Starting phenix.real_space_refine on Thu Mar 5 11:37:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnm_32042/03_2026/7vnm_32042.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnm_32042/03_2026/7vnm_32042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vnm_32042/03_2026/7vnm_32042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnm_32042/03_2026/7vnm_32042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vnm_32042/03_2026/7vnm_32042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnm_32042/03_2026/7vnm_32042.map" } resolution = 2.86 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= 0.008 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 9 5.49 5 Mg 30 5.21 5 S 82 5.16 5 C 14484 2.51 5 N 2897 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 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: 20588 Number of models: 1 Model: "" Number of chains: 55 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: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} 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: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: "1" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "2" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 270 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "L" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 327 Unusual residues: {'BCL': 2, 'BPH': 2, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 320 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 118 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 251 Unusual residues: {'BCL': 2, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "I" 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: "K" 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: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "U" 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: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} 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: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "9" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "0" 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: "X" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.59, per 1000 atoms: 0.22 Number of scatterers: 20588 At special positions: 0 Unit cell: (133.388, 125.103, 126.76, 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 82 16.00 P 9 15.00 Mg 30 11.99 O 3085 8.00 N 2897 7.00 C 14484 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=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 875.6 milliseconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 7 sheets defined 72.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 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 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.726A pdb=" N PHE L 119 " --> pdb=" O TYR L 115 " (cutoff:3.500A) removed outlier: 3.645A 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: 3.526A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 164 removed outlier: 4.066A 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 221 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: 4.206A 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 removed outlier: 4.037A pdb=" N PHE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 89 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 112 through 140 removed outlier: 3.581A 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: 3.506A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.603A pdb=" N HIS M 182 " --> pdb=" O GLY M 178 " (cutoff:3.500A) removed outlier: 3.835A 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 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 removed outlier: 3.514A 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: 3.677A 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 209 through 216 removed outlier: 3.521A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 4.004A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 6 through 11 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 3 through 10 removed outlier: 3.715A pdb=" N LYS F 6 " --> pdb=" O LYS F 3 " (cutoff:3.500A) 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 37 Processing helix chain 'I' and resid 42 through 51 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: 3.983A 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 51 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 10 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 5 No H-bonds generated for 'chain 'U' and resid 3 through 5' Processing helix chain 'U' and resid 6 through 11 removed outlier: 3.549A pdb=" N ILE U 10 " --> pdb=" O LYS U 6 " (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 Processing helix chain 'W' and resid 3 through 10 Processing helix chain 'W' and resid 12 through 38 removed outlier: 3.649A pdb=" N THR W 38 " --> pdb=" O ILE W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'C' and resid 13 through 46 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 38 removed outlier: 3.666A pdb=" N THR 7 38 " --> pdb=" O ILE 7 34 " (cutoff:3.500A) 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: 3.597A 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 54 Processing helix chain '1' and resid 13 through 38 Processing helix chain '1' and resid 42 through 51 Processing helix chain '2' and resid 19 through 46 Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 4.321A 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 'H' and resid 62 through 66 removed outlier: 4.435A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.849A pdb=" N VAL H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.621A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1198 hydrogen bonds defined for protein. 3402 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: 3.47 Time building geometry restraints manager: 2.57 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: 5337 1.34 - 1.55: 15433 1.55 - 1.76: 342 1.76 - 1.96: 159 1.96 - 2.17: 120 Bond restraints: 21391 Sorted by residual: bond pdb=" C12 SPO P 102 " pdb=" C14 SPO P 102 " ideal model delta sigma weight residual 1.359 1.581 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C32 SPO F 103 " pdb=" C33 SPO F 103 " ideal model delta sigma weight residual 1.336 1.547 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C12 SPO I 103 " pdb=" C14 SPO I 103 " ideal model delta sigma weight residual 1.359 1.567 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C12 SPO Q 102 " pdb=" C14 SPO Q 102 " ideal model delta sigma weight residual 1.359 1.567 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C12 SPO R 103 " pdb=" C14 SPO R 103 " ideal model delta sigma weight residual 1.359 1.566 -0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 21386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 28644 5.18 - 10.37: 395 10.37 - 15.55: 303 15.55 - 20.73: 52 20.73 - 25.91: 3 Bond angle restraints: 29397 Sorted by residual: angle pdb=" C11 SPO 0 102 " pdb=" C10 SPO 0 102 " pdb=" C9 SPO 0 102 " ideal model delta sigma weight residual 123.01 148.92 -25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" C8 SPO 0 102 " pdb=" C7 SPO 0 102 " pdb=" C9 SPO 0 102 " ideal model delta sigma weight residual 123.96 103.09 20.87 3.00e+00 1.11e-01 4.84e+01 angle pdb=" C36 SPO U 103 " pdb=" C37 SPO U 103 " pdb=" C38 SPO U 103 " ideal model delta sigma weight residual 128.11 107.25 20.86 3.00e+00 1.11e-01 4.84e+01 angle pdb=" C17 SPO E 102 " pdb=" C19 SPO E 102 " pdb=" C20 SPO E 102 " ideal model delta sigma weight residual 127.83 108.14 19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" C13 SPO P 102 " pdb=" C12 SPO P 102 " pdb=" C14 SPO P 102 " ideal model delta sigma weight residual 123.54 104.39 19.15 3.00e+00 1.11e-01 4.08e+01 ... (remaining 29392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 11039 35.84 - 71.68: 389 71.68 - 107.53: 43 107.53 - 143.37: 4 143.37 - 179.21: 1 Dihedral angle restraints: 11476 sinusoidal: 5364 harmonic: 6112 Sorted by residual: dihedral pdb=" C1 BCL L 305 " pdb=" C2 BCL L 305 " pdb=" C3 BCL L 305 " pdb=" C5 BCL L 305 " ideal model delta sinusoidal sigma weight residual 180.00 0.79 179.21 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C6 U10 L 304 " pdb=" C7 U10 L 304 " pdb=" C8 U10 L 304 " pdb=" C9 U10 L 304 " ideal model delta sinusoidal sigma weight residual 101.51 -133.19 -125.30 1 2.00e+01 2.50e-03 3.79e+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 244.38 127.50 116.87 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 11473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2189 0.046 - 0.093: 589 0.093 - 0.139: 88 0.139 - 0.185: 9 0.185 - 0.232: 3 Chirality restraints: 2878 Sorted by residual: chirality pdb=" C2C BPH L 306 " pdb=" C1C BPH L 306 " pdb=" C3C BPH L 306 " pdb=" CMC BPH L 306 " both_signs ideal model delta sigma weight residual False -2.81 -2.58 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C3C BPH L 302 " pdb=" C2C BPH L 302 " pdb=" C4C BPH L 302 " pdb=" CAC BPH L 302 " both_signs ideal model delta sigma weight residual False 2.83 2.65 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 2875 not shown) Planarity restraints: 3587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 SPO 0 101 " -0.419 2.00e-02 2.50e+03 3.76e-01 1.76e+03 pdb=" C12 SPO 0 101 " 0.435 2.00e-02 2.50e+03 pdb=" C13 SPO 0 101 " -0.080 2.00e-02 2.50e+03 pdb=" C14 SPO 0 101 " 0.439 2.00e-02 2.50e+03 pdb=" C15 SPO 0 101 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C36 SPO U 103 " 0.319 2.00e-02 2.50e+03 3.27e-01 1.33e+03 pdb=" C37 SPO U 103 " -0.600 2.00e-02 2.50e+03 pdb=" C38 SPO U 103 " 0.257 2.00e-02 2.50e+03 pdb=" C39 SPO U 103 " 0.064 2.00e-02 2.50e+03 pdb=" C40 SPO U 103 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C36 SPO E 102 " -0.284 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" C37 SPO E 102 " 0.570 2.00e-02 2.50e+03 pdb=" C38 SPO E 102 " -0.291 2.00e-02 2.50e+03 pdb=" C39 SPO E 102 " -0.024 2.00e-02 2.50e+03 pdb=" C40 SPO E 102 " 0.028 2.00e-02 2.50e+03 ... (remaining 3584 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 239 2.66 - 3.22: 17494 3.22 - 3.78: 33003 3.78 - 4.34: 48114 4.34 - 4.90: 76547 Nonbonded interactions: 175397 Sorted by model distance: nonbonded pdb=" OE1 GLN Q 20 " pdb=" OH TYR R 24 " model vdw 2.100 3.040 nonbonded pdb=" OG1 THR 9 38 " pdb=" O SER 9 40 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR O 38 " pdb=" O SER O 40 " model vdw 2.169 3.040 nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 2.188 3.040 nonbonded pdb=" O ALA 1 28 " pdb=" ND1 HIS 1 32 " model vdw 2.199 3.120 ... (remaining 175392 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 10 through 49) selection = (chain '8' and resid 10 through 49) selection = (chain 'B' and resid 10 through 49) selection = (chain 'E' and resid 10 through 49) selection = (chain 'G' and resid 10 through 49) selection = (chain 'J' and resid 10 through 49) selection = (chain 'N' and resid 10 through 49) selection = (chain 'P' and resid 10 through 49) selection = (chain 'R' and resid 10 through 49) selection = (chain 'T' and resid 10 through 49) selection = chain 'V' } ncs_group { reference = chain '7' selection = (chain 'W' and (resid 1 through 46 or (resid 101 and (name NB or name ND or name \ C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C1A or name C1B or name C1C or name C1D or name C2 or name C2A or name C2B o \ r name C2C or name C2D or name C3 or name C3A or name C3B or name C3C or name C3 \ D or name C4 or name C4A or name C4B or name C4C or name C4D or name C5 or name \ C6 or name C7 or name C8 or name C9 or name CAA or name CAB or name CAC or name \ CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or n \ ame CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB \ or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2 \ A or name O2D or name OBB or name OBD or name MG )))) } ncs_group { reference = (chain '9' and resid 1 through 54) selection = (chain 'A' and resid 1 through 54) selection = (chain 'D' and resid 1 through 54) selection = (chain 'F' and resid 1 through 54) selection = (chain 'I' and resid 1 through 54) selection = (chain 'K' and resid 1 through 54) selection = (chain 'O' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) selection = (chain 'U' and resid 1 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.280 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.025 0.786 21408 Z= 1.682 Angle : 1.929 25.914 29397 Z= 0.682 Chirality : 0.042 0.232 2878 Planarity : 0.047 0.376 3587 Dihedral : 16.865 179.212 7546 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.34 % Allowed : 2.44 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.54 (0.18), residues: 2052 helix: 2.62 (0.13), residues: 1312 sheet: -0.67 (0.81), residues: 34 loop : 0.01 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 53 TYR 0.012 0.002 TYR H 243 PHE 0.017 0.002 PHE H 20 TRP 0.020 0.002 TRP L 271 HIS 0.011 0.001 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.02072 (21391) covalent geometry : angle 1.92854 (29397) hydrogen bonds : bond 0.13282 ( 1196) hydrogen bonds : angle 4.42581 ( 3402) Misc. bond : bond 0.47329 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 286 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: H 35 ASN cc_start: 0.8005 (m110) cc_final: 0.7264 (m110) REVERT: B 19 GLU cc_start: 0.7811 (tt0) cc_final: 0.7556 (tt0) REVERT: J 40 LEU cc_start: 0.8958 (tp) cc_final: 0.8535 (mt) REVERT: K 10 ILE cc_start: 0.8376 (pt) cc_final: 0.8112 (pt) REVERT: R 25 MET cc_start: 0.8350 (mmt) cc_final: 0.7866 (mmm) REVERT: V 24 TYR cc_start: 0.8081 (t80) cc_final: 0.7811 (t80) REVERT: 8 26 SER cc_start: 0.7821 (m) cc_final: 0.7523 (m) REVERT: 8 40 LEU cc_start: 0.7555 (tp) cc_final: 0.7324 (tt) outliers start: 6 outliers final: 1 residues processed: 289 average time/residue: 0.5885 time to fit residues: 193.2987 Evaluate side-chains 242 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN O 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.136754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.100598 restraints weight = 22530.489| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.23 r_work: 0.2649 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21408 Z= 0.202 Angle : 0.806 14.597 29397 Z= 0.330 Chirality : 0.041 0.140 2878 Planarity : 0.005 0.049 3587 Dihedral : 16.455 179.395 3820 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.15 % Allowed : 6.41 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.39 (0.18), residues: 2052 helix: 2.37 (0.13), residues: 1380 sheet: -0.67 (0.83), residues: 34 loop : -0.02 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 14 TYR 0.012 0.002 TYR K 41 PHE 0.017 0.002 PHE M 162 TRP 0.014 0.002 TRP M 157 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00480 (21391) covalent geometry : angle 0.80615 (29397) hydrogen bonds : bond 0.06652 ( 1196) hydrogen bonds : angle 3.82619 ( 3402) Misc. bond : bond 0.00388 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.695 Fit side-chains REVERT: M 23 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: M 52 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7060 (tm) REVERT: H 35 ASN cc_start: 0.8362 (m110) cc_final: 0.7771 (m110) REVERT: H 165 VAL cc_start: 0.8620 (t) cc_final: 0.8340 (m) REVERT: B 19 GLU cc_start: 0.8645 (tt0) cc_final: 0.8358 (tt0) REVERT: K 10 ILE cc_start: 0.8160 (pt) cc_final: 0.7899 (pt) REVERT: O 6 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7958 (mtpp) REVERT: P 18 GLN cc_start: 0.7778 (mt0) cc_final: 0.7571 (mt0) REVERT: R 25 MET cc_start: 0.8505 (mmm) cc_final: 0.8169 (mmm) REVERT: R 26 SER cc_start: 0.8873 (m) cc_final: 0.8534 (m) REVERT: V 22 SER cc_start: 0.6846 (t) cc_final: 0.6621 (p) REVERT: 7 3 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8196 (mttm) REVERT: 8 40 LEU cc_start: 0.7817 (tp) cc_final: 0.7519 (tt) outliers start: 38 outliers final: 19 residues processed: 265 average time/residue: 0.6115 time to fit residues: 183.8832 Evaluate side-chains 252 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 8 residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 201 ASN S 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098321 restraints weight = 22323.736| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.33 r_work: 0.2638 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 21408 Z= 0.214 Angle : 0.805 14.205 29397 Z= 0.332 Chirality : 0.042 0.155 2878 Planarity : 0.005 0.049 3587 Dihedral : 16.090 179.465 3820 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.55 % Allowed : 8.79 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.27 (0.18), residues: 2052 helix: 2.29 (0.13), residues: 1379 sheet: -0.75 (0.83), residues: 34 loop : -0.09 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 14 TYR 0.017 0.002 TYR 2 24 PHE 0.016 0.002 PHE M 162 TRP 0.014 0.002 TRP M 157 HIS 0.009 0.002 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00521 (21391) covalent geometry : angle 0.80463 (29397) hydrogen bonds : bond 0.06759 ( 1196) hydrogen bonds : angle 3.85617 ( 3402) Misc. bond : bond 0.00252 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: L 212 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8463 (mt-10) REVERT: M 23 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: M 52 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7506 (mt) REVERT: M 60 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7750 (mt) REVERT: H 89 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7793 (mtp85) REVERT: H 165 VAL cc_start: 0.8619 (t) cc_final: 0.8384 (m) REVERT: H 199 GLN cc_start: 0.8391 (mt0) cc_final: 0.8143 (mt0) REVERT: A 1 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.4952 (tmt) REVERT: K 10 ILE cc_start: 0.8254 (pt) cc_final: 0.8016 (pt) REVERT: O 45 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8282 (mm-30) REVERT: P 18 GLN cc_start: 0.7807 (mt0) cc_final: 0.7571 (mt0) REVERT: Q 1 MET cc_start: 0.1426 (pp-130) cc_final: 0.0112 (mtt) REVERT: R 22 SER cc_start: 0.7763 (t) cc_final: 0.7408 (p) REVERT: R 26 SER cc_start: 0.8830 (m) cc_final: 0.8473 (m) REVERT: U 9 MET cc_start: 0.5677 (mmm) cc_final: 0.5421 (mmt) REVERT: V 22 SER cc_start: 0.6911 (t) cc_final: 0.6628 (p) REVERT: 8 22 SER cc_start: 0.7980 (m) cc_final: 0.7603 (p) REVERT: X 27 MET cc_start: 0.7985 (mtt) cc_final: 0.7693 (mtp) outliers start: 45 outliers final: 24 residues processed: 271 average time/residue: 0.5968 time to fit residues: 183.6167 Evaluate side-chains 269 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 195 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Q 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.135690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.099503 restraints weight = 22425.000| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.26 r_work: 0.2669 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21408 Z= 0.179 Angle : 0.734 13.600 29397 Z= 0.305 Chirality : 0.040 0.142 2878 Planarity : 0.004 0.039 3587 Dihedral : 15.671 179.412 3820 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.66 % Allowed : 10.03 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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 (0.18), residues: 2052 helix: 2.43 (0.13), residues: 1381 sheet: -0.62 (0.83), residues: 34 loop : 0.00 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 202 TYR 0.014 0.001 TYR K 41 PHE 0.016 0.002 PHE M 162 TRP 0.014 0.002 TRP M 157 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00426 (21391) covalent geometry : angle 0.73351 (29397) hydrogen bonds : bond 0.06160 ( 1196) hydrogen bonds : angle 3.74254 ( 3402) Misc. bond : bond 0.00267 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.510 Fit side-chains REVERT: M 52 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (mt) REVERT: M 236 GLU cc_start: 0.8555 (tp30) cc_final: 0.8313 (tp30) REVERT: H 165 VAL cc_start: 0.8615 (t) cc_final: 0.8408 (m) REVERT: A 1 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.4846 (tmt) REVERT: E 40 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8515 (mp) REVERT: F 5 TYR cc_start: 0.8770 (p90) cc_final: 0.8524 (p90) REVERT: K 10 ILE cc_start: 0.8272 (pt) cc_final: 0.7999 (pt) REVERT: O 1 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.4874 (mmm) REVERT: O 6 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8022 (mtpp) REVERT: O 45 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8216 (mm-30) REVERT: P 18 GLN cc_start: 0.7792 (mt0) cc_final: 0.7549 (mt0) REVERT: Q 1 MET cc_start: 0.1268 (pp-130) cc_final: -0.0212 (mtt) REVERT: R 22 SER cc_start: 0.7799 (t) cc_final: 0.7475 (p) REVERT: R 26 SER cc_start: 0.8836 (m) cc_final: 0.8477 (m) REVERT: U 9 MET cc_start: 0.5591 (mmm) cc_final: 0.5339 (mmt) REVERT: 8 14 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7740 (t70) REVERT: 8 22 SER cc_start: 0.7951 (m) cc_final: 0.7637 (p) REVERT: X 27 MET cc_start: 0.8029 (mtt) cc_final: 0.7716 (mtp) REVERT: 2 25 MET cc_start: 0.2026 (OUTLIER) cc_final: 0.1628 (tmm) outliers start: 47 outliers final: 24 residues processed: 276 average time/residue: 0.5771 time to fit residues: 181.6628 Evaluate side-chains 270 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 149 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Q 20 GLN S 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.134907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.096582 restraints weight = 22233.802| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.16 r_work: 0.2686 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21408 Z= 0.178 Angle : 0.735 13.365 29397 Z= 0.305 Chirality : 0.039 0.140 2878 Planarity : 0.004 0.051 3587 Dihedral : 15.568 179.413 3820 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 10.49 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.49 (0.18), residues: 2052 helix: 2.45 (0.13), residues: 1378 sheet: -0.56 (0.83), residues: 34 loop : 0.02 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 202 TYR 0.016 0.001 TYR V 24 PHE 0.016 0.002 PHE M 162 TRP 0.013 0.002 TRP M 271 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00423 (21391) covalent geometry : angle 0.73491 (29397) hydrogen bonds : bond 0.06206 ( 1196) hydrogen bonds : angle 3.74043 ( 3402) Misc. bond : bond 0.00274 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.715 Fit side-chains REVERT: M 52 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7583 (mt) REVERT: M 60 LEU cc_start: 0.8501 (tt) cc_final: 0.7754 (mt) REVERT: M 236 GLU cc_start: 0.8504 (tp30) cc_final: 0.8264 (tp30) REVERT: H 89 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7741 (mtp85) REVERT: H 165 VAL cc_start: 0.8604 (t) cc_final: 0.8387 (m) REVERT: A 1 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.4719 (tmt) REVERT: E 40 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8490 (mp) REVERT: F 5 TYR cc_start: 0.8756 (p90) cc_final: 0.8553 (p90) REVERT: K 10 ILE cc_start: 0.8216 (pt) cc_final: 0.7951 (pt) REVERT: O 1 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5166 (mmm) REVERT: O 6 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7987 (mtpp) REVERT: O 45 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (mm-30) REVERT: P 18 GLN cc_start: 0.7750 (mt0) cc_final: 0.7522 (mt0) REVERT: R 22 SER cc_start: 0.7760 (t) cc_final: 0.7434 (p) REVERT: R 26 SER cc_start: 0.8812 (m) cc_final: 0.8451 (m) REVERT: U 9 MET cc_start: 0.5674 (mmm) cc_final: 0.5361 (mmt) REVERT: 8 14 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7827 (t70) REVERT: 8 22 SER cc_start: 0.7950 (m) cc_final: 0.7626 (p) REVERT: X 27 MET cc_start: 0.7994 (mtt) cc_final: 0.7688 (mtp) REVERT: 2 25 MET cc_start: 0.1957 (OUTLIER) cc_final: 0.1568 (tmm) outliers start: 52 outliers final: 24 residues processed: 268 average time/residue: 0.5680 time to fit residues: 172.8814 Evaluate side-chains 267 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 141 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.138915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102739 restraints weight = 22436.357| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.38 r_work: 0.2723 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21408 Z= 0.121 Angle : 0.634 13.010 29397 Z= 0.265 Chirality : 0.036 0.132 2878 Planarity : 0.004 0.034 3587 Dihedral : 14.962 179.422 3820 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.27 % Allowed : 11.73 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.86 (0.18), residues: 2052 helix: 2.75 (0.13), residues: 1377 sheet: -0.30 (0.86), residues: 34 loop : 0.12 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 53 TYR 0.013 0.001 TYR V 24 PHE 0.016 0.001 PHE M 162 TRP 0.013 0.001 TRP M 157 HIS 0.008 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00262 (21391) covalent geometry : angle 0.63414 (29397) hydrogen bonds : bond 0.05153 ( 1196) hydrogen bonds : angle 3.55628 ( 3402) Misc. bond : bond 0.00193 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 258 time to evaluate : 0.685 Fit side-chains REVERT: M 52 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7611 (mt) REVERT: M 60 LEU cc_start: 0.8531 (tt) cc_final: 0.7772 (mt) REVERT: M 227 SER cc_start: 0.8685 (p) cc_final: 0.8478 (m) REVERT: M 236 GLU cc_start: 0.8500 (tp30) cc_final: 0.8241 (tp30) REVERT: H 35 ASN cc_start: 0.8170 (m110) cc_final: 0.7540 (m110) REVERT: H 89 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7676 (mtp85) REVERT: H 242 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8607 (ttm) REVERT: A 1 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.4726 (tmt) REVERT: A 52 ASN cc_start: 0.7679 (m110) cc_final: 0.7351 (m110) REVERT: K 5 TYR cc_start: 0.8420 (p90) cc_final: 0.8200 (p90) REVERT: K 10 ILE cc_start: 0.8020 (pt) cc_final: 0.7747 (pt) REVERT: O 1 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5029 (mmm) REVERT: O 6 LYS cc_start: 0.8273 (mtpp) cc_final: 0.8011 (mtpp) REVERT: O 45 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8188 (mm-30) REVERT: P 18 GLN cc_start: 0.7705 (mt0) cc_final: 0.7475 (mt0) REVERT: Q 1 MET cc_start: 0.0877 (pp-130) cc_final: 0.0625 (ppp) REVERT: R 22 SER cc_start: 0.7755 (t) cc_final: 0.7507 (p) REVERT: R 26 SER cc_start: 0.8845 (m) cc_final: 0.8487 (m) REVERT: U 9 MET cc_start: 0.5689 (mmm) cc_final: 0.5374 (mmt) REVERT: 7 30 MET cc_start: 0.8392 (ttm) cc_final: 0.7963 (tmm) REVERT: 8 40 LEU cc_start: 0.7755 (tp) cc_final: 0.7474 (tt) REVERT: X 27 MET cc_start: 0.7863 (mtt) cc_final: 0.7615 (mtp) REVERT: 2 25 MET cc_start: 0.1924 (OUTLIER) cc_final: 0.1567 (tmm) outliers start: 40 outliers final: 16 residues processed: 281 average time/residue: 0.5554 time to fit residues: 178.8338 Evaluate side-chains 267 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 8 residue 12 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN S 42 ASN W 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.139785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.103103 restraints weight = 22580.147| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.49 r_work: 0.2728 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21408 Z= 0.112 Angle : 0.612 12.969 29397 Z= 0.257 Chirality : 0.036 0.171 2878 Planarity : 0.003 0.033 3587 Dihedral : 14.672 179.505 3820 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.21 % Allowed : 12.36 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 3.05 (0.18), residues: 2052 helix: 2.87 (0.13), residues: 1382 sheet: -0.08 (0.88), residues: 34 loop : 0.22 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 202 TYR 0.011 0.001 TYR Q 41 PHE 0.015 0.001 PHE M 162 TRP 0.014 0.001 TRP M 157 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00237 (21391) covalent geometry : angle 0.61167 (29397) hydrogen bonds : bond 0.04872 ( 1196) hydrogen bonds : angle 3.46435 ( 3402) Misc. bond : bond 0.00174 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 0.733 Fit side-chains REVERT: M 52 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7606 (mt) REVERT: M 60 LEU cc_start: 0.8537 (tt) cc_final: 0.7779 (mt) REVERT: M 227 SER cc_start: 0.8686 (p) cc_final: 0.8485 (m) REVERT: M 236 GLU cc_start: 0.8499 (tp30) cc_final: 0.8256 (tp30) REVERT: H 89 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7676 (mtp85) REVERT: H 242 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8590 (ttm) REVERT: A 1 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.4825 (tmt) REVERT: A 52 ASN cc_start: 0.7699 (m110) cc_final: 0.7347 (m110) REVERT: G 25 MET cc_start: 0.9177 (mmm) cc_final: 0.8846 (mmp) REVERT: K 10 ILE cc_start: 0.7912 (pt) cc_final: 0.7642 (pt) REVERT: O 1 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.5102 (mmm) REVERT: O 6 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7978 (mtpp) REVERT: O 45 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: P 18 GLN cc_start: 0.7618 (mt0) cc_final: 0.7367 (mt0) REVERT: Q 1 MET cc_start: 0.0845 (pp-130) cc_final: 0.0580 (ppp) REVERT: R 22 SER cc_start: 0.7752 (t) cc_final: 0.7490 (p) REVERT: R 26 SER cc_start: 0.8833 (m) cc_final: 0.8567 (m) REVERT: T 44 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8024 (mp) REVERT: U 9 MET cc_start: 0.5578 (mmm) cc_final: 0.5268 (mmt) REVERT: U 52 ASN cc_start: 0.6757 (OUTLIER) cc_final: 0.6386 (m110) REVERT: V 24 TYR cc_start: 0.7873 (t80) cc_final: 0.7562 (t80) REVERT: 7 1 MET cc_start: 0.4739 (OUTLIER) cc_final: 0.3670 (mmt) REVERT: 7 30 MET cc_start: 0.8389 (ttm) cc_final: 0.7916 (tmm) REVERT: 8 14 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7629 (t70) REVERT: 8 40 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7496 (tt) REVERT: X 27 MET cc_start: 0.7739 (mtt) cc_final: 0.7464 (mtp) REVERT: 2 25 MET cc_start: 0.1944 (OUTLIER) cc_final: 0.1591 (tmm) outliers start: 39 outliers final: 19 residues processed: 282 average time/residue: 0.5429 time to fit residues: 175.7681 Evaluate side-chains 278 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 8 residue 12 LEU Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 192 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.140903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100562 restraints weight = 22601.010| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.48 r_work: 0.2778 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21408 Z= 0.104 Angle : 0.589 12.895 29397 Z= 0.247 Chirality : 0.035 0.130 2878 Planarity : 0.003 0.030 3587 Dihedral : 14.457 179.527 3820 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.04 % Allowed : 13.10 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 3.20 (0.18), residues: 2052 helix: 3.00 (0.13), residues: 1381 sheet: 0.01 (0.90), residues: 34 loop : 0.24 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 202 TYR 0.013 0.001 TYR K 5 PHE 0.015 0.001 PHE M 162 TRP 0.012 0.001 TRP M 66 HIS 0.005 0.001 HIS M 266 Details of bonding type rmsd covalent geometry : bond 0.00218 (21391) covalent geometry : angle 0.58945 (29397) hydrogen bonds : bond 0.04618 ( 1196) hydrogen bonds : angle 3.40069 ( 3402) Misc. bond : bond 0.00158 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.712 Fit side-chains revert: symmetry clash REVERT: M 52 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7560 (mt) REVERT: M 60 LEU cc_start: 0.8487 (tt) cc_final: 0.7731 (mt) REVERT: M 236 GLU cc_start: 0.8423 (tp30) cc_final: 0.8188 (tp30) REVERT: H 89 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7695 (mtp85) REVERT: A 52 ASN cc_start: 0.7675 (m110) cc_final: 0.7324 (m110) REVERT: G 25 MET cc_start: 0.9166 (mmm) cc_final: 0.8845 (mmp) REVERT: K 10 ILE cc_start: 0.7888 (pt) cc_final: 0.7641 (pt) REVERT: O 1 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.4953 (mmm) REVERT: O 6 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7939 (mtpp) REVERT: O 45 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: P 18 GLN cc_start: 0.7522 (mt0) cc_final: 0.7278 (mt0) REVERT: Q 1 MET cc_start: 0.0709 (OUTLIER) cc_final: 0.0287 (ppp) REVERT: R 22 SER cc_start: 0.7665 (t) cc_final: 0.7411 (p) REVERT: R 26 SER cc_start: 0.8799 (m) cc_final: 0.8512 (m) REVERT: T 25 MET cc_start: 0.8541 (mmp) cc_final: 0.8324 (mmm) REVERT: T 44 ILE cc_start: 0.8236 (mt) cc_final: 0.8000 (mp) REVERT: U 9 MET cc_start: 0.5616 (mmm) cc_final: 0.5348 (mmt) REVERT: U 52 ASN cc_start: 0.6748 (OUTLIER) cc_final: 0.6388 (m110) REVERT: V 24 TYR cc_start: 0.7903 (t80) cc_final: 0.7548 (t80) REVERT: 7 1 MET cc_start: 0.4660 (OUTLIER) cc_final: 0.3592 (mmt) REVERT: 7 30 MET cc_start: 0.8299 (ttm) cc_final: 0.7824 (tmm) REVERT: 8 14 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7529 (t70) REVERT: 8 40 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7467 (tt) REVERT: X 27 MET cc_start: 0.7630 (mtt) cc_final: 0.7409 (mtp) REVERT: 1 30 MET cc_start: 0.3306 (ttm) cc_final: 0.2965 (ttp) REVERT: 2 25 MET cc_start: 0.1827 (OUTLIER) cc_final: 0.1470 (ttt) outliers start: 36 outliers final: 17 residues processed: 279 average time/residue: 0.5510 time to fit residues: 176.7668 Evaluate side-chains 276 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 8 residue 12 LEU Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain X residue 42 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 20 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.136302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.099268 restraints weight = 22502.435| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.33 r_work: 0.2667 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21408 Z= 0.156 Angle : 0.680 12.838 29397 Z= 0.285 Chirality : 0.038 0.131 2878 Planarity : 0.004 0.035 3587 Dihedral : 14.922 179.435 3820 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.15 % Allowed : 13.27 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.95 (0.18), residues: 2052 helix: 2.81 (0.13), residues: 1379 sheet: -0.21 (0.87), residues: 34 loop : 0.17 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 53 TYR 0.012 0.001 TYR K 41 PHE 0.015 0.001 PHE M 162 TRP 0.014 0.002 TRP M 271 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00365 (21391) covalent geometry : angle 0.68029 (29397) hydrogen bonds : bond 0.05712 ( 1196) hydrogen bonds : angle 3.58039 ( 3402) Misc. bond : bond 0.00249 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7627 (mt) REVERT: M 60 LEU cc_start: 0.8526 (tt) cc_final: 0.7791 (mt) REVERT: M 95 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8470 (mm-30) REVERT: H 35 ASN cc_start: 0.8279 (m110) cc_final: 0.7702 (m110) REVERT: H 89 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: H 242 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8599 (ttm) REVERT: A 1 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.4746 (tmt) REVERT: A 52 ASN cc_start: 0.7707 (m110) cc_final: 0.7381 (m110) REVERT: G 25 MET cc_start: 0.9189 (mmm) cc_final: 0.8913 (mmp) REVERT: K 10 ILE cc_start: 0.7952 (pt) cc_final: 0.7698 (pt) REVERT: O 1 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.5003 (mmm) REVERT: O 6 LYS cc_start: 0.8310 (mtpp) cc_final: 0.8028 (mtpp) REVERT: O 45 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8174 (mm-30) REVERT: P 18 GLN cc_start: 0.7705 (mt0) cc_final: 0.7402 (mt0) REVERT: Q 1 MET cc_start: 0.0695 (OUTLIER) cc_final: 0.0279 (ppp) REVERT: R 22 SER cc_start: 0.7795 (t) cc_final: 0.7489 (p) REVERT: R 26 SER cc_start: 0.8834 (m) cc_final: 0.8554 (m) REVERT: T 44 ILE cc_start: 0.8323 (mt) cc_final: 0.8068 (mp) REVERT: U 9 MET cc_start: 0.5567 (mmm) cc_final: 0.5162 (mmt) REVERT: U 52 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6434 (m110) REVERT: V 24 TYR cc_start: 0.8007 (t80) cc_final: 0.7626 (t80) REVERT: 7 1 MET cc_start: 0.4864 (OUTLIER) cc_final: 0.3872 (mmt) REVERT: 7 30 MET cc_start: 0.8405 (ttm) cc_final: 0.7938 (tmm) REVERT: 8 14 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7748 (t70) REVERT: 8 40 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7487 (tt) REVERT: X 27 MET cc_start: 0.7837 (mtt) cc_final: 0.7584 (mtp) REVERT: 1 30 MET cc_start: 0.3392 (ttm) cc_final: 0.3024 (ttp) outliers start: 38 outliers final: 19 residues processed: 269 average time/residue: 0.5839 time to fit residues: 179.6636 Evaluate side-chains 275 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 242 MET Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.136736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.101003 restraints weight = 22469.495| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.21 r_work: 0.2680 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21408 Z= 0.166 Angle : 0.708 12.743 29397 Z= 0.296 Chirality : 0.039 0.136 2878 Planarity : 0.004 0.035 3587 Dihedral : 15.060 179.417 3820 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.76 % Allowed : 13.89 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.82 (0.18), residues: 2052 helix: 2.69 (0.13), residues: 1379 sheet: 0.43 (1.14), residues: 22 loop : 0.12 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 118 TYR 0.013 0.001 TYR K 41 PHE 0.015 0.001 PHE H 20 TRP 0.013 0.002 TRP M 271 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00390 (21391) covalent geometry : angle 0.70829 (29397) hydrogen bonds : bond 0.05939 ( 1196) hydrogen bonds : angle 3.64657 ( 3402) Misc. bond : bond 0.00270 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7558 (mt) REVERT: M 60 LEU cc_start: 0.8546 (tt) cc_final: 0.7799 (mt) REVERT: M 95 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8469 (mm-30) REVERT: H 35 ASN cc_start: 0.8261 (m110) cc_final: 0.7761 (m110) REVERT: H 89 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7752 (mtp85) REVERT: A 1 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.4691 (tmt) REVERT: E 40 LEU cc_start: 0.8907 (tp) cc_final: 0.8691 (mt) REVERT: G 25 MET cc_start: 0.9145 (mmm) cc_final: 0.8877 (mmp) REVERT: K 10 ILE cc_start: 0.8084 (pt) cc_final: 0.7825 (pt) REVERT: O 6 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8041 (mtpp) REVERT: O 45 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: P 18 GLN cc_start: 0.7721 (mt0) cc_final: 0.7426 (mt0) REVERT: Q 1 MET cc_start: 0.0546 (OUTLIER) cc_final: 0.0236 (pmm) REVERT: R 22 SER cc_start: 0.7771 (t) cc_final: 0.7450 (p) REVERT: R 26 SER cc_start: 0.8798 (m) cc_final: 0.8505 (m) REVERT: U 9 MET cc_start: 0.5463 (mmm) cc_final: 0.5114 (mmt) REVERT: U 52 ASN cc_start: 0.6654 (OUTLIER) cc_final: 0.6289 (m110) REVERT: V 24 TYR cc_start: 0.8047 (t80) cc_final: 0.7676 (t80) REVERT: 7 1 MET cc_start: 0.4815 (OUTLIER) cc_final: 0.3820 (mmt) REVERT: 7 30 MET cc_start: 0.8415 (ttm) cc_final: 0.7949 (tmm) REVERT: 8 14 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7803 (t70) REVERT: 8 22 SER cc_start: 0.7953 (m) cc_final: 0.7628 (p) REVERT: X 27 MET cc_start: 0.7968 (mtt) cc_final: 0.7725 (mtp) REVERT: 1 30 MET cc_start: 0.3408 (ttm) cc_final: 0.3005 (ttp) outliers start: 31 outliers final: 20 residues processed: 262 average time/residue: 0.5869 time to fit residues: 175.1842 Evaluate side-chains 268 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 8 residue 12 LEU Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 99 optimal weight: 0.5980 chunk 167 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 0.0000 chunk 78 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.137804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100140 restraints weight = 22546.065| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.18 r_work: 0.2710 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21408 Z= 0.132 Angle : 0.649 12.764 29397 Z= 0.272 Chirality : 0.037 0.125 2878 Planarity : 0.004 0.031 3587 Dihedral : 14.761 179.421 3820 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.76 % Allowed : 14.00 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.97 (0.18), residues: 2052 helix: 2.81 (0.13), residues: 1379 sheet: 0.48 (1.16), residues: 22 loop : 0.16 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 118 TYR 0.013 0.001 TYR K 41 PHE 0.015 0.001 PHE M 162 TRP 0.012 0.001 TRP R 29 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd covalent geometry : bond 0.00294 (21391) covalent geometry : angle 0.64932 (29397) hydrogen bonds : bond 0.05357 ( 1196) hydrogen bonds : angle 3.55222 ( 3402) Misc. bond : bond 0.00211 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6839.23 seconds wall clock time: 117 minutes 1.47 seconds (7021.47 seconds total)