Starting phenix.real_space_refine on Sun Aug 24 14:04:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yml_33931/08_2025/7yml_33931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yml_33931/08_2025/7yml_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yml_33931/08_2025/7yml_33931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yml_33931/08_2025/7yml_33931.map" model { file = "/net/cci-nas-00/data/ceres_data/7yml_33931/08_2025/7yml_33931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yml_33931/08_2025/7yml_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-2.0-5787/lib/python3.9/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: 5.51, per 1000 atoms: 0.30 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: 2.42 Conformation dependent library (CDL) restraints added in 996.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.57 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: 3.38 Time building geometry restraints manager: 2.93 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: 10485 35.10 - 70.20: 431 70.20 - 105.30: 113 105.30 - 140.41: 58 140.41 - 175.51: 19 Dihedral angle restraints: 11106 sinusoidal: 5779 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 11103 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: 7.740 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.490 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 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 : 22.916 175.507 7672 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 aren 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 covalent geometry : bond 0.01925 (19217) covalent geometry : angle 1.85686 (26320) hydrogen bonds : bond 0.19758 ( 997) hydrogen bonds : angle 6.32874 ( 2799) Misc. bond : bond 0.24852 ( 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 : 0.608 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: 0.4625 (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: 0.7776 (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: 0.8088 (tm) REVERT: W 17 GLN cc_start: 0.7268 (mm110) cc_final: 0.6978 (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: 0.5885 time to fit residues: 179.4781 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 : 0.618 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3543 r_free = 0.3543 target = 0.112645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081168 restraints weight = 43188.842| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.00 r_work: 0.2780 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 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 = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.262 19242 Z= 0.153 Angle : 0.765 16.676 26320 Z= 0.301 Chirality : 0.043 0.497 2718 Planarity : 0.004 0.053 3109 Dihedral : 21.665 175.878 4601 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.88 % Allowed : 8.66 % 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 aren not related in a simple way. whole: 2.19 (0.19), residues: 1793 helix: 2.31 (0.14), residues: 1118 sheet: -0.28 (1.04), residues: 28 loop : 0.05 (0.24), residues: 647 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 0.020 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 covalent geometry : bond 0.00350 (19217) covalent geometry : angle 0.76466 (26320) hydrogen bonds : bond 0.05176 ( 997) hydrogen bonds : angle 4.13006 ( 2799) Misc. bond : bond 0.05246 ( 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 269 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8784 (mttm) cc_final: 0.8434 (mmtp) REVERT: M 109 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8665 (ttmm) REVERT: M 137 ASP cc_start: 0.9025 (t0) cc_final: 0.8764 (t70) REVERT: H 142 MET cc_start: 0.8910 (mtt) cc_final: 0.8621 (mtt) REVERT: H 172 ASP cc_start: 0.8775 (t70) cc_final: 0.8513 (t0) REVERT: H 189 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8198 (ttpt) REVERT: D 3 LYS cc_start: 0.8597 (mptm) cc_final: 0.8167 (mmmt) REVERT: D 4 PHE cc_start: 0.9094 (m-10) cc_final: 0.8884 (m-10) REVERT: I 15 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.6875 (tmt170) REVERT: K 15 ARG cc_start: 0.8193 (mtt90) cc_final: 0.7928 (mtt90) REVERT: O 12 ASP cc_start: 0.8163 (t0) cc_final: 0.7794 (t0) REVERT: O 15 ARG cc_start: 0.7640 (mmm160) cc_final: 0.6574 (ttp-170) REVERT: Q 6 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8575 (ttmm) REVERT: R 11 LEU cc_start: 0.8711 (mp) cc_final: 0.8467 (mp) REVERT: S 5 TYR cc_start: 0.7952 (p90) cc_final: 0.7200 (p90) REVERT: S 6 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7884 (mptp) REVERT: S 9 LEU cc_start: 0.7426 (mt) cc_final: 0.7194 (mm) REVERT: T 39 LEU cc_start: 0.8825 (tp) cc_final: 0.8367 (mt) REVERT: V 30 LEU cc_start: 0.7962 (tt) cc_final: 0.7423 (tm) REVERT: X 9 ASP cc_start: 0.7175 (t0) cc_final: 0.6513 (t0) outliers start: 28 outliers final: 13 residues processed: 257 average time/residue: 0.4725 time to fit residues: 138.1822 Evaluate side-chains 225 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN H 135 GLN K 20 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 = 0.3500 r_free = 0.3500 target = 0.109714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077627 restraints weight = 45162.163| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.04 r_work: 0.2710 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19242 Z= 0.255 Angle : 0.824 16.650 26320 Z= 0.329 Chirality : 0.046 0.579 2718 Planarity : 0.004 0.054 3109 Dihedral : 19.422 177.209 4593 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.09 % Allowed : 9.73 % Favored : 87.18 % 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 aren not related in a simple way. whole: 2.17 (0.19), residues: 1793 helix: 2.35 (0.14), residues: 1120 sheet: -0.54 (1.03), residues: 28 loop : -0.07 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 179 TYR 0.031 0.002 TYR M 302 PHE 0.023 0.002 PHE H 20 TRP 0.014 0.002 TRP M 156 HIS 0.009 0.002 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00619 (19217) covalent geometry : angle 0.82428 (26320) hydrogen bonds : bond 0.05353 ( 997) hydrogen bonds : angle 4.07381 ( 2799) Misc. bond : bond 0.01378 ( 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 265 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8817 (mttm) cc_final: 0.8453 (mmtp) REVERT: M 109 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8705 (ttmm) REVERT: M 137 ASP cc_start: 0.9023 (t0) cc_final: 0.8641 (t70) REVERT: D 3 LYS cc_start: 0.8664 (mptm) cc_final: 0.8192 (mmmt) REVERT: I 14 ARG cc_start: 0.8341 (mtm110) cc_final: 0.8048 (mtt90) REVERT: I 15 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.6902 (tmt170) REVERT: J 18 GLU cc_start: 0.8526 (tp30) cc_final: 0.8314 (tm-30) REVERT: K 15 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7897 (mtt90) REVERT: O 12 ASP cc_start: 0.8202 (t0) cc_final: 0.7907 (t0) REVERT: O 15 ARG cc_start: 0.7580 (mmm160) cc_final: 0.6549 (ttp-170) REVERT: P 39 LEU cc_start: 0.9139 (tp) cc_final: 0.8815 (mp) REVERT: R 11 LEU cc_start: 0.8769 (mp) cc_final: 0.8401 (mp) REVERT: S 5 TYR cc_start: 0.7765 (p90) cc_final: 0.7148 (p90) REVERT: S 6 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7880 (mptp) REVERT: S 9 LEU cc_start: 0.7378 (mt) cc_final: 0.7133 (mm) REVERT: T 39 LEU cc_start: 0.8813 (tp) cc_final: 0.8372 (mt) REVERT: V 30 LEU cc_start: 0.7989 (tt) cc_final: 0.7272 (tm) REVERT: V 34 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7285 (mp) REVERT: X 9 ASP cc_start: 0.7305 (t0) cc_final: 0.6879 (t0) REVERT: X 15 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8053 (mtpt) REVERT: X 38 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8606 (mp) outliers start: 46 outliers final: 22 residues processed: 245 average time/residue: 0.5080 time to fit residues: 141.2436 Evaluate side-chains 229 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 19 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 39 LEU 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: 4.9990 chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN H 176 GLN N 17 GLN S 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.112508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081433 restraints weight = 41425.245| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.95 r_work: 0.2785 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19242 Z= 0.136 Angle : 0.706 14.367 26320 Z= 0.279 Chirality : 0.042 0.573 2718 Planarity : 0.004 0.053 3109 Dihedral : 17.428 176.522 4593 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.95 % Allowed : 10.40 % Favored : 86.64 % 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 aren not related in a simple way. whole: 2.43 (0.19), residues: 1793 helix: 2.59 (0.14), residues: 1118 sheet: -0.38 (1.04), residues: 28 loop : -0.05 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 179 TYR 0.027 0.001 TYR Q 5 PHE 0.016 0.001 PHE F 17 TRP 0.014 0.001 TRP M 156 HIS 0.006 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00311 (19217) covalent geometry : angle 0.70641 (26320) hydrogen bonds : bond 0.04462 ( 997) hydrogen bonds : angle 3.83530 ( 2799) Misc. bond : bond 0.00781 ( 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 277 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8801 (mttm) cc_final: 0.8440 (mmtp) REVERT: M 109 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8641 (ttmm) REVERT: M 137 ASP cc_start: 0.9007 (t0) cc_final: 0.8738 (t70) REVERT: M 213 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8842 (tp) REVERT: H 172 ASP cc_start: 0.8839 (t70) cc_final: 0.8570 (t70) REVERT: D 3 LYS cc_start: 0.8613 (mptm) cc_final: 0.8171 (mmmt) REVERT: F 16 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8637 (t) REVERT: I 14 ARG cc_start: 0.8294 (mtm110) cc_final: 0.8071 (mtt90) REVERT: I 15 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7383 (mmm160) REVERT: J 18 GLU cc_start: 0.8446 (tp30) cc_final: 0.8229 (tm-30) REVERT: K 15 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7834 (mtt90) REVERT: O 12 ASP cc_start: 0.8171 (t0) cc_final: 0.7962 (t0) REVERT: O 15 ARG cc_start: 0.7538 (mmm160) cc_final: 0.6574 (ttp-170) REVERT: R 11 LEU cc_start: 0.8765 (mp) cc_final: 0.8394 (mp) REVERT: S 3 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7821 (tptt) REVERT: S 5 TYR cc_start: 0.7812 (p90) cc_final: 0.7101 (p90) REVERT: S 6 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7873 (mptp) REVERT: S 9 LEU cc_start: 0.7415 (mt) cc_final: 0.7178 (mm) REVERT: T 39 LEU cc_start: 0.8822 (tp) cc_final: 0.8365 (mt) REVERT: V 30 LEU cc_start: 0.7990 (tt) cc_final: 0.7276 (tm) REVERT: V 34 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7243 (mp) REVERT: X 9 ASP cc_start: 0.7346 (t0) cc_final: 0.6818 (t0) outliers start: 44 outliers final: 18 residues processed: 254 average time/residue: 0.4656 time to fit residues: 134.5274 Evaluate side-chains 238 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 Q residue 2 SER 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 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: 0.6980 chunk 146 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 20 GLN N 17 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 = 0.3525 r_free = 0.3525 target = 0.111458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079260 restraints weight = 48163.329| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.11 r_work: 0.2742 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2615 r_free = 0.2615 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2002 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= 0.172 Angle : 0.721 15.382 26320 Z= 0.287 Chirality : 0.042 0.535 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.653 174.264 4587 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.89 % Allowed : 11.68 % Favored : 85.44 % 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 aren not related in a simple way. whole: 2.44 (0.19), residues: 1793 helix: 2.61 (0.14), residues: 1117 sheet: -0.52 (1.02), residues: 28 loop : -0.05 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 179 TYR 0.027 0.001 TYR M 302 PHE 0.019 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 covalent geometry : bond 0.00409 (19217) covalent geometry : angle 0.72080 (26320) hydrogen bonds : bond 0.04591 ( 997) hydrogen bonds : angle 3.83881 ( 2799) Misc. bond : bond 0.00789 ( 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 263 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8798 (mttm) cc_final: 0.8422 (mmtp) REVERT: M 109 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8635 (ttmm) REVERT: M 137 ASP cc_start: 0.9001 (t0) cc_final: 0.8611 (t70) REVERT: M 213 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8812 (tp) REVERT: D 3 LYS cc_start: 0.8615 (mptm) cc_final: 0.8165 (mmmt) REVERT: I 14 ARG cc_start: 0.8320 (mtm110) cc_final: 0.8084 (mtt90) REVERT: I 15 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7373 (mmm160) REVERT: K 15 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7845 (mtt90) REVERT: O 12 ASP cc_start: 0.8222 (t0) cc_final: 0.8006 (t0) REVERT: O 15 ARG cc_start: 0.7538 (mmm160) cc_final: 0.6569 (ttp-170) REVERT: R 11 LEU cc_start: 0.8758 (mp) cc_final: 0.8357 (mp) REVERT: R 25 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.7983 (p) REVERT: S 3 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7778 (tptt) REVERT: S 5 TYR cc_start: 0.7779 (p90) cc_final: 0.7532 (p90) REVERT: S 6 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7892 (mttm) REVERT: S 9 LEU cc_start: 0.7358 (mt) cc_final: 0.7095 (mm) REVERT: T 39 LEU cc_start: 0.8811 (tp) cc_final: 0.8352 (mt) REVERT: V 30 LEU cc_start: 0.7943 (tt) cc_final: 0.7196 (tm) REVERT: V 34 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7180 (mp) REVERT: Z 38 HIS cc_start: 0.4987 (OUTLIER) cc_final: 0.4746 (m90) REVERT: X 9 ASP cc_start: 0.7301 (t0) cc_final: 0.6847 (t0) outliers start: 43 outliers final: 20 residues processed: 241 average time/residue: 0.4790 time to fit residues: 130.7784 Evaluate side-chains 236 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain I residue 3 LYS 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 Z residue 38 HIS 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: 0.8980 chunk 116 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 37 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN H 135 GLN K 20 GLN N 17 GLN S 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076825 restraints weight = 32635.643| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.57 r_work: 0.2781 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19242 Z= 0.209 Angle : 0.744 15.944 26320 Z= 0.300 Chirality : 0.043 0.455 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.550 168.185 4587 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.75 % Allowed : 12.08 % Favored : 85.17 % 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 aren not related in a simple way. whole: 2.35 (0.19), residues: 1793 helix: 2.53 (0.14), residues: 1119 sheet: -0.65 (1.04), residues: 28 loop : -0.07 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 179 TYR 0.030 0.002 TYR Q 5 PHE 0.022 0.002 PHE F 17 TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00504 (19217) covalent geometry : angle 0.74389 (26320) hydrogen bonds : bond 0.04777 ( 997) hydrogen bonds : angle 3.90531 ( 2799) Misc. bond : bond 0.00577 ( 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 251 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8819 (mttm) cc_final: 0.8471 (mmtp) REVERT: M 109 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8634 (ttmm) REVERT: M 137 ASP cc_start: 0.8995 (t0) cc_final: 0.8599 (t70) REVERT: M 213 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8787 (tp) REVERT: D 3 LYS cc_start: 0.8622 (mptm) cc_final: 0.8180 (mmmt) REVERT: F 16 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8683 (t) REVERT: I 14 ARG cc_start: 0.8282 (mtm110) cc_final: 0.8015 (mtt90) REVERT: I 15 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.7363 (mmm160) REVERT: J 42 MET cc_start: 0.9022 (tpt) cc_final: 0.8803 (tpt) REVERT: K 15 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7841 (mtt90) REVERT: O 4 PHE cc_start: 0.8621 (m-80) cc_final: 0.8403 (m-10) REVERT: O 12 ASP cc_start: 0.8243 (t0) cc_final: 0.8028 (t0) REVERT: O 15 ARG cc_start: 0.7518 (mmm160) cc_final: 0.6563 (ttp-110) REVERT: R 25 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8001 (p) REVERT: S 5 TYR cc_start: 0.7858 (p90) cc_final: 0.7519 (p90) REVERT: S 9 LEU cc_start: 0.7401 (mt) cc_final: 0.7114 (mm) REVERT: T 39 LEU cc_start: 0.8810 (tp) cc_final: 0.8356 (mt) REVERT: V 30 LEU cc_start: 0.7966 (tt) cc_final: 0.7221 (tm) REVERT: V 34 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7199 (mp) REVERT: Z 38 HIS cc_start: 0.5013 (OUTLIER) cc_final: 0.4787 (m90) REVERT: X 9 ASP cc_start: 0.7303 (t0) cc_final: 0.6874 (t0) outliers start: 41 outliers final: 20 residues processed: 231 average time/residue: 0.4665 time to fit residues: 122.2642 Evaluate side-chains 233 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 38 HIS 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: 6.9990 chunk 170 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 104 optimal weight: 0.0010 chunk 48 optimal weight: 0.8980 chunk 172 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3556 r_free = 0.3556 target = 0.113552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081484 restraints weight = 51075.111| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.18 r_work: 0.2787 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19242 Z= 0.118 Angle : 0.649 13.052 26320 Z= 0.263 Chirality : 0.038 0.402 2718 Planarity : 0.003 0.051 3109 Dihedral : 15.752 178.113 4587 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.95 % Allowed : 13.09 % Favored : 84.97 % 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 aren not related in a simple way. whole: 2.57 (0.19), residues: 1793 helix: 2.74 (0.14), residues: 1118 sheet: -0.50 (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 M 163 TYR 0.021 0.001 TYR M 302 PHE 0.016 0.001 PHE F 17 TRP 0.014 0.001 TRP M 156 HIS 0.005 0.001 HIS M 265 Details of bonding type rmsd covalent geometry : bond 0.00265 (19217) covalent geometry : angle 0.64905 (26320) hydrogen bonds : bond 0.04153 ( 997) hydrogen bonds : angle 3.71387 ( 2799) Misc. bond : bond 0.00163 ( 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 260 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8730 (mttm) cc_final: 0.8382 (mmtp) REVERT: M 109 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8595 (ttmm) REVERT: M 137 ASP cc_start: 0.8894 (t0) cc_final: 0.8512 (t70) REVERT: M 213 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8767 (tp) REVERT: H 70 ARG cc_start: 0.7207 (mtt90) cc_final: 0.6801 (ttm110) REVERT: D 3 LYS cc_start: 0.8545 (mptm) cc_final: 0.8158 (mmmt) REVERT: I 14 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7920 (mtt90) REVERT: I 15 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.6752 (tmt170) REVERT: K 4 PHE cc_start: 0.8625 (m-80) cc_final: 0.8394 (m-10) REVERT: K 15 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7763 (mtt90) REVERT: O 15 ARG cc_start: 0.7375 (mmm160) cc_final: 0.6548 (mmt-90) REVERT: R 25 SER cc_start: 0.8493 (t) cc_final: 0.7937 (p) REVERT: S 5 TYR cc_start: 0.7774 (p90) cc_final: 0.7095 (p90) REVERT: S 6 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7787 (mttp) REVERT: S 9 LEU cc_start: 0.7416 (mt) cc_final: 0.7178 (mm) REVERT: T 39 LEU cc_start: 0.8745 (tp) cc_final: 0.8272 (mt) REVERT: V 30 LEU cc_start: 0.7931 (tt) cc_final: 0.7184 (tm) REVERT: V 34 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7132 (mp) REVERT: Z 38 HIS cc_start: 0.5205 (OUTLIER) cc_final: 0.4968 (m90) REVERT: X 9 ASP cc_start: 0.7229 (t0) cc_final: 0.6680 (t0) outliers start: 29 outliers final: 17 residues processed: 244 average time/residue: 0.4679 time to fit residues: 130.0181 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Q residue 5 TYR Chi-restraints excluded: chain R residue 7 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 Z residue 38 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 144 HIS H 53 GLN ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN S 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079169 restraints weight = 41197.467| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.94 r_work: 0.2737 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19242 Z= 0.217 Angle : 0.735 12.301 26320 Z= 0.300 Chirality : 0.042 0.384 2718 Planarity : 0.004 0.053 3109 Dihedral : 16.164 179.620 4587 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.42 % Allowed : 13.56 % 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 aren not related in a simple way. whole: 2.39 (0.19), residues: 1793 helix: 2.56 (0.14), residues: 1118 sheet: -0.60 (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 0.031 0.002 TYR M 302 PHE 0.022 0.002 PHE H 20 TRP 0.013 0.001 TRP M 156 HIS 0.009 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00523 (19217) covalent geometry : angle 0.73506 (26320) hydrogen bonds : bond 0.04759 ( 997) hydrogen bonds : angle 3.87155 ( 2799) Misc. bond : bond 0.00454 ( 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 242 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8785 (mttm) cc_final: 0.8441 (mmtp) REVERT: M 109 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8646 (ttmm) REVERT: M 137 ASP cc_start: 0.9029 (t0) cc_final: 0.8620 (t70) REVERT: M 213 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.8825 (tp) REVERT: D 3 LYS cc_start: 0.8675 (mptm) cc_final: 0.8233 (mmmt) REVERT: I 15 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7364 (mmm160) REVERT: K 4 PHE cc_start: 0.8684 (m-80) cc_final: 0.8445 (m-10) REVERT: K 15 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7841 (mtt90) REVERT: O 12 ASP cc_start: 0.8255 (t0) cc_final: 0.8038 (t0) REVERT: O 15 ARG cc_start: 0.7548 (mmm160) cc_final: 0.6616 (ttp-110) REVERT: R 25 SER cc_start: 0.8589 (t) cc_final: 0.8050 (p) REVERT: S 5 TYR cc_start: 0.7840 (p90) cc_final: 0.7079 (p90) REVERT: S 6 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7718 (mptp) REVERT: S 9 LEU cc_start: 0.7404 (mt) cc_final: 0.7156 (mm) REVERT: S 30 LEU cc_start: 0.8967 (tt) cc_final: 0.8689 (tm) REVERT: T 39 LEU cc_start: 0.8814 (tp) cc_final: 0.8360 (mt) REVERT: V 30 LEU cc_start: 0.7959 (tt) cc_final: 0.7208 (tm) REVERT: V 34 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7253 (mp) REVERT: Z 38 HIS cc_start: 0.5051 (OUTLIER) cc_final: 0.4786 (m90) REVERT: X 9 ASP cc_start: 0.7273 (t0) cc_final: 0.6908 (t0) outliers start: 36 outliers final: 21 residues processed: 228 average time/residue: 0.4739 time to fit residues: 122.3942 Evaluate side-chains 229 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 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 Z residue 38 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 170 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3524 r_free = 0.3524 target = 0.111317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.079252 restraints weight = 46735.502| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.08 r_work: 0.2744 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19242 Z= 0.175 Angle : 0.701 13.023 26320 Z= 0.287 Chirality : 0.040 0.375 2718 Planarity : 0.004 0.053 3109 Dihedral : 15.975 176.665 4587 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.81 % Allowed : 14.23 % Favored : 83.96 % 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 aren not related in a simple way. whole: 2.41 (0.19), residues: 1793 helix: 2.58 (0.14), residues: 1118 sheet: -0.35 (1.07), residues: 28 loop : -0.07 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 179 TYR 0.028 0.001 TYR M 302 PHE 0.019 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 covalent geometry : bond 0.00416 (19217) covalent geometry : angle 0.70132 (26320) hydrogen bonds : bond 0.04558 ( 997) hydrogen bonds : angle 3.82394 ( 2799) Misc. bond : bond 0.00288 ( 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 234 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8797 (mttm) cc_final: 0.8423 (mmtp) REVERT: M 109 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8656 (ttmm) REVERT: M 137 ASP cc_start: 0.9033 (t0) cc_final: 0.8656 (t70) REVERT: M 213 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8823 (tp) REVERT: D 3 LYS cc_start: 0.8641 (mptm) cc_final: 0.8212 (mmmt) REVERT: I 14 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8094 (mtt90) REVERT: I 15 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.7324 (mmm160) REVERT: J 42 MET cc_start: 0.9067 (tpt) cc_final: 0.8838 (tpt) REVERT: K 4 PHE cc_start: 0.8682 (m-80) cc_final: 0.8434 (m-10) REVERT: K 15 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7853 (mtt90) REVERT: O 12 ASP cc_start: 0.8264 (t0) cc_final: 0.8047 (t0) REVERT: O 15 ARG cc_start: 0.7547 (mmm160) cc_final: 0.6615 (ttp-110) REVERT: R 25 SER cc_start: 0.8569 (t) cc_final: 0.8028 (p) REVERT: S 5 TYR cc_start: 0.7869 (p90) cc_final: 0.7136 (p90) REVERT: S 6 LYS cc_start: 0.8143 (mtpt) cc_final: 0.7732 (mptp) REVERT: S 9 LEU cc_start: 0.7418 (mt) cc_final: 0.7161 (mm) REVERT: T 39 LEU cc_start: 0.8806 (tp) cc_final: 0.8355 (mt) REVERT: V 30 LEU cc_start: 0.7944 (tt) cc_final: 0.7184 (tm) REVERT: V 34 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7226 (mp) REVERT: Z 38 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4795 (m90) REVERT: X 9 ASP cc_start: 0.7222 (t0) cc_final: 0.6760 (t0) outliers start: 27 outliers final: 20 residues processed: 223 average time/residue: 0.5045 time to fit residues: 127.1520 Evaluate side-chains 229 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 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 Z residue 38 HIS 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: 7.9990 chunk 174 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 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 = 0.3524 r_free = 0.3524 target = 0.111327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079972 restraints weight = 41493.888| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.97 r_work: 0.2756 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19242 Z= 0.170 Angle : 0.699 13.069 26320 Z= 0.287 Chirality : 0.039 0.361 2718 Planarity : 0.004 0.053 3109 Dihedral : 15.854 172.866 4587 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.95 % Allowed : 14.16 % Favored : 83.89 % 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 aren not related in a simple way. whole: 2.39 (0.19), residues: 1793 helix: 2.59 (0.14), residues: 1118 sheet: -0.37 (1.06), residues: 28 loop : -0.12 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 179 TYR 0.027 0.001 TYR M 302 PHE 0.024 0.001 PHE F 17 TRP 0.014 0.001 TRP V 8 HIS 0.007 0.001 HIS M 181 Details of bonding type rmsd covalent geometry : bond 0.00406 (19217) covalent geometry : angle 0.69939 (26320) hydrogen bonds : bond 0.04518 ( 997) hydrogen bonds : angle 3.82092 ( 2799) Misc. bond : bond 0.00284 ( 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 237 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8799 (mttm) cc_final: 0.8432 (mmtp) REVERT: M 109 LYS cc_start: 0.9017 (ttmm) cc_final: 0.8665 (ttmm) REVERT: M 137 ASP cc_start: 0.9029 (t0) cc_final: 0.8645 (t70) REVERT: M 213 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8822 (tp) REVERT: H 70 ARG cc_start: 0.7333 (mtt90) cc_final: 0.7100 (ttt90) REVERT: D 3 LYS cc_start: 0.8659 (mptm) cc_final: 0.8242 (mmmt) REVERT: I 15 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.6860 (tmt170) REVERT: J 42 MET cc_start: 0.9068 (tpt) cc_final: 0.8837 (tpt) REVERT: K 4 PHE cc_start: 0.8685 (m-80) cc_final: 0.8448 (m-10) REVERT: K 15 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7858 (mtt90) REVERT: O 12 ASP cc_start: 0.8245 (t0) cc_final: 0.8015 (t0) REVERT: O 15 ARG cc_start: 0.7540 (mmm160) cc_final: 0.6617 (ttp-110) REVERT: R 25 SER cc_start: 0.8572 (t) cc_final: 0.8035 (p) REVERT: S 5 TYR cc_start: 0.7800 (p90) cc_final: 0.7387 (p90) REVERT: S 6 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7927 (mttm) REVERT: S 9 LEU cc_start: 0.7402 (mt) cc_final: 0.7099 (mm) REVERT: T 39 LEU cc_start: 0.8820 (tp) cc_final: 0.8363 (mt) REVERT: V 30 LEU cc_start: 0.7970 (tt) cc_final: 0.7197 (tm) REVERT: V 34 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7249 (mp) REVERT: Z 38 HIS cc_start: 0.5099 (OUTLIER) cc_final: 0.4821 (m90) REVERT: X 9 ASP cc_start: 0.7217 (t0) cc_final: 0.6789 (t0) outliers start: 29 outliers final: 21 residues processed: 225 average time/residue: 0.4492 time to fit residues: 114.3037 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 5 TYR Chi-restraints excluded: chain Q residue 16 VAL 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 Z residue 38 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 20 GLN S 20 GLN Z 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.111748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.079998 restraints weight = 44815.611| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.04 r_work: 0.2759 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 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 = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19242 Z= 0.154 Angle : 0.685 15.510 26320 Z= 0.282 Chirality : 0.039 0.351 2718 Planarity : 0.004 0.053 3109 Dihedral : 15.713 176.741 4587 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.95 % Allowed : 14.36 % Favored : 83.69 % 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 aren not related in a simple way. whole: 2.43 (0.19), residues: 1793 helix: 2.62 (0.14), residues: 1118 sheet: -0.35 (1.08), residues: 28 loop : -0.10 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 179 TYR 0.026 0.001 TYR M 302 PHE 0.017 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 covalent geometry : bond 0.00363 (19217) covalent geometry : angle 0.68487 (26320) hydrogen bonds : bond 0.04414 ( 997) hydrogen bonds : angle 3.79507 ( 2799) Misc. bond : bond 0.00252 ( 25) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6985.28 seconds wall clock time: 119 minutes 30.69 seconds (7170.69 seconds total)