Starting phenix.real_space_refine on Sat Jul 4 11:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yml_33931/07_2026/7yml_33931.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 25 5.21 5 S 72 5.16 5 C 13028 2.51 5 N 2496 2.21 5 O 2923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18554 Number of models: 1 Model: "" Number of chains: 50 Chain: "L" Number of atoms: 2239 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Conformer: "B" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} bond proxies already assigned to first conformer: 2308 Chain: "M" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2417 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 291} Chain: "H" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1956 Classifications: {'peptide': 248} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 227} Chain: "A" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "F" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 452 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 453 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 334 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 56, 454 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 56, 454 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 460 Chain: "T" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 309 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 335 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 224 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "X" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 502 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 513 Unusual residues: {'BCL': 2, 'BPH': 1, 'LDA': 1, 'LMT': 3, 'PEE': 1, 'PGV': 1, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 685 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'LDA': 4, 'LMT': 5, 'PGV': 4, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'PGV:plan-3': 3} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'LDA': 2, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'BCL': 1, 'LDA': 1, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'BCL': 2, 'MYR': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" 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: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 166 Unusual residues: {'BCL': 1, 'LDA': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" 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: "Q" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 157 Unusual residues: {'BCL': 1, 'LDA': 2, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" 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: "S" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "T" 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: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" 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: "Y" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.45, per 1000 atoms: 0.24 Number of scatterers: 18554 At special positions: 0 Unit cell: (128.74, 104.96, 126.28, 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 72 16.00 P 9 15.00 Mg 25 11.99 O 2923 8.00 N 2496 7.00 C 13028 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=25, symmetry=0 Number of additional bonds: simple=25, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 801.1 milliseconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3434 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 9 sheets defined 71.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 58 Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.666A pdb=" N GLN L 88 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.783A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.641A pdb=" N TYR L 145 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 221 removed outlier: 3.527A pdb=" N GLU L 213 " --> pdb=" O THR L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 252 removed outlier: 3.781A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 264 removed outlier: 3.747A pdb=" N TRP L 263 " --> pdb=" O LEU L 259 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TRP L 264 " --> pdb=" O TRP L 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 259 through 264' Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.104A pdb=" N VAL L 268 " --> pdb=" O TRP L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 30 Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.985A pdb=" N TRP M 41 " --> pdb=" O ILE M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.548A pdb=" N GLY M 102 " --> pdb=" O ALA M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 110 Processing helix chain 'M' and resid 111 through 139 removed outlier: 3.507A pdb=" N ALA M 136 " --> pdb=" O VAL M 132 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU M 139 " --> pdb=" O ARG M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 161 removed outlier: 3.519A pdb=" N ALA M 152 " --> pdb=" O ALA M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 168 Processing helix chain 'M' and resid 169 through 173 removed outlier: 3.924A pdb=" N VAL M 172 " --> pdb=" O SER M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 192 removed outlier: 3.630A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 198 through 225 Processing helix chain 'M' and resid 226 through 229 Processing helix chain 'M' and resid 232 through 239 Processing helix chain 'M' and resid 241 through 256 removed outlier: 3.624A pdb=" N TRP M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 263 through 289 removed outlier: 3.790A pdb=" N VAL M 275 " --> pdb=" O MET M 271 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY M 287 " --> pdb=" O ILE M 283 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR M 288 " --> pdb=" O LEU M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 300 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 106 through 111 Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'H' and resid 138 through 140 No H-bonds generated for 'chain 'H' and resid 138 through 140' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 228 through 241 Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 37 removed outlier: 4.039A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 45 Processing helix chain 'D' and resid 3 through 10 Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'I' and resid 3 through 10 removed outlier: 3.583A pdb=" N LYS I 6 " --> pdb=" O LYS I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 42 through 51 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.613A pdb=" N TRP K 8 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'N' and resid 12 through 45 removed outlier: 3.518A pdb=" N VAL N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.640A pdb=" N TRP O 8 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 Processing helix chain 'O' and resid 42 through 52 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.551A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 52 Processing helix chain 'R' and resid 12 through 45 Processing helix chain 'S' and resid 3 through 10 removed outlier: 3.751A pdb=" N LYS S 6 " --> pdb=" O LYS S 3 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE S 7 " --> pdb=" O PHE S 4 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP S 8 " --> pdb=" O TYR S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 43 through 51 removed outlier: 3.579A pdb=" N ALA S 47 " --> pdb=" O TRP S 43 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 45 Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 12 through 38 Processing helix chain 'V' and resid 42 through 52 Processing helix chain 'W' and resid 12 through 45 removed outlier: 3.921A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU W 19 " --> pdb=" O GLN W 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 38 Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 42 through 52 Processing helix chain 'Z' and resid 19 through 45 Processing helix chain 'X' and resid 14 through 52 Proline residue: X 36 - end of helix Processing helix chain 'X' and resid 57 through 61 removed outlier: 3.570A pdb=" N GLN X 60 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA X 61 " --> pdb=" O ALA X 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 57 through 61' Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.634A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'M' and resid 11 through 14 removed outlier: 6.448A pdb=" N ALA M 14 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL H 144 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 34 through 35 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.882A pdb=" N PHE H 7 " --> pdb=" O PHE H 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 62 through 64 Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'H' and resid 134 through 136 removed outlier: 5.981A pdb=" N GLY H 164 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU H 185 " --> pdb=" O GLY H 164 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE H 166 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL H 183 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP H 168 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU H 181 " --> pdb=" O ASP H 168 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TRP H 170 " --> pdb=" O ARG H 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.830A pdb=" N GLY H 164 " --> pdb=" O VAL H 155 " (cutoff:3.500A) 999 hydrogen bonds defined for protein. 2799 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: 3.17 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 5532 1.37 - 1.54: 13298 1.54 - 1.71: 147 1.71 - 1.88: 140 1.88 - 2.05: 100 Bond restraints: 19217 Sorted by residual: bond pdb=" NA BCL Z 101 " pdb="MG BCL Z 101 " ideal model delta sigma weight residual 2.170 1.991 0.179 2.40e-02 1.74e+03 5.59e+01 bond pdb=" C8 U10 M 407 " pdb=" C9 U10 M 407 " ideal model delta sigma weight residual 1.470 1.320 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C8 U10 L 303 " pdb=" C9 U10 L 303 " ideal model delta sigma weight residual 1.470 1.321 0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" NA BCL A 101 " pdb="MG BCL A 101 " ideal model delta sigma weight residual 2.170 1.993 0.177 2.40e-02 1.74e+03 5.44e+01 bond pdb=" C8 U10 M 401 " pdb=" C9 U10 M 401 " ideal model delta sigma weight residual 1.470 1.323 0.147 2.00e-02 2.50e+03 5.44e+01 ... (remaining 19212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 25068 4.70 - 9.40: 1152 9.40 - 14.10: 83 14.10 - 18.80: 15 18.80 - 23.49: 2 Bond angle restraints: 26320 Sorted by residual: angle pdb=" C2 SPO R 101 " pdb=" C1 SPO R 101 " pdb=" C4 SPO R 101 " ideal model delta sigma weight residual 110.23 86.74 23.49 3.00e+00 1.11e-01 6.13e+01 angle pdb=" C1D BCL A 101 " pdb=" C2D BCL A 101 " pdb=" CMD BCL A 101 " ideal model delta sigma weight residual 125.57 139.44 -13.87 1.83e+00 2.99e-01 5.76e+01 angle pdb=" C1D BCL V 101 " pdb=" C2D BCL V 101 " pdb=" CMD BCL V 101 " ideal model delta sigma weight residual 125.57 139.33 -13.76 1.83e+00 2.99e-01 5.67e+01 angle pdb=" C1D BCL S 103 " pdb=" C2D BCL S 103 " pdb=" CMD BCL S 103 " ideal model delta sigma weight residual 125.57 139.32 -13.74 1.83e+00 2.99e-01 5.65e+01 angle pdb=" C1D BCL F 101 " pdb=" C2D BCL F 101 " pdb=" CMD BCL F 101 " ideal model delta sigma weight residual 125.57 139.10 -13.53 1.83e+00 2.99e-01 5.48e+01 ... (remaining 26315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 9660 35.10 - 70.20: 321 70.20 - 105.30: 23 105.30 - 140.41: 4 140.41 - 175.51: 16 Dihedral angle restraints: 10024 sinusoidal: 4697 harmonic: 5327 Sorted by residual: dihedral pdb=" C1 BCL M 403 " pdb=" CGA BCL M 403 " pdb=" O2A BCL M 403 " pdb=" CBA BCL M 403 " ideal model delta sinusoidal sigma weight residual 180.00 109.53 70.47 1 6.00e+00 2.78e-02 1.78e+02 dihedral pdb=" C1 BCL B 101 " pdb=" CGA BCL B 101 " pdb=" O2A BCL B 101 " pdb=" CBA BCL B 101 " ideal model delta sinusoidal sigma weight residual 180.00 110.38 69.62 1 6.00e+00 2.78e-02 1.74e+02 dihedral pdb=" CBD BCL Z 101 " pdb=" CGD BCL Z 101 " pdb=" O2D BCL Z 101 " pdb=" CED BCL Z 101 " ideal model delta sinusoidal sigma weight residual 180.00 135.84 44.16 1 5.00e+00 4.00e-02 1.09e+02 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2169 0.057 - 0.115: 405 0.115 - 0.172: 103 0.172 - 0.229: 29 0.229 - 0.287: 12 Chirality restraints: 2718 Sorted by residual: chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV H 304 " pdb=" C04 PGV H 304 " pdb=" C06 PGV H 304 " pdb=" O05 PGV H 304 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C05 PGV H 303 " pdb=" C04 PGV H 303 " pdb=" C06 PGV H 303 " pdb=" O05 PGV H 303 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2715 not shown) Planarity restraints: 3109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 403 " 0.372 3.00e-02 1.11e+03 3.02e-01 5.08e+02 pdb=" CBA BCL M 403 " 0.178 3.00e-02 1.11e+03 pdb=" CGA BCL M 403 " -0.086 3.00e-02 1.11e+03 pdb=" O1A BCL M 403 " 0.061 3.00e-02 1.11e+03 pdb=" O2A BCL M 403 " -0.525 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL B 101 " 0.359 3.00e-02 1.11e+03 2.94e-01 4.81e+02 pdb=" CBA BCL B 101 " 0.173 3.00e-02 1.11e+03 pdb=" CGA BCL B 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL B 101 " 0.061 3.00e-02 1.11e+03 pdb=" O2A BCL B 101 " -0.515 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL A 101 " 0.123 3.10e-02 1.04e+03 2.69e-01 3.77e+02 pdb=" C4C BCL A 101 " 0.056 3.10e-02 1.04e+03 pdb=" CHC BCL A 101 " -0.321 3.10e-02 1.04e+03 pdb=" CHD BCL A 101 " -0.269 3.10e-02 1.04e+03 pdb=" NC BCL A 101 " 0.411 3.10e-02 1.04e+03 ... (remaining 3106 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 200 2.61 - 3.18: 14903 3.18 - 3.75: 30670 3.75 - 4.33: 46006 4.33 - 4.90: 73002 Nonbonded interactions: 164781 Sorted by model distance: nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 406 " model vdw 2.035 2.260 nonbonded pdb=" OE1 GLU M 233 " pdb="FE FE M 406 " model vdw 2.078 2.260 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 406 " model vdw 2.094 2.340 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 406 " model vdw 2.140 2.340 nonbonded pdb=" O6' LMT M 409 " pdb=" O1 LDA H 301 " model vdw 2.167 3.040 ... (remaining 164776 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 'B' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'E' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'G' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'J' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'N' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'P' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'R' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 48)) selection = (chain 'T' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 48)) selection = (chain 'W' and resid 8 through 48) } ncs_group { reference = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'I' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 14 or resid 16 through 54)) selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'S' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'V' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 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=0.50 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: 6.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.920 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.564 19242 Z= 1.165 Angle : 1.857 23.495 26320 Z= 0.775 Chirality : 0.056 0.287 2718 Planarity : 0.018 0.302 3109 Dihedral : 17.845 175.507 6590 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.88 % Allowed : 4.09 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1793 helix: 1.44 (0.14), residues: 1098 sheet: -0.46 (1.04), residues: 28 loop : 0.12 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 45 TYR 0.032 0.002 TYR M 302 PHE 0.017 0.002 PHE L 147 TRP 0.012 0.002 TRP S 8 HIS 0.007 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.01925 / 0.85 (19217) covalent geometry : angle 1.85686 / 0.78 (26320) hydrogen bonds : bond 0.19758 / 13.07 ( 997) hydrogen bonds : angle 6.32874 / 4.51 ( 2799) Misc. bond : bond 0.24852 / 16.36 ( 25) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8672 (mttm) cc_final: 0.8460 (mmtp) REVERT: M 109 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8561 (ttmm) REVERT: M 137 ASP cc_start: 0.8919 (t0) cc_final: 0.8547 (t70) REVERT: E 6 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4626 (tm) REVERT: I 15 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7187 (tmt170) REVERT: K 4 PHE cc_start: 0.8797 (m-80) cc_final: 0.8557 (m-10) REVERT: K 15 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7828 (mtt90) REVERT: O 15 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6438 (ttp-110) REVERT: P 24 MET cc_start: 0.8658 (mmm) cc_final: 0.8398 (mmm) REVERT: Q 6 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8614 (ttmm) REVERT: R 13 ASP cc_start: 0.8016 (t0) cc_final: 0.7775 (t0) REVERT: S 5 TYR cc_start: 0.7954 (p90) cc_final: 0.6997 (p90) REVERT: T 17 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7723 (mp10) REVERT: V 11 PHE cc_start: 0.7278 (m-80) cc_final: 0.6788 (m-10) REVERT: V 30 LEU cc_start: 0.8317 (tt) cc_final: 0.8087 (tm) REVERT: W 17 GLN cc_start: 0.7268 (mm110) cc_final: 0.6977 (mm110) REVERT: X 9 ASP cc_start: 0.7256 (t0) cc_final: 0.6918 (t0) outliers start: 28 outliers final: 11 residues processed: 270 average time/residue: 0.5695 time to fit residues: 174.1006 Evaluate side-chains 225 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 213 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 32 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 77 ASN L 117 HIS M 12 GLN M 44 ASN M 110 GLN M 144 HIS H 44 ASN H 52 ASN I 20 GLN K 20 GLN N 15 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081107 restraints weight = 43189.461| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.00 r_work: 0.2777 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.269 19242 Z= 0.152 Angle : 0.715 17.376 26320 Z= 0.288 Chirality : 0.038 0.308 2718 Planarity : 0.004 0.053 3109 Dihedral : 18.434 176.332 3519 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.95 % Allowed : 8.59 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.22 (0.19), residues: 1793 helix: 2.32 (0.14), residues: 1120 sheet: -0.30 (1.04), residues: 28 loop : 0.06 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 14 TYR 0.026 0.001 TYR M 302 PHE 0.019 0.001 PHE L 272 TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (19217) covalent geometry : angle 0.71535 / 0.29 (26320) hydrogen bonds : bond 0.05345 / 3.40 ( 997) hydrogen bonds : angle 4.15817 / 2.93 ( 2799) Misc. bond : bond 0.05391 / 4.18 ( 25) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8798 (mttm) cc_final: 0.8448 (mmtp) REVERT: M 109 LYS cc_start: 0.8948 (ttmm) cc_final: 0.8687 (ttmm) REVERT: M 137 ASP cc_start: 0.9031 (t0) cc_final: 0.8768 (t70) REVERT: H 142 MET cc_start: 0.8920 (mtt) cc_final: 0.8617 (mtt) REVERT: H 172 ASP cc_start: 0.8803 (t70) cc_final: 0.8551 (t0) REVERT: H 189 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8167 (ttpt) REVERT: D 3 LYS cc_start: 0.8606 (mptm) cc_final: 0.8161 (mmmt) REVERT: I 15 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.6872 (tmt170) REVERT: K 15 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7939 (mtt90) REVERT: O 12 ASP cc_start: 0.8152 (t0) cc_final: 0.7808 (t0) REVERT: O 15 ARG cc_start: 0.7643 (mmm160) cc_final: 0.6570 (ttp-170) REVERT: Q 6 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8580 (ttmm) REVERT: R 11 LEU cc_start: 0.8710 (mp) cc_final: 0.8459 (mp) REVERT: R 17 GLN cc_start: 0.8036 (tt0) cc_final: 0.7632 (tt0) REVERT: S 5 TYR cc_start: 0.7980 (p90) cc_final: 0.7309 (p90) REVERT: S 6 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7890 (mptp) REVERT: S 9 LEU cc_start: 0.7437 (mt) cc_final: 0.7205 (mm) REVERT: T 39 LEU cc_start: 0.8842 (tp) cc_final: 0.8377 (mt) REVERT: V 30 LEU cc_start: 0.7968 (tt) cc_final: 0.7426 (tm) REVERT: X 9 ASP cc_start: 0.7159 (t0) cc_final: 0.6576 (t0) outliers start: 29 outliers final: 13 residues processed: 255 average time/residue: 0.5191 time to fit residues: 151.6293 Evaluate side-chains 226 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 189 LYS Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain Q residue 5 TYR Chi-restraints excluded: chain Y residue 31 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 ASN H 135 GLN K 20 GLN N 17 GLN S 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.108884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076966 restraints weight = 45299.779| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.03 r_work: 0.2698 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 19242 Z= 0.308 Angle : 0.830 17.218 26320 Z= 0.334 Chirality : 0.045 0.297 2718 Planarity : 0.005 0.055 3109 Dihedral : 18.456 176.896 3511 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.09 % Allowed : 9.66 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.07 (0.19), residues: 1793 helix: 2.27 (0.14), residues: 1120 sheet: -0.68 (1.02), residues: 28 loop : -0.11 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 179 TYR 0.032 0.002 TYR M 302 PHE 0.025 0.002 PHE H 20 TRP 0.014 0.002 TRP M 156 HIS 0.010 0.002 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.31 (19217) covalent geometry : angle 0.82965 / 0.33 (26320) hydrogen bonds : bond 0.05572 / 3.57 ( 997) hydrogen bonds : angle 4.13430 / 2.92 ( 2799) Misc. bond : bond 0.01564 / 1.20 ( 25) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8845 (mttm) cc_final: 0.8479 (mmtp) REVERT: M 109 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8736 (ttmm) REVERT: M 137 ASP cc_start: 0.9035 (t0) cc_final: 0.8659 (t70) REVERT: D 3 LYS cc_start: 0.8692 (mptm) cc_final: 0.8223 (mmmt) REVERT: G 14 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: I 14 ARG cc_start: 0.8372 (mtm110) cc_final: 0.8060 (mtt90) REVERT: I 15 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.6903 (tmt170) REVERT: K 15 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7889 (mtt90) REVERT: N 12 THR cc_start: 0.8819 (p) cc_final: 0.8496 (p) REVERT: N 14 GLU cc_start: 0.8063 (pm20) cc_final: 0.7782 (pm20) REVERT: O 12 ASP cc_start: 0.8208 (t0) cc_final: 0.7808 (t0) REVERT: O 15 ARG cc_start: 0.7595 (mmm160) cc_final: 0.6545 (ttp-170) REVERT: Q 6 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8291 (mppt) REVERT: R 11 LEU cc_start: 0.8720 (mp) cc_final: 0.8365 (mp) REVERT: S 3 LYS cc_start: 0.8311 (tppt) cc_final: 0.8098 (tptt) REVERT: S 5 TYR cc_start: 0.7762 (p90) cc_final: 0.7217 (p90) REVERT: S 6 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7877 (mptp) REVERT: S 9 LEU cc_start: 0.7383 (mt) cc_final: 0.7115 (mm) REVERT: T 39 LEU cc_start: 0.8831 (tp) cc_final: 0.8381 (mt) REVERT: V 30 LEU cc_start: 0.8006 (tt) cc_final: 0.7277 (tm) REVERT: V 34 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7277 (mp) REVERT: W 24 MET cc_start: 0.8555 (mmm) cc_final: 0.8339 (tpp) REVERT: X 9 ASP cc_start: 0.7239 (t0) cc_final: 0.6761 (t0) REVERT: X 15 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8045 (mtpt) REVERT: X 38 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8629 (mp) outliers start: 46 outliers final: 23 residues processed: 242 average time/residue: 0.5491 time to fit residues: 151.1992 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 ASN H 176 GLN N 15 GLN N 17 GLN P 20 HIS S 20 GLN T 20 HIS ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081190 restraints weight = 41382.771| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.96 r_work: 0.2784 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19242 Z= 0.134 Angle : 0.674 13.930 26320 Z= 0.270 Chirality : 0.038 0.278 2718 Planarity : 0.004 0.053 3109 Dihedral : 17.259 172.682 3511 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.68 % Allowed : 10.74 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.38 (0.19), residues: 1793 helix: 2.55 (0.14), residues: 1118 sheet: -0.49 (1.03), residues: 28 loop : -0.06 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.032 0.001 TYR Q 5 PHE 0.019 0.001 PHE F 17 TRP 0.015 0.001 TRP M 156 HIS 0.006 0.001 HIS M 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (19217) covalent geometry : angle 0.67396 / 0.27 (26320) hydrogen bonds : bond 0.04529 / 2.89 ( 997) hydrogen bonds : angle 3.85187 / 2.71 ( 2799) Misc. bond : bond 0.00736 / 0.56 ( 25) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8802 (mttm) cc_final: 0.8445 (mmtp) REVERT: M 109 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8722 (ttmm) REVERT: M 137 ASP cc_start: 0.9001 (t0) cc_final: 0.8728 (t70) REVERT: M 213 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.8844 (tp) REVERT: H 172 ASP cc_start: 0.8846 (t70) cc_final: 0.8606 (t70) REVERT: D 3 LYS cc_start: 0.8623 (mptm) cc_final: 0.8206 (mmmt) REVERT: F 16 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8632 (t) REVERT: I 14 ARG cc_start: 0.8308 (mtm110) cc_final: 0.8092 (mtt90) REVERT: I 15 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.6891 (tmt170) REVERT: J 18 GLU cc_start: 0.8417 (tp30) cc_final: 0.8215 (tm-30) REVERT: K 15 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7844 (mtt90) REVERT: O 12 ASP cc_start: 0.8174 (t0) cc_final: 0.7863 (t0) REVERT: O 15 ARG cc_start: 0.7543 (mmm160) cc_final: 0.6546 (ttp-170) REVERT: Q 5 TYR cc_start: 0.8573 (p90) cc_final: 0.8315 (p90) REVERT: R 11 LEU cc_start: 0.8776 (mp) cc_final: 0.8396 (mp) REVERT: R 17 GLN cc_start: 0.8034 (tt0) cc_final: 0.7765 (tp40) REVERT: S 5 TYR cc_start: 0.7798 (p90) cc_final: 0.7244 (p90) REVERT: S 6 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7872 (mptp) REVERT: S 9 LEU cc_start: 0.7415 (mt) cc_final: 0.7181 (mm) REVERT: T 39 LEU cc_start: 0.8812 (tp) cc_final: 0.8362 (mt) REVERT: V 30 LEU cc_start: 0.7981 (tt) cc_final: 0.7246 (tm) REVERT: V 34 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7264 (mp) REVERT: X 6 LYS cc_start: 0.8368 (mmtp) cc_final: 0.8112 (mmtm) REVERT: X 9 ASP cc_start: 0.7243 (t0) cc_final: 0.6718 (t0) outliers start: 40 outliers final: 17 residues processed: 247 average time/residue: 0.5713 time to fit residues: 161.2353 Evaluate side-chains 231 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 17 GLN S 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.077945 restraints weight = 48208.737| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.12 r_work: 0.2719 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19242 Z= 0.220 Angle : 0.735 12.948 26320 Z= 0.296 Chirality : 0.041 0.272 2718 Planarity : 0.004 0.053 3109 Dihedral : 17.173 178.819 3507 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.02 % Allowed : 11.28 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.31 (0.19), residues: 1793 helix: 2.50 (0.14), residues: 1117 sheet: -0.70 (1.01), residues: 28 loop : -0.09 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 179 TYR 0.029 0.002 TYR M 302 PHE 0.022 0.001 PHE H 20 TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (19217) covalent geometry : angle 0.73457 / 0.30 (26320) hydrogen bonds : bond 0.04865 / 3.11 ( 997) hydrogen bonds : angle 3.92423 / 2.77 ( 2799) Misc. bond : bond 0.00719 / 0.54 ( 25) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8798 (mttm) cc_final: 0.8429 (mmtp) REVERT: M 109 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8794 (ttmm) REVERT: M 137 ASP cc_start: 0.9037 (t0) cc_final: 0.8653 (t70) REVERT: M 213 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8819 (tp) REVERT: D 3 LYS cc_start: 0.8657 (mptm) cc_final: 0.8215 (mmmt) REVERT: I 14 ARG cc_start: 0.8336 (mtm110) cc_final: 0.8079 (mtt90) REVERT: I 15 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.6884 (tmt170) REVERT: K 15 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7867 (mtt90) REVERT: O 15 ARG cc_start: 0.7541 (mmm160) cc_final: 0.6575 (ttp-170) REVERT: R 11 LEU cc_start: 0.8777 (mp) cc_final: 0.8371 (mp) REVERT: R 17 GLN cc_start: 0.8069 (tt0) cc_final: 0.7773 (tp40) REVERT: R 25 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.7967 (p) REVERT: S 3 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7922 (tptt) REVERT: S 5 TYR cc_start: 0.7844 (p90) cc_final: 0.7236 (p90) REVERT: S 6 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7861 (mptp) REVERT: S 9 LEU cc_start: 0.7350 (mt) cc_final: 0.7099 (mm) REVERT: T 39 LEU cc_start: 0.8827 (tp) cc_final: 0.8375 (mt) REVERT: V 30 LEU cc_start: 0.7975 (tt) cc_final: 0.7229 (tm) REVERT: V 34 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7210 (mp) REVERT: X 9 ASP cc_start: 0.7226 (t0) cc_final: 0.6736 (t0) outliers start: 45 outliers final: 22 residues processed: 237 average time/residue: 0.5696 time to fit residues: 153.7287 Evaluate side-chains 235 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 ASN S 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077797 restraints weight = 32633.300| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.57 r_work: 0.2804 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19242 Z= 0.158 Angle : 0.678 11.999 26320 Z= 0.276 Chirality : 0.038 0.266 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.615 172.859 3507 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.55 % Allowed : 11.88 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.41 (0.19), residues: 1793 helix: 2.58 (0.14), residues: 1118 sheet: -0.59 (1.02), residues: 28 loop : -0.05 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.027 0.001 TYR M 302 PHE 0.018 0.001 PHE H 20 TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (19217) covalent geometry : angle 0.67809 / 0.28 (26320) hydrogen bonds : bond 0.04555 / 2.92 ( 997) hydrogen bonds : angle 3.84049 / 2.70 ( 2799) Misc. bond : bond 0.00379 / 0.27 ( 25) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8801 (mttm) cc_final: 0.8448 (mmtp) REVERT: M 109 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8773 (ttmm) REVERT: M 137 ASP cc_start: 0.8986 (t0) cc_final: 0.8625 (t70) REVERT: M 213 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8806 (tp) REVERT: D 3 LYS cc_start: 0.8625 (mptm) cc_final: 0.8188 (mmmt) REVERT: I 14 ARG cc_start: 0.8272 (mtm110) cc_final: 0.8037 (mtt90) REVERT: I 15 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7355 (mmm160) REVERT: K 15 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7829 (mtt90) REVERT: O 4 PHE cc_start: 0.8600 (m-80) cc_final: 0.8387 (m-10) REVERT: O 15 ARG cc_start: 0.7513 (mmm160) cc_final: 0.6557 (ttp-170) REVERT: R 25 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8002 (p) REVERT: S 5 TYR cc_start: 0.7835 (p90) cc_final: 0.7285 (p90) REVERT: S 6 LYS cc_start: 0.8266 (mtpt) cc_final: 0.8007 (mttm) REVERT: S 9 LEU cc_start: 0.7413 (mt) cc_final: 0.7145 (mm) REVERT: T 39 LEU cc_start: 0.8822 (tp) cc_final: 0.8362 (mt) REVERT: V 30 LEU cc_start: 0.7947 (tt) cc_final: 0.7207 (tm) REVERT: V 34 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7212 (mp) REVERT: X 3 MET cc_start: 0.7429 (ttm) cc_final: 0.7212 (ttt) REVERT: X 9 ASP cc_start: 0.7152 (t0) cc_final: 0.6644 (t0) outliers start: 38 outliers final: 20 residues processed: 235 average time/residue: 0.5649 time to fit residues: 151.4932 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 32 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 20 GLN S 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.078529 restraints weight = 53043.973| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.31 r_work: 0.2727 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19242 Z= 0.170 Angle : 0.682 11.963 26320 Z= 0.280 Chirality : 0.039 0.262 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.454 173.136 3507 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.55 % Allowed : 12.42 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.19), residues: 1793 helix: 2.58 (0.14), residues: 1118 sheet: -0.63 (1.00), residues: 28 loop : -0.09 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.030 0.001 TYR Q 5 PHE 0.020 0.001 PHE F 17 TRP 0.013 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (19217) covalent geometry : angle 0.68188 / 0.28 (26320) hydrogen bonds : bond 0.04564 / 2.92 ( 997) hydrogen bonds : angle 3.83128 / 2.70 ( 2799) Misc. bond : bond 0.00307 / 0.20 ( 25) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8750 (mttm) cc_final: 0.8395 (mmtp) REVERT: M 109 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8722 (ttmm) REVERT: M 137 ASP cc_start: 0.8926 (t0) cc_final: 0.8543 (t70) REVERT: M 213 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8758 (tp) REVERT: D 3 LYS cc_start: 0.8594 (mptm) cc_final: 0.8189 (mmmt) REVERT: F 16 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8585 (t) REVERT: I 14 ARG cc_start: 0.8207 (mtm110) cc_final: 0.7953 (mtt90) REVERT: I 15 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7252 (mmm160) REVERT: K 15 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7751 (mtt90) REVERT: O 4 PHE cc_start: 0.8589 (m-80) cc_final: 0.8377 (m-10) REVERT: O 15 ARG cc_start: 0.7380 (mmm160) cc_final: 0.6488 (ttp-170) REVERT: Q 5 TYR cc_start: 0.8520 (p90) cc_final: 0.8256 (p90) REVERT: R 25 SER cc_start: 0.8479 (OUTLIER) cc_final: 0.7921 (p) REVERT: S 5 TYR cc_start: 0.7793 (p90) cc_final: 0.7165 (p90) REVERT: S 6 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7808 (mptp) REVERT: S 9 LEU cc_start: 0.7298 (mt) cc_final: 0.7053 (mm) REVERT: T 39 LEU cc_start: 0.8754 (tp) cc_final: 0.8290 (mt) REVERT: V 30 LEU cc_start: 0.7854 (tt) cc_final: 0.7108 (tm) REVERT: V 34 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7099 (mp) REVERT: X 9 ASP cc_start: 0.7164 (t0) cc_final: 0.6738 (t0) outliers start: 38 outliers final: 21 residues processed: 232 average time/residue: 0.5916 time to fit residues: 155.6921 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 59 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 ASN K 20 GLN S 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080352 restraints weight = 41236.414| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.95 r_work: 0.2762 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19242 Z= 0.167 Angle : 0.680 11.792 26320 Z= 0.280 Chirality : 0.038 0.263 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.345 177.833 3507 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.15 % Allowed : 13.22 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.40 (0.19), residues: 1793 helix: 2.58 (0.14), residues: 1118 sheet: -0.53 (1.02), residues: 28 loop : -0.08 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.029 0.001 TYR Q 5 PHE 0.020 0.001 PHE X 4 TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (19217) covalent geometry : angle 0.68015 / 0.28 (26320) hydrogen bonds : bond 0.04523 / 2.89 ( 997) hydrogen bonds : angle 3.82130 / 2.69 ( 2799) Misc. bond : bond 0.00279 / 0.18 ( 25) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8809 (mttm) cc_final: 0.8432 (mmtp) REVERT: M 109 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8793 (ttmm) REVERT: M 137 ASP cc_start: 0.9016 (t0) cc_final: 0.8643 (t70) REVERT: M 213 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8825 (tp) REVERT: D 3 LYS cc_start: 0.8683 (mptm) cc_final: 0.8260 (mmmt) REVERT: I 14 ARG cc_start: 0.8301 (mtm110) cc_final: 0.8066 (mtt90) REVERT: I 15 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.7381 (mmm160) REVERT: K 15 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7882 (mtt90) REVERT: O 15 ARG cc_start: 0.7504 (mmm160) cc_final: 0.6597 (ttp-110) REVERT: Q 5 TYR cc_start: 0.8531 (p90) cc_final: 0.8250 (p90) REVERT: R 25 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8025 (p) REVERT: S 5 TYR cc_start: 0.7830 (p90) cc_final: 0.7183 (p90) REVERT: S 6 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7854 (mptp) REVERT: S 9 LEU cc_start: 0.7377 (mt) cc_final: 0.7124 (mm) REVERT: T 39 LEU cc_start: 0.8828 (tp) cc_final: 0.8371 (mt) REVERT: V 30 LEU cc_start: 0.7965 (tt) cc_final: 0.7218 (tm) REVERT: V 34 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7268 (mp) REVERT: X 3 MET cc_start: 0.7441 (ptp) cc_final: 0.7184 (ptp) REVERT: X 9 ASP cc_start: 0.7221 (t0) cc_final: 0.6830 (t0) outliers start: 32 outliers final: 22 residues processed: 224 average time/residue: 0.5842 time to fit residues: 148.5607 Evaluate side-chains 229 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 170 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 ASN K 20 GLN S 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078089 restraints weight = 46869.298| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.09 r_work: 0.2722 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19242 Z= 0.222 Angle : 0.734 13.262 26320 Z= 0.302 Chirality : 0.041 0.265 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.625 179.831 3507 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.08 % Allowed : 13.49 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1793 helix: 2.48 (0.14), residues: 1119 sheet: -0.67 (1.00), residues: 28 loop : -0.12 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.030 0.002 TYR M 302 PHE 0.025 0.002 PHE F 17 TRP 0.013 0.001 TRP M 156 HIS 0.008 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (19217) covalent geometry : angle 0.73360 / 0.30 (26320) hydrogen bonds : bond 0.04802 / 3.07 ( 997) hydrogen bonds : angle 3.90180 / 2.75 ( 2799) Misc. bond : bond 0.00516 / 0.37 ( 25) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8781 (mttm) cc_final: 0.8430 (mmtp) REVERT: M 109 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8798 (ttmm) REVERT: M 137 ASP cc_start: 0.9033 (t0) cc_final: 0.8640 (t70) REVERT: H 198 LEU cc_start: 0.8427 (mp) cc_final: 0.8201 (pp) REVERT: D 3 LYS cc_start: 0.8703 (mptm) cc_final: 0.8273 (mmmt) REVERT: F 16 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8700 (t) REVERT: I 14 ARG cc_start: 0.8333 (mtm110) cc_final: 0.8087 (mtt90) REVERT: I 15 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.7343 (mmm160) REVERT: K 4 PHE cc_start: 0.8713 (m-80) cc_final: 0.8480 (m-10) REVERT: K 15 ARG cc_start: 0.8216 (mtt90) cc_final: 0.7843 (mpt180) REVERT: O 15 ARG cc_start: 0.7498 (mmm160) cc_final: 0.6576 (ttp-170) REVERT: Q 5 TYR cc_start: 0.8523 (p90) cc_final: 0.8237 (p90) REVERT: R 25 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8016 (p) REVERT: S 5 TYR cc_start: 0.7821 (p90) cc_final: 0.7575 (p90) REVERT: S 6 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7907 (mttm) REVERT: S 9 LEU cc_start: 0.7410 (mt) cc_final: 0.7103 (mm) REVERT: T 39 LEU cc_start: 0.8816 (tp) cc_final: 0.8363 (mt) REVERT: V 30 LEU cc_start: 0.7952 (tt) cc_final: 0.7189 (tm) REVERT: V 34 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7216 (mp) REVERT: X 9 ASP cc_start: 0.7201 (t0) cc_final: 0.6809 (t0) outliers start: 31 outliers final: 22 residues processed: 223 average time/residue: 0.5903 time to fit residues: 149.5962 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 32 HIS Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 24 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 174 optimal weight: 0.0870 chunk 37 optimal weight: 0.0170 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 ASN K 20 GLN S 20 GLN Z 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.112086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080967 restraints weight = 41543.001| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.97 r_work: 0.2783 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19242 Z= 0.135 Angle : 0.666 13.110 26320 Z= 0.275 Chirality : 0.038 0.262 2718 Planarity : 0.003 0.053 3109 Dihedral : 16.159 174.565 3507 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.61 % Allowed : 14.36 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.19), residues: 1793 helix: 2.64 (0.14), residues: 1118 sheet: -0.49 (1.02), residues: 28 loop : -0.08 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 15 TYR 0.029 0.001 TYR Q 5 PHE 0.021 0.001 PHE F 17 TRP 0.015 0.001 TRP M 156 HIS 0.006 0.001 HIS M 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (19217) covalent geometry : angle 0.66591 / 0.27 (26320) hydrogen bonds : bond 0.04350 / 2.79 ( 997) hydrogen bonds : angle 3.77957 / 2.66 ( 2799) Misc. bond : bond 0.00284 / 0.20 ( 25) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8800 (mttm) cc_final: 0.8421 (mmtp) REVERT: M 109 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8757 (ttmm) REVERT: M 137 ASP cc_start: 0.9014 (t0) cc_final: 0.8640 (t70) REVERT: H 70 ARG cc_start: 0.7316 (mtt90) cc_final: 0.7095 (ttt90) REVERT: H 172 ASP cc_start: 0.8845 (t70) cc_final: 0.8636 (t70) REVERT: D 3 LYS cc_start: 0.8696 (mptm) cc_final: 0.8280 (mmmt) REVERT: I 14 ARG cc_start: 0.8273 (mtm110) cc_final: 0.8047 (mtt90) REVERT: I 15 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7328 (mmm160) REVERT: K 4 PHE cc_start: 0.8685 (m-80) cc_final: 0.8453 (m-10) REVERT: K 15 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7897 (mtt90) REVERT: O 15 ARG cc_start: 0.7495 (mmm160) cc_final: 0.6606 (ttp-170) REVERT: Q 5 TYR cc_start: 0.8488 (p90) cc_final: 0.8227 (p90) REVERT: R 25 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8010 (p) REVERT: S 5 TYR cc_start: 0.7897 (p90) cc_final: 0.7517 (p90) REVERT: S 9 LEU cc_start: 0.7396 (mt) cc_final: 0.7085 (mm) REVERT: T 39 LEU cc_start: 0.8816 (tp) cc_final: 0.8364 (mt) REVERT: V 30 LEU cc_start: 0.7935 (tt) cc_final: 0.7168 (tm) REVERT: V 34 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7245 (mp) REVERT: X 9 ASP cc_start: 0.7167 (t0) cc_final: 0.6751 (t0) outliers start: 24 outliers final: 18 residues processed: 223 average time/residue: 0.5899 time to fit residues: 149.4287 Evaluate side-chains 223 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 174 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 20 GLN S 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080703 restraints weight = 44846.583| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.06 r_work: 0.2779 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19242 Z= 0.134 Angle : 0.657 12.809 26320 Z= 0.273 Chirality : 0.037 0.260 2718 Planarity : 0.003 0.052 3109 Dihedral : 15.892 175.711 3507 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.68 % Allowed : 14.23 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.53 (0.19), residues: 1793 helix: 2.70 (0.14), residues: 1118 sheet: -0.48 (1.04), residues: 28 loop : -0.07 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 15 TYR 0.029 0.001 TYR Q 5 PHE 0.016 0.001 PHE O 11 TRP 0.015 0.001 TRP M 156 HIS 0.006 0.001 HIS M 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (19217) covalent geometry : angle 0.65692 / 0.27 (26320) hydrogen bonds : bond 0.04283 / 2.75 ( 997) hydrogen bonds : angle 3.74085 / 2.63 ( 2799) Misc. bond : bond 0.00215 / 0.14 ( 25) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7912.81 seconds wall clock time: 135 minutes 35.64 seconds (8135.64 seconds total)