3.53246 ( 3717) Misc. bond : bond 0.00151 ( 31) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4434 Ramachandran restraints generated. 2217 Oldfield, 0 Emsley, 2217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 0.716 Fit side-chains REVERT: L 73 TYR cc_start: 0.8693 (m-80) cc_final: 0.8477 (m-80) REVERT: L 216 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: M 168 MET cc_start: 0.8847 (mmm) cc_final: 0.8301 (mmm) REVERT: H 60 LYS cc_start: 0.7191 (mptp) cc_final: 0.6896 (mttt) REVERT: H 106 LYS cc_start: 0.7558 (mmtt) cc_final: 0.7178 (tttp) REVERT: H 177 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7384 (mtp180) REVERT: E 46 ARG cc_start: 0.7466 (mtt180) cc_final: 0.7256 (ttm170) REVERT: F 3 LYS cc_start: 0.7997 (mttp) cc_final: 0.7746 (mttm) REVERT: I 5 TYR cc_start: 0.8394 (p90) cc_final: 0.7905 (p90) REVERT: I 9 MET cc_start: 0.8329 (mtm) cc_final: 0.7994 (mtt) REVERT: I 15 ARG cc_start: 0.6928 (mtm110) cc_final: 0.6059 (mtt-85) REVERT: N 24 TYR cc_start: 0.8522 (t80) cc_final: 0.8249 (t80) REVERT: O 5 TYR cc_start: 0.8260 (p90) cc_final: 0.8023 (p90) REVERT: O 9 MET cc_start: 0.8106 (mtp) cc_final: 0.7874 (mtp) REVERT: O 52 ASN cc_start: 0.7255 (m-40) cc_final: 0.6952 (m-40) REVERT: P 13 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.6073 (t) REVERT: Q 1 MET cc_start: 0.1884 (mpt) cc_final: -0.0829 (pp-130) REVERT: R 18 GLN cc_start: 0.8122 (mt0) cc_final: 0.7321 (mt0) REVERT: S 1 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.4832 (ptp) REVERT: U 9 MET cc_start: 0.7823 (mtm) cc_final: 0.7352 (mtm) REVERT: U 45 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7524 (mm-30) REVERT: 3 1 MET cc_start: 0.2637 (mtm) cc_final: 0.2076 (mtt) REVERT: 3 52 ASN cc_start: 0.6492 (m110) cc_final: 0.5743 (t0) REVERT: 1 38 THR cc_start: 0.6579 (m) cc_final: 0.6077 (p) REVERT: 1 47 SER cc_start: 0.8312 (t) cc_final: 0.7934 (p) REVERT: 8 12 LEU cc_start: 0.7861 (mp) cc_final: 0.7574 (mt) REVERT: 8 14 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: 8 36 ILE cc_start: 0.8272 (mt) cc_final: 0.7778 (mt) REVERT: 8 37 VAL cc_start: 0.8149 (p) cc_final: 0.7736 (m) REVERT: 8 43 TYR cc_start: 0.8326 (t80) cc_final: 0.8086 (t80) REVERT: 0 19 GLU cc_start: 0.7402 (tp30) cc_final: 0.7019 (mm-30) REVERT: X 27 MET cc_start: 0.7366 (mtt) cc_final: 0.7119 (mtt) REVERT: Y 6 GLU cc_start: 0.6179 (tp30) cc_final: 0.5914 (tm-30) outliers start: 29 outliers final: 18 residues processed: 301 average time/residue: 0.6328 time to fit residues: 216.8809 Evaluate side-chains 299 residues out of total 1901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain 3 residue 26 LEU Chi-restraints excluded: chain 2 residue 37 VAL Chi-restraints excluded: chain 8 residue 14 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 194 GLN O 20 GLN ** T 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.123516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.098150 restraints weight = 23651.058| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.12 r_work: 0.2736 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23359 Z= 0.160 Angle : 0.988 42.582 32006 Z= 0.374 Chirality : 0.039 0.190 3105 Planarity : 0.004 0.056 3909 Dihedral : 16.273 179.696 4267 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.89 % Allowed : 14.99 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 2.46 (0.17), residues: 2217 helix: 2.53 (0.12), residues: 1507 sheet: -0.97 (0.86), residues: 36 loop : -0.33 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 15 TYR 0.032 0.002 TYR U 5 PHE 0.017 0.001 PHE L 216 TRP 0.026 0.002 TRP N 29 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00375 (23328) covalent geometry : angle 0.98821 (32006) hydrogen bonds : bond 0.05766 ( 1310) hydrogen bonds : angle 3.67131 ( 3717) Misc. bond : bond 0.00220 ( 31) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7376.79 seconds wall clock time: 126 minutes 3.67 seconds (7563.67 seconds total)