Starting phenix.real_space_refine on Tue May 20 20:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yml_33931/05_2025/7yml_33931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yml_33931/05_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_33931/05_2025/7yml_33931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yml_33931/05_2025/7yml_33931.map" model { file = "/net/cci-nas-00/data/ceres_data/7yml_33931/05_2025/7yml_33931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yml_33931/05_2025/7yml_33931.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP: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: {'PGV:plan-3': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 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: {'PGV:plan-3': 3, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-11': 2, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 2, 'U10:plan-3': 1} 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: 13.52, per 1000 atoms: 0.73 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: 6.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.54 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: 4.78 Time building geometry restraints manager: 7.27 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 44.400 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.570 ------------------------------------------------------------------------------- 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 : 11.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP S 8 HIS 0.007 0.001 HIS L 154 PHE 0.017 0.002 PHE L 147 TYR 0.032 0.002 TYR M 302 ARG 0.003 0.001 ARG T 45 Details of bonding type rmsd hydrogen bonds : bond 0.19758 ( 997) hydrogen bonds : angle 6.32874 ( 2799) covalent geometry : bond 0.01925 (19217) covalent geometry : angle 1.85686 (26320) 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 : 1.680 Fit side-chains revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8672 (mttm) cc_final: 0.8460 (mmtp) REVERT: M 109 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8561 (ttmm) REVERT: M 137 ASP cc_start: 0.8919 (t0) cc_final: 0.8547 (t70) REVERT: E 6 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4626 (tm) REVERT: I 15 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7187 (tmt170) REVERT: K 4 PHE cc_start: 0.8797 (m-80) cc_final: 0.8557 (m-10) REVERT: K 15 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7828 (mtt90) REVERT: O 15 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6438 (ttp-110) REVERT: P 24 MET cc_start: 0.8658 (mmm) cc_final: 0.8398 (mmm) REVERT: Q 6 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8614 (ttmm) REVERT: R 13 ASP cc_start: 0.8016 (t0) cc_final: 0.7775 (t0) REVERT: S 5 TYR cc_start: 0.7954 (p90) cc_final: 0.6997 (p90) REVERT: T 17 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7723 (mp10) REVERT: V 11 PHE cc_start: 0.7278 (m-80) cc_final: 0.6788 (m-10) REVERT: V 30 LEU cc_start: 0.8317 (tt) cc_final: 0.8087 (tm) REVERT: W 17 GLN cc_start: 0.7268 (mm110) cc_final: 0.6977 (mm110) REVERT: X 9 ASP cc_start: 0.7256 (t0) cc_final: 0.6918 (t0) outliers start: 28 outliers final: 11 residues processed: 270 average time/residue: 1.1658 time to fit residues: 357.1578 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 : 1.808 ------------------------------------------------------------------------------- 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 147 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 F 20 GLN I 20 GLN K 20 GLN N 15 GLN ** S 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079775 restraints weight = 48080.263| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.12 r_work: 0.2754 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 19242 Z= 0.167 Angle : 0.756 17.920 26320 Z= 0.301 Chirality : 0.043 0.504 2718 Planarity : 0.004 0.053 3109 Dihedral : 21.994 176.252 4601 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 8.46 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1793 helix: 2.35 (0.14), residues: 1120 sheet: -0.32 (1.04), residues: 28 loop : 0.07 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 PHE 0.019 0.001 PHE L 272 TYR 0.027 0.001 TYR M 302 ARG 0.005 0.000 ARG I 14 Details of bonding type rmsd hydrogen bonds : bond 0.05597 ( 997) hydrogen bonds : angle 4.18270 ( 2799) covalent geometry : bond 0.00384 (19217) covalent geometry : angle 0.75563 (26320) Misc. bond : bond 0.05341 ( 25) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8820 (mttm) cc_final: 0.8468 (mmtp) REVERT: M 109 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8671 (ttmm) REVERT: M 137 ASP cc_start: 0.9027 (t0) cc_final: 0.8759 (t70) REVERT: H 142 MET cc_start: 0.8930 (mtt) cc_final: 0.8590 (mtt) REVERT: H 189 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8193 (ttpt) REVERT: D 4 PHE cc_start: 0.9101 (m-10) cc_final: 0.8883 (m-10) REVERT: I 15 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.6865 (tmt170) REVERT: K 4 PHE cc_start: 0.8744 (m-80) cc_final: 0.8509 (m-10) REVERT: K 15 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7920 (mtt90) REVERT: O 12 ASP cc_start: 0.8148 (t0) cc_final: 0.7822 (t0) REVERT: O 15 ARG cc_start: 0.7595 (mmm160) cc_final: 0.6522 (ttp-170) REVERT: P 24 MET cc_start: 0.8570 (mmm) cc_final: 0.8367 (mmt) REVERT: Q 6 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8588 (ttmm) REVERT: R 11 LEU cc_start: 0.8716 (mp) cc_final: 0.8459 (mp) REVERT: R 17 GLN cc_start: 0.8051 (tt0) cc_final: 0.7651 (tt0) REVERT: S 5 TYR cc_start: 0.7981 (p90) cc_final: 0.7303 (p90) REVERT: S 6 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7892 (mptp) REVERT: S 9 LEU cc_start: 0.7415 (mt) cc_final: 0.7180 (mm) REVERT: T 39 LEU cc_start: 0.8842 (tp) cc_final: 0.8372 (mt) REVERT: V 30 LEU cc_start: 0.7978 (tt) cc_final: 0.7305 (tm) REVERT: V 34 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7330 (mp) REVERT: X 9 ASP cc_start: 0.7149 (t0) cc_final: 0.6556 (t0) outliers start: 32 outliers final: 15 residues processed: 252 average time/residue: 1.0931 time to fit residues: 315.6754 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 G residue 19 LEU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain Q residue 5 TYR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 96 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN N 17 GLN P 20 HIS T 20 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.110307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.077569 restraints weight = 52161.167| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.26 r_work: 0.2704 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 19242 Z= 0.234 Angle : 0.798 16.135 26320 Z= 0.317 Chirality : 0.045 0.563 2718 Planarity : 0.004 0.054 3109 Dihedral : 19.542 178.899 4595 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.95 % Allowed : 9.26 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.19), residues: 1793 helix: 2.41 (0.14), residues: 1119 sheet: -0.52 (1.02), residues: 28 loop : -0.05 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 156 HIS 0.009 0.001 HIS M 181 PHE 0.022 0.002 PHE H 20 TYR 0.030 0.002 TYR M 302 ARG 0.004 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 997) hydrogen bonds : angle 4.04278 ( 2799) covalent geometry : bond 0.00567 (19217) covalent geometry : angle 0.79756 (26320) Misc. bond : bond 0.01805 ( 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 263 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8754 (mttm) cc_final: 0.8421 (mmtp) REVERT: M 109 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8568 (ttmm) REVERT: M 137 ASP cc_start: 0.8918 (t0) cc_final: 0.8524 (t70) REVERT: D 3 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8137 (mmmt) REVERT: G 14 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: I 14 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7928 (mtt90) REVERT: I 15 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.6813 (tmt170) REVERT: J 18 GLU cc_start: 0.8321 (tp30) cc_final: 0.8120 (tm-30) REVERT: K 15 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7755 (mtt90) REVERT: N 12 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8066 (p) REVERT: N 14 GLU cc_start: 0.7877 (pm20) cc_final: 0.7579 (pm20) REVERT: O 12 ASP cc_start: 0.8074 (t0) cc_final: 0.7773 (t0) REVERT: O 15 ARG cc_start: 0.7473 (mmm160) cc_final: 0.6474 (ttp-170) REVERT: O 20 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: R 11 LEU cc_start: 0.8728 (mp) cc_final: 0.8363 (mp) REVERT: S 5 TYR cc_start: 0.7738 (p90) cc_final: 0.7179 (p90) REVERT: S 6 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7837 (mptp) REVERT: S 9 LEU cc_start: 0.7377 (mt) cc_final: 0.7138 (mm) REVERT: T 39 LEU cc_start: 0.8753 (tp) cc_final: 0.8305 (mt) REVERT: V 30 LEU cc_start: 0.7901 (tt) cc_final: 0.7193 (tm) REVERT: V 34 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7176 (mp) REVERT: X 9 ASP cc_start: 0.7212 (t0) cc_final: 0.6704 (t0) REVERT: X 15 LYS cc_start: 0.8307 (mtpt) cc_final: 0.8067 (mtpt) outliers start: 44 outliers final: 21 residues processed: 244 average time/residue: 1.1630 time to fit residues: 322.5342 Evaluate side-chains 232 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 20 GLN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain T residue 17 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 94 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 H 176 GLN N 17 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 = 0.3508 r_free = 0.3508 target = 0.110224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076370 restraints weight = 33477.552| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.60 r_work: 0.2779 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19242 Z= 0.227 Angle : 0.785 14.525 26320 Z= 0.311 Chirality : 0.045 0.575 2718 Planarity : 0.004 0.054 3109 Dihedral : 18.066 173.678 4595 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.02 % Allowed : 10.81 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.19), residues: 1793 helix: 2.42 (0.14), residues: 1119 sheet: -0.65 (1.04), residues: 28 loop : -0.13 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 156 HIS 0.009 0.001 HIS M 181 PHE 0.021 0.002 PHE H 20 TYR 0.029 0.002 TYR M 302 ARG 0.006 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 997) hydrogen bonds : angle 3.98112 ( 2799) covalent geometry : bond 0.00549 (19217) covalent geometry : angle 0.78503 (26320) Misc. bond : bond 0.00709 ( 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 264 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8801 (mttm) cc_final: 0.8462 (mmtp) REVERT: M 109 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8625 (ttmm) REVERT: M 137 ASP cc_start: 0.8985 (t0) cc_final: 0.8601 (t70) REVERT: H 233 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8506 (t70) REVERT: I 14 ARG cc_start: 0.8316 (mtm110) cc_final: 0.8026 (mtt90) REVERT: I 15 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.6863 (tmt170) REVERT: J 18 GLU cc_start: 0.8414 (tp30) cc_final: 0.8191 (tm-30) REVERT: K 15 ARG cc_start: 0.8207 (mtt90) cc_final: 0.7847 (mtt90) REVERT: N 12 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.7866 (p) REVERT: N 14 GLU cc_start: 0.7933 (pm20) cc_final: 0.7621 (pm20) REVERT: O 12 ASP cc_start: 0.8214 (t0) cc_final: 0.7942 (t0) REVERT: O 15 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6552 (ttp-170) REVERT: R 11 LEU cc_start: 0.8761 (mp) cc_final: 0.8367 (mp) REVERT: S 5 TYR cc_start: 0.7790 (p90) cc_final: 0.7205 (p90) REVERT: S 6 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7894 (mptp) REVERT: S 9 LEU cc_start: 0.7375 (mt) cc_final: 0.7129 (mm) REVERT: T 39 LEU cc_start: 0.8811 (tp) cc_final: 0.8362 (mt) REVERT: V 30 LEU cc_start: 0.7933 (tt) cc_final: 0.7204 (tm) REVERT: V 34 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7193 (mp) REVERT: X 9 ASP cc_start: 0.7221 (t0) cc_final: 0.6717 (t0) REVERT: X 15 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8102 (mtpt) outliers start: 45 outliers final: 25 residues processed: 241 average time/residue: 1.1370 time to fit residues: 312.0071 Evaluate side-chains 238 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 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 I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 26 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 T residue 17 GLN Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 20 GLN N 15 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 = 0.3548 r_free = 0.3548 target = 0.113073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082198 restraints weight = 40895.545| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.95 r_work: 0.2799 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19242 Z= 0.126 Angle : 0.686 15.582 26320 Z= 0.272 Chirality : 0.040 0.531 2718 Planarity : 0.003 0.052 3109 Dihedral : 16.727 178.991 4595 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.82 % Allowed : 11.28 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.19), residues: 1793 helix: 2.62 (0.14), residues: 1118 sheet: -0.52 (1.03), residues: 28 loop : -0.06 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 156 HIS 0.006 0.001 HIS M 265 PHE 0.019 0.001 PHE F 17 TYR 0.032 0.001 TYR Q 5 ARG 0.003 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04324 ( 997) hydrogen bonds : angle 3.78914 ( 2799) covalent geometry : bond 0.00283 (19217) covalent geometry : angle 0.68620 (26320) Misc. bond : bond 0.00272 ( 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 278 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8801 (mttm) cc_final: 0.8446 (mmtp) REVERT: M 109 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8629 (ttmm) REVERT: M 137 ASP cc_start: 0.9004 (t0) cc_final: 0.8756 (t70) REVERT: M 213 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8821 (tp) REVERT: H 172 ASP cc_start: 0.8802 (t70) cc_final: 0.8583 (t70) REVERT: D 3 LYS cc_start: 0.8587 (mmtp) cc_final: 0.8143 (mmmt) REVERT: I 14 ARG cc_start: 0.8292 (mtm110) cc_final: 0.8076 (mtt90) REVERT: I 15 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7377 (mmm160) REVERT: K 15 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7844 (mtt90) REVERT: N 12 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7978 (p) REVERT: O 4 PHE cc_start: 0.8580 (m-80) cc_final: 0.8357 (m-10) REVERT: O 12 ASP cc_start: 0.8204 (t0) cc_final: 0.7999 (t0) REVERT: O 15 ARG cc_start: 0.7548 (mmm160) cc_final: 0.6588 (ttp-170) REVERT: R 11 LEU cc_start: 0.8754 (mp) cc_final: 0.8347 (mp) REVERT: R 17 GLN cc_start: 0.7962 (tt0) cc_final: 0.7676 (tp40) REVERT: R 25 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.7995 (p) REVERT: S 5 TYR cc_start: 0.7802 (p90) cc_final: 0.7108 (p90) REVERT: S 6 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7838 (mptp) REVERT: S 9 LEU cc_start: 0.7400 (mt) cc_final: 0.7158 (mm) REVERT: T 39 LEU cc_start: 0.8827 (tp) cc_final: 0.8380 (mt) REVERT: V 30 LEU cc_start: 0.7984 (tt) cc_final: 0.7240 (tm) REVERT: V 34 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7224 (mp) REVERT: X 9 ASP cc_start: 0.7272 (t0) cc_final: 0.6724 (t0) outliers start: 42 outliers final: 16 residues processed: 259 average time/residue: 1.1153 time to fit residues: 328.8514 Evaluate side-chains 239 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 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 I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain T residue 17 GLN Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 55 optimal weight: 0.6980 chunk 80 optimal weight: 0.2980 chunk 135 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 162 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN A 20 GLN 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 = 0.3532 r_free = 0.3532 target = 0.111900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.080125 restraints weight = 45019.041| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.03 r_work: 0.2763 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19242 Z= 0.158 Angle : 0.695 16.018 26320 Z= 0.280 Chirality : 0.041 0.472 2718 Planarity : 0.004 0.052 3109 Dihedral : 16.328 170.061 4589 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.28 % Allowed : 12.68 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 1793 helix: 2.66 (0.14), residues: 1118 sheet: -0.48 (1.05), residues: 28 loop : -0.06 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 PHE 0.018 0.001 PHE H 20 TYR 0.028 0.001 TYR M 302 ARG 0.004 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 997) hydrogen bonds : angle 3.79111 ( 2799) covalent geometry : bond 0.00376 (19217) covalent geometry : angle 0.69523 (26320) Misc. bond : bond 0.00405 ( 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 249 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8807 (mttm) cc_final: 0.8434 (mmtp) REVERT: M 109 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8652 (ttmm) REVERT: M 137 ASP cc_start: 0.9008 (t0) cc_final: 0.8620 (t70) REVERT: M 213 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8826 (tp) REVERT: H 172 ASP cc_start: 0.8821 (t70) cc_final: 0.8594 (t70) REVERT: I 14 ARG cc_start: 0.8302 (mtm110) cc_final: 0.8070 (mtt90) REVERT: I 15 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7377 (mmm160) REVERT: J 42 MET cc_start: 0.9047 (tpt) cc_final: 0.8824 (tpt) REVERT: K 15 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7840 (mtt90) REVERT: N 12 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8165 (p) REVERT: O 15 ARG cc_start: 0.7528 (mmm160) cc_final: 0.6689 (mmt-90) REVERT: R 11 LEU cc_start: 0.8764 (mp) cc_final: 0.8345 (mp) REVERT: R 17 GLN cc_start: 0.8028 (tt0) cc_final: 0.7742 (tp40) REVERT: R 25 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8006 (p) REVERT: S 5 TYR cc_start: 0.7831 (p90) cc_final: 0.7194 (p90) REVERT: S 6 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7827 (mptp) REVERT: S 9 LEU cc_start: 0.7395 (mt) cc_final: 0.7151 (mm) REVERT: T 39 LEU cc_start: 0.8815 (tp) cc_final: 0.8357 (mt) REVERT: V 30 LEU cc_start: 0.7958 (tt) cc_final: 0.7210 (tm) REVERT: V 34 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7219 (mp) REVERT: X 3 MET cc_start: 0.7356 (ttm) cc_final: 0.7132 (ttt) REVERT: X 9 ASP cc_start: 0.7214 (t0) cc_final: 0.6730 (t0) outliers start: 34 outliers final: 20 residues processed: 234 average time/residue: 1.1683 time to fit residues: 311.1121 Evaluate side-chains 232 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 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 I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 162 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078172 restraints weight = 33056.225| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.59 r_work: 0.2810 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2160 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= 0.158 Angle : 0.691 14.463 26320 Z= 0.280 Chirality : 0.041 0.415 2718 Planarity : 0.004 0.052 3109 Dihedral : 16.099 175.917 4589 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.35 % Allowed : 12.95 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 1793 helix: 2.68 (0.14), residues: 1118 sheet: -0.47 (1.03), residues: 28 loop : -0.10 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 PHE 0.021 0.001 PHE F 17 TYR 0.028 0.001 TYR M 302 ARG 0.006 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 997) hydrogen bonds : angle 3.77927 ( 2799) covalent geometry : bond 0.00375 (19217) covalent geometry : angle 0.69067 (26320) Misc. bond : bond 0.00365 ( 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 252 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8794 (mttm) cc_final: 0.8439 (mmtp) REVERT: M 109 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8622 (ttmm) REVERT: M 137 ASP cc_start: 0.8980 (t0) cc_final: 0.8592 (t70) REVERT: M 213 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8791 (tp) REVERT: D 3 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8188 (mmmt) REVERT: I 14 ARG cc_start: 0.8259 (mtm110) cc_final: 0.8022 (mtt90) REVERT: I 15 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7319 (mmm160) REVERT: J 42 MET cc_start: 0.8996 (tpt) cc_final: 0.8766 (tpt) REVERT: K 15 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7824 (mtt90) REVERT: N 12 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8090 (p) REVERT: O 15 ARG cc_start: 0.7504 (mmm160) cc_final: 0.6642 (mmt-90) REVERT: R 17 GLN cc_start: 0.8018 (tt0) cc_final: 0.7671 (tp40) REVERT: R 25 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.7981 (p) REVERT: S 5 TYR cc_start: 0.7801 (p90) cc_final: 0.7475 (p90) REVERT: S 9 LEU cc_start: 0.7409 (mt) cc_final: 0.7135 (mm) REVERT: T 39 LEU cc_start: 0.8796 (tp) cc_final: 0.8340 (mt) REVERT: V 30 LEU cc_start: 0.7931 (tt) cc_final: 0.7186 (tm) REVERT: V 34 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7215 (mp) REVERT: X 9 ASP cc_start: 0.7199 (t0) cc_final: 0.6753 (t0) outliers start: 35 outliers final: 20 residues processed: 233 average time/residue: 1.2008 time to fit residues: 317.3270 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 : 1.685 ------------------------------------------------------------------------------- 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 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 I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 20 GLN N 17 GLN S 20 GLN Z 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080975 restraints weight = 46177.754| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.08 r_work: 0.2783 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2299 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= 0.134 Angle : 0.660 11.534 26320 Z= 0.269 Chirality : 0.039 0.390 2718 Planarity : 0.003 0.052 3109 Dihedral : 15.760 178.095 4589 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.35 % Allowed : 13.49 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.19), residues: 1793 helix: 2.73 (0.14), residues: 1118 sheet: -0.46 (1.04), residues: 28 loop : -0.09 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.006 0.001 HIS M 181 PHE 0.016 0.001 PHE H 20 TYR 0.025 0.001 TYR M 302 ARG 0.005 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 997) hydrogen bonds : angle 3.72913 ( 2799) covalent geometry : bond 0.00312 (19217) covalent geometry : angle 0.65978 (26320) Misc. bond : bond 0.00232 ( 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 252 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8801 (mttm) cc_final: 0.8429 (mmtp) REVERT: M 109 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8655 (ttmm) REVERT: M 137 ASP cc_start: 0.9009 (t0) cc_final: 0.8633 (t70) REVERT: M 213 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8801 (tp) REVERT: D 3 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8235 (mmmt) REVERT: I 14 ARG cc_start: 0.8279 (mtm110) cc_final: 0.8054 (mtt90) REVERT: I 15 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.6832 (tmt170) REVERT: K 15 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7859 (mtt90) REVERT: N 12 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8094 (p) REVERT: O 12 ASP cc_start: 0.8324 (t0) cc_final: 0.8102 (t0) REVERT: O 15 ARG cc_start: 0.7491 (mmm160) cc_final: 0.6579 (ttp-170) REVERT: R 17 GLN cc_start: 0.7994 (tt0) cc_final: 0.7734 (tp40) REVERT: R 25 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.7994 (p) REVERT: S 5 TYR cc_start: 0.7755 (p90) cc_final: 0.7345 (p90) REVERT: S 9 LEU cc_start: 0.7405 (mt) cc_final: 0.7147 (mm) REVERT: T 39 LEU cc_start: 0.8808 (tp) cc_final: 0.8352 (mt) REVERT: V 30 LEU cc_start: 0.7970 (tt) cc_final: 0.7211 (tm) REVERT: V 34 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7229 (mp) REVERT: Z 24 MET cc_start: 0.6099 (ppp) cc_final: 0.5860 (pmm) REVERT: X 3 MET cc_start: 0.7371 (ptp) cc_final: 0.6503 (ptt) REVERT: X 6 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8043 (mmtm) REVERT: X 9 ASP cc_start: 0.7218 (t0) cc_final: 0.6777 (t0) outliers start: 35 outliers final: 22 residues processed: 236 average time/residue: 1.1351 time to fit residues: 305.5088 Evaluate side-chains 230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 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 I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR 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 R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 160 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 144 HIS 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 = 0.3515 r_free = 0.3515 target = 0.110710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.079698 restraints weight = 35504.267| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.82 r_work: 0.2741 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19242 Z= 0.216 Angle : 0.738 12.375 26320 Z= 0.301 Chirality : 0.042 0.372 2718 Planarity : 0.004 0.054 3109 Dihedral : 16.141 175.762 4589 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.21 % Allowed : 13.69 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.19), residues: 1793 helix: 2.58 (0.14), residues: 1117 sheet: -0.53 (1.04), residues: 28 loop : -0.13 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 156 HIS 0.008 0.001 HIS M 181 PHE 0.024 0.002 PHE F 17 TYR 0.031 0.002 TYR M 302 ARG 0.005 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 997) hydrogen bonds : angle 3.85557 ( 2799) covalent geometry : bond 0.00521 (19217) covalent geometry : angle 0.73778 (26320) Misc. bond : bond 0.00413 ( 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 241 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8778 (mttm) cc_final: 0.8440 (mmtp) REVERT: M 109 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8656 (ttmm) REVERT: M 137 ASP cc_start: 0.9002 (t0) cc_final: 0.8623 (t70) REVERT: F 16 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8698 (t) REVERT: I 14 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8089 (mtt90) REVERT: I 15 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7380 (mmm160) REVERT: J 42 MET cc_start: 0.9050 (tpt) cc_final: 0.8818 (tpt) REVERT: K 4 PHE cc_start: 0.8718 (m-80) cc_final: 0.8494 (m-10) REVERT: K 15 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7849 (mtt90) REVERT: N 12 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8048 (p) REVERT: O 12 ASP cc_start: 0.8345 (t0) cc_final: 0.8123 (t0) REVERT: O 15 ARG cc_start: 0.7528 (mmm160) cc_final: 0.6613 (ttp-110) REVERT: R 17 GLN cc_start: 0.8136 (tt0) cc_final: 0.7875 (tp40) REVERT: R 25 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8010 (p) REVERT: S 5 TYR cc_start: 0.7727 (p90) cc_final: 0.7340 (p90) REVERT: S 6 LYS cc_start: 0.8202 (mttm) cc_final: 0.7939 (mttp) REVERT: S 9 LEU cc_start: 0.7445 (mt) cc_final: 0.7181 (mm) REVERT: T 39 LEU cc_start: 0.8816 (tp) cc_final: 0.8368 (mt) REVERT: V 30 LEU cc_start: 0.7965 (tt) cc_final: 0.7207 (tm) REVERT: V 34 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7264 (mp) REVERT: X 9 ASP cc_start: 0.7238 (t0) cc_final: 0.6849 (t0) outliers start: 33 outliers final: 21 residues processed: 227 average time/residue: 1.1660 time to fit residues: 301.7950 Evaluate side-chains 231 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 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 I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR 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 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 32 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 132 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 164 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 K 20 GLN N 15 GLN N 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.113434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082527 restraints weight = 37389.845| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.84 r_work: 0.2808 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19242 Z= 0.118 Angle : 0.653 11.601 26320 Z= 0.268 Chirality : 0.038 0.363 2718 Planarity : 0.003 0.052 3109 Dihedral : 15.550 172.803 4589 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.68 % Allowed : 14.23 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.19), residues: 1793 helix: 2.74 (0.14), residues: 1118 sheet: -0.28 (1.09), residues: 28 loop : -0.07 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 156 HIS 0.005 0.001 HIS M 265 PHE 0.014 0.001 PHE L 147 TYR 0.022 0.001 TYR M 302 ARG 0.004 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 997) hydrogen bonds : angle 3.71192 ( 2799) covalent geometry : bond 0.00269 (19217) covalent geometry : angle 0.65325 (26320) Misc. bond : bond 0.00159 ( 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 243 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8781 (mttm) cc_final: 0.8412 (mmtp) REVERT: M 109 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8661 (ttmm) REVERT: M 137 ASP cc_start: 0.8997 (t0) cc_final: 0.8618 (t70) REVERT: H 172 ASP cc_start: 0.8766 (t70) cc_final: 0.8557 (t70) REVERT: D 3 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8275 (mmmt) REVERT: I 14 ARG cc_start: 0.8263 (mtm110) cc_final: 0.8037 (mtt90) REVERT: I 15 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.6812 (tmt170) REVERT: K 4 PHE cc_start: 0.8681 (m-80) cc_final: 0.8460 (m-10) REVERT: K 15 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7872 (mtt90) REVERT: N 12 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8102 (p) REVERT: O 12 ASP cc_start: 0.8281 (t0) cc_final: 0.7944 (t0) REVERT: O 15 ARG cc_start: 0.7484 (mmm160) cc_final: 0.6600 (ttp-110) REVERT: R 17 GLN cc_start: 0.7980 (tt0) cc_final: 0.7725 (tp40) REVERT: R 25 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8015 (p) REVERT: S 5 TYR cc_start: 0.7714 (p90) cc_final: 0.7488 (p90) REVERT: S 9 LEU cc_start: 0.7575 (mt) cc_final: 0.7303 (mm) REVERT: T 39 LEU cc_start: 0.8810 (tp) cc_final: 0.8355 (mt) REVERT: V 30 LEU cc_start: 0.7962 (tt) cc_final: 0.7344 (tm) REVERT: X 9 ASP cc_start: 0.7186 (t0) cc_final: 0.6768 (t0) outliers start: 25 outliers final: 19 residues processed: 230 average time/residue: 1.1539 time to fit residues: 301.4065 Evaluate side-chains 232 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain 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 I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR 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 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain Y residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 160 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.112722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079978 restraints weight = 53842.147| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.34 r_work: 0.2755 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2382 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= 0.139 Angle : 0.667 11.668 26320 Z= 0.274 Chirality : 0.038 0.353 2718 Planarity : 0.003 0.053 3109 Dihedral : 15.448 176.203 4589 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.61 % Allowed : 14.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.19), residues: 1793 helix: 2.74 (0.14), residues: 1118 sheet: -0.29 (1.09), residues: 28 loop : -0.09 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS M 181 PHE 0.020 0.001 PHE F 17 TYR 0.025 0.001 TYR M 302 ARG 0.004 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 997) hydrogen bonds : angle 3.71010 ( 2799) covalent geometry : bond 0.00325 (19217) covalent geometry : angle 0.66730 (26320) Misc. bond : bond 0.00323 ( 25) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15172.18 seconds wall clock time: 261 minutes 57.75 seconds (15717.75 seconds total)