Starting phenix.real_space_refine on Sat Jul 4 13:10:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vy3_32193/07_2026/7vy3_32193.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 16 5.49 5 Mg 25 5.21 5 S 69 5.16 5 C 13266 2.51 5 N 2513 2.21 5 O 2941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18831 Number of models: 1 Model: "" Number of chains: 49 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} 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 Conformer: "B" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} 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 bond proxies already assigned to first conformer: 1910 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 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: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 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: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 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: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 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: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 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: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 441 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "W" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 339 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} 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: "Y" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 318 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "Z" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "1" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "X" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 384 Unusual residues: {'BCL': 2, 'BPH': 1, 'LDA': 1, 'LMT': 2, 'PGV': 1, 'U10': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2, 'U10:plan-5': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 2, 'PGV': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 270 Unusual residues: {'CDL': 1, 'LDA': 1, 'LMT': 3, 'PGV': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 240 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 260 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 2, 'PTY': 1, 'SPO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 16 Chain: "J" 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: "K" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 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: "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: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 256 Unusual residues: {'BCL': 2, 'LMT': 2, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'CDL:plan-1': 1, 'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" 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: "1" 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LDA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 3.32, per 1000 atoms: 0.18 Number of scatterers: 18831 At special positions: 0 Unit cell: (121.36, 125.46, 113.16, 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 69 16.00 P 16 15.00 Mg 25 11.99 O 2941 8.00 N 2513 7.00 C 13266 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 572.6 milliseconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 7 sheets defined 71.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.553A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.538A pdb=" N TYR L 144 " --> pdb=" O ALA L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 163 Processing helix chain 'L' and resid 164 through 165 No H-bonds generated for 'chain 'L' and resid 164 through 165' Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 221 removed outlier: 3.519A pdb=" N GLU L 212 " --> pdb=" O THR L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 250 removed outlier: 3.866A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 262 No H-bonds generated for 'chain 'L' and resid 260 through 262' Processing helix chain 'L' and resid 263 through 268 removed outlier: 3.927A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 98 through 102 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.628A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.560A pdb=" N GLU M 173 " --> pdb=" O SER M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 removed outlier: 3.664A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.983A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.705A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE H 216 " --> pdb=" O PHE H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 244 removed outlier: 3.508A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.569A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (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 51 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 51 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'I' and resid 3 through 10 Processing helix chain 'I' and resid 12 through 38 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 42 through 52 removed outlier: 3.505A pdb=" N ALA I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 3 through 10 Processing helix chain 'K' and resid 12 through 38 Processing helix chain 'K' and resid 42 through 51 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 'O' and resid 3 through 5 No H-bonds generated for 'chain 'O' and resid 3 through 5' Processing helix chain 'O' and resid 6 through 11 removed outlier: 3.871A pdb=" N ILE O 10 " --> pdb=" O LYS O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 38 removed outlier: 3.552A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 51 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 52 Processing helix chain 'R' and resid 12 through 45 Processing helix chain 'S' and resid 3 through 8 removed outlier: 3.836A pdb=" N LYS S 6 " --> pdb=" O LYS S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 38 Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 12 through 45 Processing helix chain 'V' and resid 3 through 5 No H-bonds generated for 'chain 'V' and resid 3 through 5' Processing helix chain 'V' and resid 6 through 11 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: 4.144A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 38 removed outlier: 3.943A pdb=" N PHE Y 17 " --> pdb=" O PRO Y 13 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL Y 18 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) 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 47 Processing helix chain 'Z' and resid 19 through 45 removed outlier: 3.629A pdb=" N SER Z 25 " --> pdb=" O SER Z 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Z 33 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 38 Processing helix chain 'X' and resid 18 through 55 Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.573A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.558A pdb=" N GLN M 11 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 62 through 65 Processing sheet with id=AA5, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA6, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.769A pdb=" N VAL H 164 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.656A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2865 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: 2.37 Time building geometry restraints manager: 1.81 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: 5433 1.37 - 1.54: 13750 1.54 - 1.71: 111 1.71 - 1.88: 133 1.88 - 2.05: 100 Bond restraints: 19527 Sorted by residual: bond pdb=" CA7 CDL M 408 " pdb=" OA8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL H 307 " pdb=" OA8 CDL H 307 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CA7 CDL Y 102 " pdb=" OA8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL H 307 " pdb=" OB8 CDL H 307 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CB7 CDL M 408 " pdb=" OB8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 ... (remaining 19522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 25593 4.95 - 9.89: 1019 9.89 - 14.84: 72 14.84 - 19.79: 11 19.79 - 24.73: 1 Bond angle restraints: 26696 Sorted by residual: angle pdb=" C2 SPO P 102 " pdb=" C1 SPO P 102 " pdb=" C4 SPO P 102 " ideal model delta sigma weight residual 110.23 85.50 24.73 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C1D BCL 1 101 " pdb=" C2D BCL 1 101 " pdb=" CMD BCL 1 101 " ideal model delta sigma weight residual 125.57 139.20 -13.63 1.83e+00 2.99e-01 5.56e+01 angle pdb=" C1D BCL M 402 " pdb=" C2D BCL M 402 " pdb=" CMD BCL M 402 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL Y 103 " pdb=" C2D BCL Y 103 " pdb=" CMD BCL Y 103 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.13 -13.55 1.83e+00 2.99e-01 5.50e+01 ... (remaining 26691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9791 35.92 - 71.85: 373 71.85 - 107.77: 35 107.77 - 143.69: 7 143.69 - 179.61: 12 Dihedral angle restraints: 10218 sinusoidal: 4895 harmonic: 5323 Sorted by residual: dihedral pdb=" C1 BCL L 309 " pdb=" C2 BCL L 309 " pdb=" C3 BCL L 309 " pdb=" C5 BCL L 309 " ideal model delta sinusoidal sigma weight residual -180.00 -0.95 -179.05 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL B 103 " pdb=" CGA BCL B 103 " pdb=" O2A BCL B 103 " pdb=" CBA BCL B 103 " ideal model delta sinusoidal sigma weight residual 180.00 116.19 63.81 1 6.00e+00 2.78e-02 1.49e+02 dihedral pdb=" CBD BCL Z 102 " pdb=" CGD BCL Z 102 " pdb=" O2D BCL Z 102 " pdb=" CED BCL Z 102 " ideal model delta sinusoidal sigma weight residual 180.00 140.82 39.18 1 5.00e+00 4.00e-02 8.63e+01 ... (remaining 10215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2177 0.059 - 0.118: 360 0.118 - 0.177: 102 0.177 - 0.236: 18 0.236 - 0.295: 10 Chirality restraints: 2667 Sorted by residual: chirality pdb=" C05 PGV H 301 " pdb=" C04 PGV H 301 " pdb=" C06 PGV H 301 " pdb=" O05 PGV H 301 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C05 PGV M 409 " pdb=" C04 PGV M 409 " pdb=" C06 PGV M 409 " pdb=" O05 PGV M 409 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C05 PGV F 102 " pdb=" C04 PGV F 102 " pdb=" C06 PGV F 102 " pdb=" O05 PGV F 102 " 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 2664 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 D 105 " 0.062 2.00e-02 2.50e+03 1.93e-01 6.53e+02 pdb=" C1M U10 D 105 " -0.255 2.00e-02 2.50e+03 pdb=" C2 U10 D 105 " 0.145 2.00e-02 2.50e+03 pdb=" C3 U10 D 105 " 0.096 2.00e-02 2.50e+03 pdb=" C4 U10 D 105 " -0.289 2.00e-02 2.50e+03 pdb=" C5 U10 D 105 " -0.037 2.00e-02 2.50e+03 pdb=" C6 U10 D 105 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL B 103 " 0.343 3.00e-02 1.11e+03 2.80e-01 4.36e+02 pdb=" CBA BCL B 103 " 0.182 3.00e-02 1.11e+03 pdb=" CGA BCL B 103 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL B 103 " 0.037 3.00e-02 1.11e+03 pdb=" O2A BCL B 103 " -0.485 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 1 101 " -0.310 3.10e-02 1.04e+03 2.87e-01 4.30e+02 pdb=" C4C BCL 1 101 " -0.265 3.10e-02 1.04e+03 pdb=" CHC BCL 1 101 " 0.055 3.10e-02 1.04e+03 pdb=" CHD BCL 1 101 " 0.028 3.10e-02 1.04e+03 pdb=" NC BCL 1 101 " 0.492 3.10e-02 1.04e+03 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 173 2.61 - 3.18: 14663 3.18 - 3.75: 31381 3.75 - 4.33: 46398 4.33 - 4.90: 73859 Nonbonded interactions: 166474 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 404 " model vdw 2.032 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 404 " model vdw 2.066 2.260 nonbonded pdb=" OG SER A 37 " pdb=" O2' LMT A 102 " model vdw 2.102 3.040 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 404 " model vdw 2.119 2.340 nonbonded pdb=" OE1 GLN S 20 " pdb=" OH TYR T 23 " model vdw 2.184 3.040 ... (remaining 166469 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 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 45)) selection = (chain 'O' and resid 3 through 45) selection = (chain 'V' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 45)) } ncs_group { reference = (chain 'B' and (resid 7 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 7 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 7 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 7 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 7 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 7 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 7 through 48) selection = (chain 'T' and (resid 7 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 7 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 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 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) 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 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) 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 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) 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 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'S' and (resid 1 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) } 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: 3.200 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.730 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.019 0.326 19551 Z= 1.001 Angle : 1.837 24.733 26696 Z= 0.773 Chirality : 0.053 0.295 2667 Planarity : 0.017 0.287 3163 Dihedral : 18.697 179.613 6802 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.30 % Allowed : 3.49 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1789 helix: 1.12 (0.14), residues: 1147 sheet: -0.62 (1.08), residues: 24 loop : 0.25 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 45 TYR 0.011 0.001 TYR L 164 PHE 0.015 0.001 PHE H 10 TRP 0.012 0.001 TRP M 268 HIS 0.005 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.01874 / 0.85 (19527) covalent geometry : angle 1.83673 / 0.77 (26696) hydrogen bonds : bond 0.20238 / 13.45 ( 1008) hydrogen bonds : angle 6.24206 / 4.53 ( 2865) Misc. bond : bond 0.15242 / 9.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.477 Fit side-chains REVERT: M 168 MET cc_start: 0.8939 (mmm) cc_final: 0.8511 (mmm) REVERT: H 134 MET cc_start: 0.8539 (ttp) cc_final: 0.8229 (ttp) REVERT: A 37 SER cc_start: 0.8204 (t) cc_final: 0.7988 (t) REVERT: G 42 TYR cc_start: 0.8853 (t80) cc_final: 0.8559 (t80) REVERT: I 3 LYS cc_start: 0.8496 (mttt) cc_final: 0.8289 (mttm) REVERT: O 24 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8478 (mp) REVERT: S 52 ASN cc_start: 0.7630 (m110) cc_final: 0.7110 (m110) REVERT: Z 24 MET cc_start: 0.5136 (mmm) cc_final: 0.4558 (mtp) REVERT: 1 36 LEU cc_start: 0.4018 (OUTLIER) cc_final: 0.3314 (mt) REVERT: X 29 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7406 (ttmm) REVERT: X 47 PHE cc_start: 0.7735 (t80) cc_final: 0.7494 (t80) outliers start: 35 outliers final: 15 residues processed: 317 average time/residue: 0.4911 time to fit residues: 176.2967 Evaluate side-chains 231 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain 1 residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 264 GLN M 301 HIS H 199 GLN E 17 GLN I 20 GLN Q 20 GLN S 20 GLN V 20 GLN 1 20 GLN X 66 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108708 restraints weight = 21288.782| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.16 r_work: 0.2945 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19551 Z= 0.144 Angle : 0.696 15.355 26696 Z= 0.277 Chirality : 0.038 0.250 2667 Planarity : 0.004 0.038 3163 Dihedral : 19.482 179.832 3644 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.62 % Allowed : 8.62 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 1789 helix: 2.07 (0.14), residues: 1180 sheet: -0.64 (1.10), residues: 24 loop : 0.25 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 202 TYR 0.012 0.001 TYR K 5 PHE 0.015 0.001 PHE H 20 TRP 0.012 0.001 TRP M 252 HIS 0.007 0.001 HIS S 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (19527) covalent geometry : angle 0.69581 / 0.28 (26696) hydrogen bonds : bond 0.05390 / 3.51 ( 1008) hydrogen bonds : angle 4.04582 / 2.91 ( 2865) Misc. bond : bond 0.00272 / 0.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 222 time to evaluate : 0.656 Fit side-chains REVERT: M 100 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: M 218 MET cc_start: 0.9283 (mtp) cc_final: 0.8891 (mtp) REVERT: H 134 MET cc_start: 0.8635 (ttp) cc_final: 0.8383 (ttp) REVERT: B 12 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8445 (t) REVERT: G 42 TYR cc_start: 0.9137 (t80) cc_final: 0.8856 (t80) REVERT: I 3 LYS cc_start: 0.8715 (mttt) cc_final: 0.8332 (mttm) REVERT: P 18 GLU cc_start: 0.7502 (tt0) cc_final: 0.7296 (tt0) REVERT: Q 5 TYR cc_start: 0.7808 (p90) cc_final: 0.7461 (p90) REVERT: Q 45 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8063 (pt0) REVERT: V 45 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: W 31 SER cc_start: 0.8087 (m) cc_final: 0.7768 (m) REVERT: Z 24 MET cc_start: 0.4659 (mmm) cc_final: 0.3773 (mtp) REVERT: X 53 ARG cc_start: 0.6446 (mtm110) cc_final: 0.6126 (mtp85) REVERT: X 67 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6899 (pp) outliers start: 55 outliers final: 17 residues processed: 253 average time/residue: 0.5125 time to fit residues: 146.8390 Evaluate side-chains 227 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 ASN A 20 GLN E 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105044 restraints weight = 25222.673| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.34 r_work: 0.2840 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19551 Z= 0.217 Angle : 0.779 16.037 26696 Z= 0.312 Chirality : 0.042 0.255 2667 Planarity : 0.004 0.039 3163 Dihedral : 19.537 179.752 3624 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.09 % Allowed : 10.27 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.19), residues: 1789 helix: 1.99 (0.14), residues: 1181 sheet: -0.79 (1.09), residues: 24 loop : 0.01 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 202 TYR 0.014 0.002 TYR L 164 PHE 0.025 0.002 PHE H 20 TRP 0.018 0.002 TRP M 271 HIS 0.008 0.002 HIS S 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (19527) covalent geometry : angle 0.77914 / 0.31 (26696) hydrogen bonds : bond 0.05590 / 3.65 ( 1008) hydrogen bonds : angle 4.05230 / 2.92 ( 2865) Misc. bond : bond 0.00446 / 0.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.408 Fit side-chains REVERT: M 100 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: M 218 MET cc_start: 0.9310 (mtp) cc_final: 0.8975 (mtp) REVERT: H 134 MET cc_start: 0.8718 (ttp) cc_final: 0.8353 (ttp) REVERT: A 9 MET cc_start: 0.8351 (mtp) cc_final: 0.8149 (mmm) REVERT: B 12 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8406 (t) REVERT: D 45 GLU cc_start: 0.8382 (pt0) cc_final: 0.8144 (tt0) REVERT: G 11 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8820 (mp) REVERT: Q 5 TYR cc_start: 0.7881 (p90) cc_final: 0.7592 (p90) REVERT: W 31 SER cc_start: 0.8235 (m) cc_final: 0.7971 (m) REVERT: Y 30 MET cc_start: 0.3602 (tmm) cc_final: 0.3366 (tmm) REVERT: Z 24 MET cc_start: 0.4657 (mmm) cc_final: 0.3838 (mtp) REVERT: X 53 ARG cc_start: 0.6560 (mtm110) cc_final: 0.6151 (mtp85) REVERT: X 67 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6928 (pp) outliers start: 47 outliers final: 24 residues processed: 231 average time/residue: 0.5195 time to fit residues: 135.8500 Evaluate side-chains 223 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN E 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.107673 restraints weight = 25085.936| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.32 r_work: 0.2891 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19551 Z= 0.140 Angle : 0.677 14.023 26696 Z= 0.267 Chirality : 0.038 0.244 2667 Planarity : 0.003 0.038 3163 Dihedral : 18.500 179.653 3624 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.09 % Allowed : 11.13 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.19), residues: 1789 helix: 2.31 (0.14), residues: 1174 sheet: -0.54 (1.10), residues: 24 loop : 0.13 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 15 TYR 0.013 0.001 TYR I 5 PHE 0.019 0.001 PHE H 20 TRP 0.013 0.001 TRP M 157 HIS 0.006 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (19527) covalent geometry : angle 0.67710 / 0.27 (26696) hydrogen bonds : bond 0.04827 / 3.14 ( 1008) hydrogen bonds : angle 3.79556 / 2.73 ( 2865) Misc. bond : bond 0.00302 / 0.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.533 Fit side-chains REVERT: L 216 PHE cc_start: 0.8703 (m-80) cc_final: 0.8422 (m-80) REVERT: M 100 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: M 218 MET cc_start: 0.9278 (mtp) cc_final: 0.8960 (mtp) REVERT: H 45 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7843 (mm-30) REVERT: H 134 MET cc_start: 0.8688 (ttp) cc_final: 0.8327 (ttp) REVERT: A 9 MET cc_start: 0.8280 (mtp) cc_final: 0.8029 (mmm) REVERT: E 14 GLU cc_start: 0.7760 (mp0) cc_final: 0.7542 (pt0) REVERT: G 11 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (mp) REVERT: I 3 LYS cc_start: 0.8685 (mttt) cc_final: 0.8219 (mttm) REVERT: Q 5 TYR cc_start: 0.7877 (p90) cc_final: 0.7534 (p90) REVERT: Q 45 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8141 (pt0) REVERT: V 45 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7743 (mm-30) REVERT: W 24 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7083 (mmm) REVERT: W 31 SER cc_start: 0.8135 (m) cc_final: 0.7845 (m) REVERT: W 43 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7723 (mp) REVERT: Y 30 MET cc_start: 0.3736 (tmm) cc_final: 0.3475 (tmm) REVERT: Z 24 MET cc_start: 0.4585 (mmm) cc_final: 0.3782 (mtp) REVERT: X 53 ARG cc_start: 0.6472 (mtm110) cc_final: 0.6099 (mtp85) REVERT: X 67 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6955 (pp) outliers start: 47 outliers final: 20 residues processed: 241 average time/residue: 0.5376 time to fit residues: 146.1669 Evaluate side-chains 225 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN E 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.139954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109675 restraints weight = 29951.617| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.42 r_work: 0.2936 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19551 Z= 0.118 Angle : 0.635 14.947 26696 Z= 0.249 Chirality : 0.037 0.245 2667 Planarity : 0.003 0.036 3163 Dihedral : 17.466 179.763 3623 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.70 % Allowed : 11.13 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.19), residues: 1789 helix: 2.55 (0.14), residues: 1175 sheet: -0.33 (1.15), residues: 24 loop : 0.13 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 202 TYR 0.016 0.001 TYR K 5 PHE 0.017 0.001 PHE H 20 TRP 0.013 0.001 TRP M 157 HIS 0.006 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (19527) covalent geometry : angle 0.63463 / 0.25 (26696) hydrogen bonds : bond 0.04465 / 2.91 ( 1008) hydrogen bonds : angle 3.63254 / 2.62 ( 2865) Misc. bond : bond 0.00238 / 0.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 217 time to evaluate : 0.562 Fit side-chains REVERT: L 216 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8413 (m-80) REVERT: M 218 MET cc_start: 0.9244 (mtp) cc_final: 0.8942 (mtp) REVERT: H 45 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7838 (mm-30) REVERT: H 134 MET cc_start: 0.8663 (ttp) cc_final: 0.8371 (ttp) REVERT: G 11 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8799 (mp) REVERT: I 3 LYS cc_start: 0.8728 (mttt) cc_final: 0.8323 (mttm) REVERT: Q 5 TYR cc_start: 0.7894 (p90) cc_final: 0.7522 (p90) REVERT: Q 45 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8065 (pt0) REVERT: T 39 LEU cc_start: 0.8082 (tp) cc_final: 0.7880 (mp) REVERT: V 45 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7718 (mm-30) REVERT: W 27 LEU cc_start: 0.7206 (tt) cc_final: 0.6744 (tm) REVERT: W 31 SER cc_start: 0.8115 (m) cc_final: 0.7789 (m) REVERT: W 43 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7708 (mp) REVERT: Y 30 MET cc_start: 0.3959 (tmm) cc_final: 0.3555 (tmm) REVERT: Z 24 MET cc_start: 0.4433 (mmm) cc_final: 0.3327 (ttp) REVERT: X 53 ARG cc_start: 0.6447 (mtm110) cc_final: 0.6068 (mtp85) REVERT: X 67 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6948 (pp) outliers start: 41 outliers final: 19 residues processed: 240 average time/residue: 0.5574 time to fit residues: 151.0772 Evaluate side-chains 229 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 121 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 17 GLN I 20 GLN S 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108377 restraints weight = 21231.917| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.13 r_work: 0.2949 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19551 Z= 0.137 Angle : 0.658 15.502 26696 Z= 0.262 Chirality : 0.038 0.242 2667 Planarity : 0.003 0.040 3163 Dihedral : 17.132 179.669 3620 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.90 % Allowed : 11.26 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.19), residues: 1789 helix: 2.48 (0.14), residues: 1175 sheet: -0.32 (1.16), residues: 24 loop : 0.13 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 202 TYR 0.015 0.001 TYR K 5 PHE 0.020 0.001 PHE H 20 TRP 0.014 0.001 TRP M 157 HIS 0.006 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19527) covalent geometry : angle 0.65753 / 0.26 (26696) hydrogen bonds : bond 0.04627 / 3.01 ( 1008) hydrogen bonds : angle 3.67400 / 2.64 ( 2865) Misc. bond : bond 0.00300 / 0.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.408 Fit side-chains REVERT: M 23 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: M 100 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: M 218 MET cc_start: 0.9240 (mtp) cc_final: 0.8908 (mtp) REVERT: H 83 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7844 (ptm160) REVERT: H 134 MET cc_start: 0.8651 (ttp) cc_final: 0.8343 (ttp) REVERT: B 12 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8367 (t) REVERT: D 20 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: G 11 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8816 (mp) REVERT: I 3 LYS cc_start: 0.8626 (mttt) cc_final: 0.8189 (mttm) REVERT: J 39 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8544 (tp) REVERT: P 14 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: Q 5 TYR cc_start: 0.7799 (p90) cc_final: 0.7435 (p90) REVERT: T 19 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7205 (tp) REVERT: T 39 LEU cc_start: 0.8075 (tp) cc_final: 0.7847 (mp) REVERT: W 24 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7036 (mmm) REVERT: W 27 LEU cc_start: 0.7167 (tt) cc_final: 0.6695 (tm) REVERT: W 31 SER cc_start: 0.8009 (m) cc_final: 0.7679 (m) REVERT: W 43 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7670 (mp) REVERT: Y 30 MET cc_start: 0.3836 (tmm) cc_final: 0.3470 (tmm) REVERT: Z 24 MET cc_start: 0.4336 (mmm) cc_final: 0.3703 (mtp) REVERT: X 53 ARG cc_start: 0.6357 (mtm110) cc_final: 0.6016 (mtp85) REVERT: X 67 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6945 (pp) outliers start: 44 outliers final: 20 residues processed: 233 average time/residue: 0.5940 time to fit residues: 155.9956 Evaluate side-chains 232 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 116 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102124 restraints weight = 29722.766| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.37 r_work: 0.2857 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19551 Z= 0.229 Angle : 0.799 15.596 26696 Z= 0.319 Chirality : 0.043 0.241 2667 Planarity : 0.004 0.041 3163 Dihedral : 17.962 179.424 3620 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.96 % Allowed : 11.13 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.19), residues: 1789 helix: 2.05 (0.14), residues: 1177 sheet: -0.73 (1.12), residues: 24 loop : -0.05 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 15 TYR 0.016 0.002 TYR K 5 PHE 0.028 0.002 PHE H 20 TRP 0.019 0.002 TRP M 271 HIS 0.010 0.002 HIS S 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (19527) covalent geometry : angle 0.79901 / 0.32 (26696) hydrogen bonds : bond 0.05377 / 3.50 ( 1008) hydrogen bonds : angle 3.95962 / 2.85 ( 2865) Misc. bond : bond 0.00473 / 0.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.568 Fit side-chains REVERT: M 68 PHE cc_start: 0.8008 (m-80) cc_final: 0.7807 (m-10) REVERT: H 122 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: H 134 MET cc_start: 0.8710 (ttp) cc_final: 0.8353 (ttp) REVERT: G 11 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8811 (mp) REVERT: I 3 LYS cc_start: 0.8661 (mttt) cc_final: 0.8240 (mttm) REVERT: P 14 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: Q 5 TYR cc_start: 0.7854 (p90) cc_final: 0.7594 (p90) REVERT: Q 45 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8001 (pt0) REVERT: T 19 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7170 (tp) REVERT: W 24 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7008 (mmm) REVERT: W 27 LEU cc_start: 0.7184 (tt) cc_final: 0.6740 (tm) REVERT: W 31 SER cc_start: 0.8196 (m) cc_final: 0.7906 (m) REVERT: W 43 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7670 (mp) REVERT: Y 30 MET cc_start: 0.3857 (tmm) cc_final: 0.3408 (tmm) REVERT: Z 24 MET cc_start: 0.4694 (mmm) cc_final: 0.3824 (mtp) REVERT: X 53 ARG cc_start: 0.6481 (mtm110) cc_final: 0.6036 (mtp85) REVERT: X 67 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6907 (pp) outliers start: 45 outliers final: 25 residues processed: 225 average time/residue: 0.6129 time to fit residues: 155.6525 Evaluate side-chains 233 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 243 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 17 GLN S 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.106594 restraints weight = 28294.938| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.30 r_work: 0.2932 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19551 Z= 0.121 Angle : 0.645 15.500 26696 Z= 0.256 Chirality : 0.037 0.242 2667 Planarity : 0.003 0.038 3163 Dihedral : 16.769 179.710 3620 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.17 % Allowed : 12.05 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.19), residues: 1789 helix: 2.47 (0.14), residues: 1175 sheet: -0.39 (1.16), residues: 24 loop : 0.09 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 202 TYR 0.015 0.001 TYR K 5 PHE 0.019 0.001 PHE H 20 TRP 0.014 0.001 TRP M 157 HIS 0.005 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (19527) covalent geometry : angle 0.64505 / 0.26 (26696) hydrogen bonds : bond 0.04533 / 2.95 ( 1008) hydrogen bonds : angle 3.66488 / 2.64 ( 2865) Misc. bond : bond 0.00243 / 0.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.688 Fit side-chains REVERT: M 68 PHE cc_start: 0.7979 (m-80) cc_final: 0.7761 (m-10) REVERT: M 218 MET cc_start: 0.9257 (mtp) cc_final: 0.8934 (mtp) REVERT: H 134 MET cc_start: 0.8641 (ttp) cc_final: 0.8321 (ttp) REVERT: G 11 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8784 (mp) REVERT: I 3 LYS cc_start: 0.8632 (mttt) cc_final: 0.8193 (mttm) REVERT: J 39 LEU cc_start: 0.8772 (tm) cc_final: 0.8568 (tp) REVERT: Q 5 TYR cc_start: 0.7846 (p90) cc_final: 0.7519 (p90) REVERT: Q 45 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8020 (pt0) REVERT: T 19 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7173 (tp) REVERT: T 39 LEU cc_start: 0.8081 (mt) cc_final: 0.7865 (mp) REVERT: W 27 LEU cc_start: 0.7179 (tt) cc_final: 0.6710 (tm) REVERT: W 31 SER cc_start: 0.8047 (m) cc_final: 0.7722 (m) REVERT: W 43 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7674 (mp) REVERT: Y 30 MET cc_start: 0.3779 (tmm) cc_final: 0.3403 (tmm) REVERT: Z 24 MET cc_start: 0.4348 (mmm) cc_final: 0.3707 (mtp) REVERT: X 53 ARG cc_start: 0.6307 (mtm110) cc_final: 0.5916 (mtp85) REVERT: X 67 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6946 (pp) outliers start: 33 outliers final: 19 residues processed: 232 average time/residue: 0.6148 time to fit residues: 161.0107 Evaluate side-chains 223 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 136 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106670 restraints weight = 25288.472| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.36 r_work: 0.2894 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19551 Z= 0.161 Angle : 0.699 15.538 26696 Z= 0.279 Chirality : 0.039 0.245 2667 Planarity : 0.003 0.040 3163 Dihedral : 16.901 179.541 3620 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.11 % Allowed : 12.57 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.19), residues: 1789 helix: 2.34 (0.14), residues: 1175 sheet: -0.47 (1.17), residues: 24 loop : 0.07 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 202 TYR 0.017 0.002 TYR K 5 PHE 0.037 0.002 PHE L 41 TRP 0.015 0.001 TRP M 271 HIS 0.007 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (19527) covalent geometry : angle 0.69935 / 0.28 (26696) hydrogen bonds : bond 0.04837 / 3.15 ( 1008) hydrogen bonds : angle 3.75763 / 2.71 ( 2865) Misc. bond : bond 0.00353 / 0.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.636 Fit side-chains REVERT: M 68 PHE cc_start: 0.7997 (m-80) cc_final: 0.7785 (m-10) REVERT: M 218 MET cc_start: 0.9257 (mtp) cc_final: 0.8922 (mtp) REVERT: H 134 MET cc_start: 0.8690 (ttp) cc_final: 0.8345 (ttp) REVERT: G 11 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8821 (mp) REVERT: I 3 LYS cc_start: 0.8680 (mttt) cc_final: 0.8216 (mttm) REVERT: J 39 LEU cc_start: 0.8796 (tm) cc_final: 0.8594 (tp) REVERT: P 14 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: Q 5 TYR cc_start: 0.7846 (p90) cc_final: 0.7531 (p90) REVERT: Q 45 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7971 (pt0) REVERT: T 19 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7166 (tp) REVERT: T 24 MET cc_start: 0.8359 (mmt) cc_final: 0.8028 (mmt) REVERT: W 27 LEU cc_start: 0.7218 (tt) cc_final: 0.6742 (tm) REVERT: W 31 SER cc_start: 0.8135 (m) cc_final: 0.7830 (m) REVERT: Y 30 MET cc_start: 0.3896 (tmm) cc_final: 0.3518 (tmm) REVERT: Z 24 MET cc_start: 0.4367 (mmm) cc_final: 0.3703 (mtp) REVERT: X 53 ARG cc_start: 0.6446 (mtm110) cc_final: 0.6001 (mtp85) REVERT: X 67 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6917 (pp) outliers start: 32 outliers final: 21 residues processed: 223 average time/residue: 0.6150 time to fit residues: 154.3810 Evaluate side-chains 226 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain P residue 14 GLU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 164 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 161 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107173 restraints weight = 21188.955| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.07 r_work: 0.2936 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19551 Z= 0.156 Angle : 0.690 15.812 26696 Z= 0.276 Chirality : 0.039 0.246 2667 Planarity : 0.003 0.040 3163 Dihedral : 16.764 179.538 3620 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 12.77 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 1789 helix: 2.33 (0.14), residues: 1175 sheet: -0.49 (1.17), residues: 24 loop : 0.03 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 202 TYR 0.016 0.002 TYR K 5 PHE 0.030 0.001 PHE L 41 TRP 0.017 0.001 TRP X 22 HIS 0.006 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (19527) covalent geometry : angle 0.69027 / 0.28 (26696) hydrogen bonds : bond 0.04794 / 3.12 ( 1008) hydrogen bonds : angle 3.74757 / 2.70 ( 2865) Misc. bond : bond 0.00338 / 0.22 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 0.645 Fit side-chains REVERT: M 218 MET cc_start: 0.9174 (mtp) cc_final: 0.8778 (mtp) REVERT: H 134 MET cc_start: 0.8682 (ttp) cc_final: 0.8337 (ttp) REVERT: G 11 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8826 (mp) REVERT: Q 5 TYR cc_start: 0.7873 (p90) cc_final: 0.7573 (p90) REVERT: Q 45 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8018 (pt0) REVERT: T 19 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (tp) REVERT: T 24 MET cc_start: 0.8358 (mmt) cc_final: 0.8013 (mmt) REVERT: W 27 LEU cc_start: 0.7291 (tt) cc_final: 0.6809 (tm) REVERT: W 31 SER cc_start: 0.8120 (m) cc_final: 0.7815 (m) REVERT: Y 30 MET cc_start: 0.4007 (tmm) cc_final: 0.3599 (tmm) REVERT: Z 24 MET cc_start: 0.4448 (mmm) cc_final: 0.3767 (mtp) REVERT: X 53 ARG cc_start: 0.6473 (mtm110) cc_final: 0.6047 (mtp85) REVERT: X 67 ILE cc_start: 0.7227 (OUTLIER) cc_final: 0.6930 (pp) outliers start: 26 outliers final: 21 residues processed: 222 average time/residue: 0.5818 time to fit residues: 145.4109 Evaluate side-chains 227 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Chi-restraints excluded: chain X residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107827 restraints weight = 23344.173| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.33 r_work: 0.2914 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19551 Z= 0.137 Angle : 0.662 15.721 26696 Z= 0.265 Chirality : 0.038 0.245 2667 Planarity : 0.003 0.039 3163 Dihedral : 16.496 179.602 3620 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.84 % Allowed : 12.57 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.19), residues: 1789 helix: 2.42 (0.14), residues: 1175 sheet: -0.42 (1.17), residues: 24 loop : 0.05 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 15 TYR 0.017 0.001 TYR K 5 PHE 0.026 0.001 PHE L 41 TRP 0.015 0.001 TRP X 22 HIS 0.006 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (19527) covalent geometry : angle 0.66150 / 0.27 (26696) hydrogen bonds : bond 0.04631 / 3.01 ( 1008) hydrogen bonds : angle 3.68867 / 2.66 ( 2865) Misc. bond : bond 0.00290 / 0.19 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6747.72 seconds wall clock time: 115 minutes 45.80 seconds (6945.80 seconds total)