Starting phenix.real_space_refine on Sun Sep 13 17:28:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.map" model { file = "/net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z5s_11081/09_2026/6z5s_11081.cif" } resolution = 2.65 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= 0.001 sd= 0.015 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 32 5.21 5 S 56 5.16 5 C 16082 2.51 5 N 3074 2.21 5 O 3533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22794 Number of models: 1 Model: "" Number of chains: 66 Chain: "W" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 682 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "M" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2381 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 280} Chain: "L" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2185 Classifications: {'peptide': 276} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain: "H" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1894 Classifications: {'peptide': 251} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 223} Chain: "1" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "2" Number of atoms: 393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Conformer: "B" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} bond proxies already assigned to first conformer: 384 Chain: "5" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "6" Number of atoms: 356 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Conformer: "B" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} bond proxies already assigned to first conformer: 346 Chain: "3" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "4" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 374 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "Y" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "Z" Number of atoms: 393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Conformer: "B" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} bond proxies already assigned to first conformer: 384 Chain: "V" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "X" Number of atoms: 393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Conformer: "B" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} bond proxies already assigned to first conformer: 384 Chain: "T" Number of atoms: 408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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 Conformer: "B" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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 bond proxies already assigned to first conformer: 398 Chain: "U" Number of atoms: 393 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Conformer: "B" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} bond proxies already assigned to first conformer: 384 Chain: "A" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 352 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "B" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "D" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "R" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "S" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "P" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "Q" Number of atoms: 399 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Conformer: "B" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} bond proxies already assigned to first conformer: 390 Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "O" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "J" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 392 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: "K" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "G" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "I" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 382 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "E" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 397 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} 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: "F" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "M" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {' FE': 1, '6PL': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'QAK': 1, 'U10': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 340 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 139 Unusual residues: {'6PL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "1" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 19 Chain: "2" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 195 Unusual residues: {'BCL': 1, 'CDL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "4" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 211 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 211 Unusual residues: {'BCL': 2, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 182 Unusual residues: {'BCL': 2, 'PGT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 167 Unusual residues: {'BCL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 310 Unusual residues: {'BCL': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "I" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 172 Unusual residues: {'6PL': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N APHE 2 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE 2 26 " occ=0.50 residue: pdb=" N APHE 6 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE 6 26 " occ=0.50 residue: pdb=" N APHE Z 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE Z 26 " occ=0.50 residue: pdb=" N APHE X 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE X 26 " occ=0.50 residue: pdb=" N APHE T 30 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE T 30 " occ=0.50 residue: pdb=" N APHE U 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE U 26 " occ=0.50 residue: pdb=" N APHE D 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 26 " occ=0.50 residue: pdb=" N APHE S 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE S 26 " occ=0.50 residue: pdb=" N APHE Q 26 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE Q 26 " occ=0.50 Time building chain proxies: 5.60, per 1000 atoms: 0.25 Number of scatterers: 22794 At special positions: 0 Unit cell: (136.24, 131, 112.136, 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 56 16.00 P 16 15.00 Mg 32 11.99 O 3533 8.00 N 3074 7.00 C 16082 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4144 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 5 sheets defined 67.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'W' and resid 9 through 25 Processing helix chain 'W' and resid 36 through 58 removed outlier: 4.575A pdb=" N GLY W 44 " --> pdb=" O SER W 40 " (cutoff:3.500A) Proline residue: W 45 - end of helix removed outlier: 3.661A pdb=" N LYS W 57 " --> pdb=" O PHE W 53 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA W 58 " --> pdb=" O VAL W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 90 removed outlier: 4.929A pdb=" N LEU W 76 " --> pdb=" O ARG W 72 " (cutoff:3.500A) Proline residue: W 77 - end of helix removed outlier: 3.617A pdb=" N PHE W 83 " --> pdb=" O PHE W 79 " (cutoff:3.500A) Proline residue: W 86 - end of helix Processing helix chain 'M' and resid 37 through 44 Processing helix chain 'M' and resid 54 through 78 Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 91 through 93 No H-bonds generated for 'chain 'M' and resid 91 through 93' Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 139 Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.640A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.679A 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 Processing helix chain 'M' and resid 178 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 Processing helix chain 'M' and resid 263 through 287 Proline residue: M 277 - end of helix Processing helix chain 'M' and resid 293 through 302 Processing helix chain 'L' and resid 6 through 10 removed outlier: 4.059A pdb=" N LYS L 9 " --> pdb=" O PHE L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.569A pdb=" N VAL L 37 " --> pdb=" O GLY L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 113 Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.667A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 Processing helix chain 'L' and resid 152 through 164 Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 Processing helix chain 'L' and resid 225 through 251 removed outlier: 3.684A pdb=" N GLY L 229 " --> pdb=" O ILE L 225 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 266 removed outlier: 3.795A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 271 removed outlier: 3.759A pdb=" N ARG L 270 " --> pdb=" O TRP L 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 32 Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 75 through 79 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' 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 212 through 218 removed outlier: 3.614A pdb=" N PHE H 215 " --> pdb=" O GLY H 212 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL H 218 " --> pdb=" O PHE H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 246 removed outlier: 3.942A pdb=" N GLY H 242 " --> pdb=" O TYR H 238 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR H 243 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 8 Processing helix chain '1' and resid 9 through 14 Processing helix chain '1' and resid 14 through 35 Processing helix chain '2' and resid 10 through 15 removed outlier: 3.817A pdb=" N ALA 2 14 " --> pdb=" O SER 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 43 Processing helix chain '5' and resid 9 through 35 removed outlier: 3.618A pdb=" N THR 5 35 " --> pdb=" O ILE 5 31 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 43 Processing helix chain '3' and resid 9 through 35 Processing helix chain '4' and resid 10 through 43 removed outlier: 3.861A pdb=" N THR 4 23 " --> pdb=" O SER 4 19 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU 4 27 " --> pdb=" O THR 4 23 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU 4 38 " --> pdb=" O VAL 4 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.711A pdb=" N TRP Y 5 " --> pdb=" O TRP Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 4.217A pdb=" N VAL Y 15 " --> pdb=" O ARG Y 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 43 Processing helix chain 'V' and resid 3 through 8 removed outlier: 3.900A pdb=" N LEU V 7 " --> pdb=" O ARG V 3 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 35 Processing helix chain 'X' and resid 11 through 43 Processing helix chain 'T' and resid 3 through 8 removed outlier: 4.040A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 35 removed outlier: 3.786A pdb=" N VAL T 15 " --> pdb=" O ARG T 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 43 Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 14 through 35 removed outlier: 3.596A pdb=" N THR A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 removed outlier: 3.970A pdb=" N ILE B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.778A pdb=" N LEU C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 35 Processing helix chain 'D' and resid 10 through 43 removed outlier: 3.537A pdb=" N ILE D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 8 removed outlier: 3.706A pdb=" N LEU R 7 " --> pdb=" O ARG R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 35 Processing helix chain 'S' and resid 13 through 43 Processing helix chain 'P' and resid 3 through 8 removed outlier: 3.734A pdb=" N LEU P 7 " --> pdb=" O ARG P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 35 Processing helix chain 'Q' and resid 10 through 43 removed outlier: 3.637A pdb=" N ILE Q 20 " --> pdb=" O GLU Q 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 7 Processing helix chain 'N' and resid 9 through 35 removed outlier: 3.522A pdb=" N THR N 35 " --> pdb=" O ILE N 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 43 removed outlier: 3.755A pdb=" N GLU O 16 " --> pdb=" O ALA O 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 8 Processing helix chain 'J' and resid 9 through 35 Processing helix chain 'K' and resid 10 through 43 Processing helix chain 'G' and resid 1 through 7 Processing helix chain 'G' and resid 9 through 35 Processing helix chain 'I' and resid 10 through 43 Processing helix chain 'E' and resid 1 through 7 Processing helix chain 'E' and resid 9 through 35 Processing helix chain 'F' and resid 10 through 43 Processing sheet with id=AA1, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA3, first strand: chain 'H' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'H' and resid 129 through 131 removed outlier: 5.593A pdb=" N VAL H 163 " --> pdb=" O GLU H 181 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU H 181 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU H 165 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP H 169 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA H 175 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 152 through 153 1146 hydrogen bonds defined for protein. 3333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 2.55 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: 6752 1.37 - 1.54: 16447 1.54 - 1.71: 289 1.71 - 1.88: 100 1.88 - 2.05: 128 Bond restraints: 23716 Sorted by residual: bond pdb=" CZ2 QAK M 401 " pdb=" C4 QAK M 401 " ideal model delta sigma weight residual 1.330 1.540 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CE3 QAK M 401 " pdb=" CZ3 QAK M 401 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" NA BCL 4 101 " pdb="MG BCL 4 101 " ideal model delta sigma weight residual 2.170 1.992 0.178 2.40e-02 1.74e+03 5.53e+01 bond pdb=" NA BCL 5 102 " pdb="MG BCL 5 102 " ideal model delta sigma weight residual 2.170 1.992 0.178 2.40e-02 1.74e+03 5.53e+01 bond pdb=" NA BCL M 407 " pdb="MG BCL M 407 " ideal model delta sigma weight residual 2.170 1.993 0.177 2.40e-02 1.74e+03 5.44e+01 ... (remaining 23711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 30492 3.70 - 7.40: 1724 7.40 - 11.10: 248 11.10 - 14.80: 54 14.80 - 18.50: 13 Bond angle restraints: 32531 Sorted by residual: angle pdb=" C1D BCL 5 101 " pdb=" C2D BCL 5 101 " pdb=" CMD BCL 5 101 " ideal model delta sigma weight residual 125.57 140.14 -14.57 1.83e+00 2.99e-01 6.35e+01 angle pdb=" C1D BCL J 102 " pdb=" C2D BCL J 102 " pdb=" CMD BCL J 102 " ideal model delta sigma weight residual 125.57 139.78 -14.21 1.83e+00 2.99e-01 6.04e+01 angle pdb=" C1D BCL Y 101 " pdb=" C2D BCL Y 101 " pdb=" CMD BCL Y 101 " ideal model delta sigma weight residual 125.57 139.50 -13.93 1.83e+00 2.99e-01 5.81e+01 angle pdb=" C1D BCL 1 101 " pdb=" C2D BCL 1 101 " pdb=" CMD BCL 1 101 " ideal model delta sigma weight residual 125.57 139.36 -13.79 1.83e+00 2.99e-01 5.69e+01 angle pdb=" C1D BCL C 100 " pdb=" C2D BCL C 100 " pdb=" CMD BCL C 100 " ideal model delta sigma weight residual 125.57 139.22 -13.65 1.83e+00 2.99e-01 5.57e+01 ... (remaining 32526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 11669 36.00 - 72.00: 587 72.00 - 108.00: 24 108.00 - 144.00: 1 144.00 - 180.00: 27 Dihedral angle restraints: 12308 sinusoidal: 5918 harmonic: 6390 Sorted by residual: dihedral pdb=" C1 BCL 4 101 " pdb=" C2 BCL 4 101 " pdb=" C3 BCL 4 101 " pdb=" C5 BCL 4 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 2 101 " pdb=" C2 BCL 2 101 " pdb=" C3 BCL 2 101 " pdb=" C5 BCL 2 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.08 -179.92 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL L 401 " pdb=" C2 BCL L 401 " pdb=" C3 BCL L 401 " pdb=" C5 BCL L 401 " ideal model delta sinusoidal sigma weight residual -180.00 -0.10 -179.90 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 12305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.029: 3386 1.029 - 2.059: 0 2.059 - 3.088: 0 3.088 - 4.117: 0 4.117 - 5.146: 5 Chirality restraints: 3391 Sorted by residual: chirality pdb=" CE2 QAK M 401 " pdb=" CD2 QAK M 401 " pdb=" CZ2 QAK M 401 " pdb=" C39 QAK M 401 " both_signs ideal model delta sigma weight residual False -2.48 2.67 -5.15 2.00e-01 2.50e+01 6.62e+02 chirality pdb=" C8 BPH M 403 " pdb=" C10 BPH M 403 " pdb=" C7 BPH M 403 " pdb=" C9 BPH M 403 " both_signs ideal model delta sigma weight residual False 2.55 -2.56 5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" C13 BPH M 403 " pdb=" C12 BPH M 403 " pdb=" C14 BPH M 403 " pdb=" C15 BPH M 403 " both_signs ideal model delta sigma weight residual False 2.60 -2.50 5.10 2.00e-01 2.50e+01 6.51e+02 ... (remaining 3388 not shown) Planarity restraints: 3711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL N 101 " -0.395 3.00e-02 1.11e+03 3.24e-01 5.83e+02 pdb=" CBA BCL N 101 " -0.133 3.00e-02 1.11e+03 pdb=" CGA BCL N 101 " 0.089 3.00e-02 1.11e+03 pdb=" O1A BCL N 101 " -0.132 3.00e-02 1.11e+03 pdb=" O2A BCL N 101 " 0.570 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 5 102 " -0.184 3.10e-02 1.04e+03 2.83e-01 4.18e+02 pdb=" C4C BCL 5 102 " -0.188 3.10e-02 1.04e+03 pdb=" CHC BCL 5 102 " -0.095 3.10e-02 1.04e+03 pdb=" CHD BCL 5 102 " -0.093 3.10e-02 1.04e+03 pdb=" NC BCL 5 102 " 0.561 3.10e-02 1.04e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 5 102 " -0.333 3.00e-02 1.11e+03 2.68e-01 4.00e+02 pdb=" CBA BCL 5 102 " -0.196 3.00e-02 1.11e+03 pdb=" CGA BCL 5 102 " 0.082 3.00e-02 1.11e+03 pdb=" O1A BCL 5 102 " -0.004 3.00e-02 1.11e+03 pdb=" O2A BCL 5 102 " 0.451 3.00e-02 1.11e+03 ... (remaining 3708 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 228 2.56 - 3.15: 17525 3.15 - 3.73: 37986 3.73 - 4.32: 57431 4.32 - 4.90: 90038 Nonbonded interactions: 203208 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 408 " model vdw 1.977 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 408 " model vdw 2.054 2.260 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 408 " model vdw 2.073 2.340 nonbonded pdb=" OG SER G 36 " pdb=" O PRO G 44 " model vdw 2.142 3.040 nonbonded pdb=" O THR M 255 " pdb=" NH2 ARG L 104 " model vdw 2.151 3.120 ... (remaining 203203 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 '1' and (resid 2 through 29 or resid 31 through 41)) selection = (chain '3' and (resid 2 through 29 or resid 31 through 41)) selection = (chain '5' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'A' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'C' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'E' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'G' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'J' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'N' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'P' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'R' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'T' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'V' and (resid 2 through 29 or resid 31 through 41)) selection = (chain 'Y' and (resid 2 through 29 or resid 31 through 41)) } ncs_group { reference = (chain '2' and (resid 7 through 25 or resid 27 through 52)) selection = (chain '4' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'B' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'D' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'F' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'I' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'K' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'O' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'Q' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'S' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'U' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'X' and (resid 7 through 25 or resid 27 through 52)) selection = (chain 'Z' and (resid 7 through 25 or resid 27 through 52)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.250 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 : 0.027 0.698 23746 Z= 2.060 Angle : 1.820 18.503 32531 Z= 0.797 Chirality : 0.205 5.146 3391 Planarity : 0.020 0.324 3711 Dihedral : 20.705 179.996 8164 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.19 (0.16), residues: 2164 helix: 0.14 (0.13), residues: 1340 sheet: -1.83 (0.87), residues: 30 loop : -2.37 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 43 TYR 0.015 0.002 TYR M 198 PHE 0.074 0.002 PHE M 216 TRP 0.016 0.002 TRP 5 2 HIS 0.008 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.01987 / 0.88 (23716) covalent geometry : angle 1.82030 / 0.80 (32531) hydrogen bonds : bond 0.11021 / 7.17 ( 1146) hydrogen bonds : angle 5.02640 / 3.60 ( 3333) Misc. bond : bond 0.52447 / 31.72 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 46 PHE cc_start: 0.8600 (m-80) cc_final: 0.8397 (m-80) REVERT: M 39 TRP cc_start: 0.7874 (m100) cc_final: 0.7487 (m-10) REVERT: M 218 MET cc_start: 0.9337 (mtp) cc_final: 0.8991 (mtp) REVERT: L 175 MET cc_start: 0.9142 (mtm) cc_final: 0.8804 (mtp) REVERT: 5 38 PHE cc_start: 0.8653 (m-80) cc_final: 0.8420 (m-80) REVERT: Z 50 THR cc_start: 0.8411 (p) cc_final: 0.8100 (m) REVERT: T 4 ILE cc_start: 0.9097 (tp) cc_final: 0.8845 (tp) REVERT: A 3 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7017 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.7371 time to fit residues: 267.8243 Evaluate side-chains 247 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN M 47 GLN M 187 ASN L 64 GLN L 160 ASN L 267 ASN L 271 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 18 HIS Z 18 HIS X 18 HIS ** U 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 HIS S 18 HIS Q 18 HIS O 18 HIS K 18 HIS I 18 HIS F 18 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.057277 restraints weight = 170855.341| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.50 r_work: 0.2789 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23746 Z= 0.157 Angle : 0.795 15.637 32531 Z= 0.314 Chirality : 0.041 0.292 3391 Planarity : 0.005 0.076 3711 Dihedral : 22.801 179.993 4302 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.34 % Allowed : 11.36 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.36 (0.18), residues: 2164 helix: 1.47 (0.13), residues: 1341 sheet: -1.52 (0.89), residues: 30 loop : -1.92 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 45 TYR 0.011 0.001 TYR M 198 PHE 0.033 0.002 PHE M 216 TRP 0.014 0.001 TRP M 252 HIS 0.006 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (23716) covalent geometry : angle 0.79488 / 0.31 (32531) hydrogen bonds : bond 0.04473 / 2.92 ( 1146) hydrogen bonds : angle 4.06672 / 2.91 ( 3333) Misc. bond : bond 0.00217 / 0.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 6 ASN cc_start: 0.7782 (t0) cc_final: 0.7572 (t160) REVERT: M 39 TRP cc_start: 0.8004 (m100) cc_final: 0.7422 (m-10) REVERT: M 218 MET cc_start: 0.9482 (mtp) cc_final: 0.9179 (mtp) REVERT: L 175 MET cc_start: 0.9320 (mtm) cc_final: 0.9005 (mtt) REVERT: H 202 PHE cc_start: 0.6262 (OUTLIER) cc_final: 0.6022 (p90) REVERT: 5 38 PHE cc_start: 0.8772 (m-80) cc_final: 0.8513 (m-80) REVERT: 4 11 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7955 (mm-30) REVERT: 4 15 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6407 (pttp) REVERT: Z 15 LYS cc_start: 0.8560 (mtpm) cc_final: 0.8310 (mttm) REVERT: Z 48 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8686 (mttp) REVERT: Z 50 THR cc_start: 0.8488 (p) cc_final: 0.8099 (m) REVERT: V 9 ASP cc_start: 0.8589 (p0) cc_final: 0.8360 (p0) REVERT: A 12 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8038 (mpt-90) REVERT: F 48 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8484 (mttp) outliers start: 43 outliers final: 13 residues processed: 302 average time/residue: 0.6509 time to fit residues: 223.1950 Evaluate side-chains 265 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 5 residue 28 ILE Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 15 LYS Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain K residue 27 LEU Chi-restraints excluded: chain F residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 174 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 10 GLN M 47 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 HIS B 18 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057405 restraints weight = 156043.435| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.39 r_work: 0.2793 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23746 Z= 0.157 Angle : 0.753 13.981 32531 Z= 0.302 Chirality : 0.040 0.268 3391 Planarity : 0.005 0.074 3711 Dihedral : 21.868 179.975 4302 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.55 % Allowed : 13.32 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.87 (0.18), residues: 2164 helix: 1.88 (0.14), residues: 1353 sheet: -1.51 (0.87), residues: 30 loop : -1.80 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 45 TYR 0.012 0.001 TYR M 198 PHE 0.033 0.001 PHE X 25 TRP 0.014 0.001 TRP T 5 HIS 0.005 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (23716) covalent geometry : angle 0.75268 / 0.30 (32531) hydrogen bonds : bond 0.04373 / 2.84 ( 1146) hydrogen bonds : angle 3.95355 / 2.85 ( 3333) Misc. bond : bond 0.00247 / 0.16 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 274 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 39 TRP cc_start: 0.7953 (m100) cc_final: 0.7361 (m-10) REVERT: M 218 MET cc_start: 0.9485 (mtp) cc_final: 0.9191 (mtp) REVERT: L 175 MET cc_start: 0.9356 (mtm) cc_final: 0.9056 (mtt) REVERT: H 202 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.6037 (p90) REVERT: 5 38 PHE cc_start: 0.8733 (m-80) cc_final: 0.8473 (m-80) REVERT: Z 48 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8664 (mttp) REVERT: Z 50 THR cc_start: 0.8439 (p) cc_final: 0.8056 (m) REVERT: A 3 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7279 (ptp90) REVERT: A 12 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7931 (mpt-90) REVERT: Q 10 SER cc_start: 0.8847 (p) cc_final: 0.8522 (m) outliers start: 47 outliers final: 18 residues processed: 290 average time/residue: 0.6192 time to fit residues: 205.6309 Evaluate side-chains 270 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 84 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 48 LYS Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain S residue 9 LEU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN M 47 GLN H 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.076815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057562 restraints weight = 176251.730| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.54 r_work: 0.2797 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23746 Z= 0.145 Angle : 0.734 13.705 32531 Z= 0.294 Chirality : 0.039 0.213 3391 Planarity : 0.005 0.075 3711 Dihedral : 21.287 179.997 4302 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.50 % Allowed : 15.16 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.14 (0.18), residues: 2164 helix: 2.09 (0.13), residues: 1352 sheet: -1.34 (0.88), residues: 30 loop : -1.68 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 45 TYR 0.011 0.001 TYR M 198 PHE 0.035 0.001 PHE X 25 TRP 0.015 0.001 TRP V 2 HIS 0.005 0.001 HIS M 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (23716) covalent geometry : angle 0.73433 / 0.29 (32531) hydrogen bonds : bond 0.04193 / 2.73 ( 1146) hydrogen bonds : angle 3.87779 / 2.79 ( 3333) Misc. bond : bond 0.00226 / 0.15 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 39 TRP cc_start: 0.7967 (m100) cc_final: 0.7357 (m-10) REVERT: M 218 MET cc_start: 0.9508 (mtp) cc_final: 0.9244 (mtp) REVERT: L 175 MET cc_start: 0.9377 (mtm) cc_final: 0.9077 (mtt) REVERT: H 202 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5893 (p90) REVERT: 5 31 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8855 (tp) REVERT: 5 38 PHE cc_start: 0.8746 (m-80) cc_final: 0.8499 (m-80) REVERT: 6 11 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8160 (tp30) REVERT: 4 18 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.6629 (t-170) REVERT: 4 27 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7575 (mt) REVERT: Z 48 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8659 (mttp) REVERT: Z 50 THR cc_start: 0.8292 (p) cc_final: 0.7936 (m) REVERT: A 3 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7256 (ptp90) REVERT: A 12 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7969 (mpt-90) REVERT: K 6 ILE cc_start: 0.6964 (tp) cc_final: 0.6716 (tp) outliers start: 46 outliers final: 19 residues processed: 291 average time/residue: 0.6285 time to fit residues: 210.1436 Evaluate side-chains 271 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 84 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 18 HIS Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain 4 residue 48 LYS Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 114 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055909 restraints weight = 206467.361| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.75 r_work: 0.2743 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23746 Z= 0.218 Angle : 0.798 16.494 32531 Z= 0.322 Chirality : 0.042 0.193 3391 Planarity : 0.005 0.076 3711 Dihedral : 21.340 179.998 4302 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.93 % Allowed : 15.60 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.16 (0.18), residues: 2164 helix: 2.07 (0.13), residues: 1346 sheet: -1.22 (0.89), residues: 30 loop : -1.54 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG V 45 TYR 0.015 0.001 TYR M 198 PHE 0.036 0.002 PHE X 25 TRP 0.015 0.001 TRP T 5 HIS 0.008 0.002 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (23716) covalent geometry : angle 0.79812 / 0.32 (32531) hydrogen bonds : bond 0.04614 / 2.99 ( 1146) hydrogen bonds : angle 3.97802 / 2.86 ( 3333) Misc. bond : bond 0.00341 / 0.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 39 TRP cc_start: 0.7952 (m100) cc_final: 0.7371 (m-10) REVERT: M 218 MET cc_start: 0.9541 (mtp) cc_final: 0.9202 (mtp) REVERT: L 83 GLU cc_start: 0.8847 (mp0) cc_final: 0.8472 (mp0) REVERT: L 175 MET cc_start: 0.9443 (mtm) cc_final: 0.9148 (mtt) REVERT: H 202 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.6106 (p90) REVERT: 5 38 PHE cc_start: 0.8745 (m-80) cc_final: 0.8511 (m-80) REVERT: 6 11 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7883 (tp30) REVERT: 4 27 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7585 (mt) REVERT: Y 3 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8343 (tpp-160) REVERT: Y 11 ARG cc_start: 0.7703 (tmm160) cc_final: 0.7324 (ttm-80) REVERT: Z 15 LYS cc_start: 0.8674 (mttm) cc_final: 0.8413 (mmmt) REVERT: Z 48 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8673 (mttm) REVERT: Z 50 THR cc_start: 0.8386 (p) cc_final: 0.8048 (m) REVERT: A 3 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7495 (ptp90) REVERT: A 12 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7949 (mpt-90) REVERT: P 3 ARG cc_start: 0.8983 (mtt-85) cc_final: 0.8707 (mtt90) outliers start: 54 outliers final: 26 residues processed: 279 average time/residue: 0.6219 time to fit residues: 198.9585 Evaluate side-chains 271 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 84 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain 4 residue 48 LYS Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain K residue 9 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 90 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 198 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 37 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057901 restraints weight = 159786.301| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.43 r_work: 0.2811 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23746 Z= 0.133 Angle : 0.734 13.005 32531 Z= 0.294 Chirality : 0.039 0.174 3391 Planarity : 0.005 0.076 3711 Dihedral : 20.891 179.967 4302 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.28 % Allowed : 16.85 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.34 (0.18), residues: 2164 helix: 2.26 (0.13), residues: 1344 sheet: -1.13 (0.89), residues: 30 loop : -1.57 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG V 45 TYR 0.010 0.001 TYR M 198 PHE 0.033 0.001 PHE X 25 TRP 0.020 0.001 TRP 3 2 HIS 0.007 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (23716) covalent geometry : angle 0.73389 / 0.29 (32531) hydrogen bonds : bond 0.04133 / 2.69 ( 1146) hydrogen bonds : angle 3.88265 / 2.79 ( 3333) Misc. bond : bond 0.00202 / 0.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 261 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 218 MET cc_start: 0.9509 (mtp) cc_final: 0.9231 (mtp) REVERT: L 83 GLU cc_start: 0.8739 (mp0) cc_final: 0.8388 (mp0) REVERT: L 175 MET cc_start: 0.9362 (mtm) cc_final: 0.9072 (mtt) REVERT: H 202 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.6032 (p90) REVERT: 5 38 PHE cc_start: 0.8670 (m-80) cc_final: 0.8431 (m-80) REVERT: 6 11 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8001 (tp30) REVERT: 4 27 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (mt) REVERT: Y 3 ARG cc_start: 0.8593 (mpt-90) cc_final: 0.8280 (tpp-160) REVERT: Z 20 ILE cc_start: 0.8797 (mm) cc_final: 0.8583 (tp) REVERT: A 3 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7495 (mtm-85) REVERT: A 4 ILE cc_start: 0.8640 (tp) cc_final: 0.8336 (tt) REVERT: A 12 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7904 (mpt-90) outliers start: 42 outliers final: 19 residues processed: 279 average time/residue: 0.6495 time to fit residues: 207.6030 Evaluate side-chains 267 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 18 HIS Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain X residue 27 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain N residue 11 ARG Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain K residue 9 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.057415 restraints weight = 172180.628| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.52 r_work: 0.2797 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23746 Z= 0.152 Angle : 0.745 13.361 32531 Z= 0.300 Chirality : 0.040 0.172 3391 Planarity : 0.005 0.074 3711 Dihedral : 20.665 179.974 4302 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.07 % Allowed : 17.93 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.42 (0.18), residues: 2164 helix: 2.30 (0.13), residues: 1348 sheet: -1.28 (0.85), residues: 32 loop : -1.50 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 45 TYR 0.011 0.001 TYR M 198 PHE 0.033 0.001 PHE X 25 TRP 0.016 0.001 TRP 3 2 HIS 0.008 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (23716) covalent geometry : angle 0.74508 / 0.30 (32531) hydrogen bonds : bond 0.04205 / 2.74 ( 1146) hydrogen bonds : angle 3.86583 / 2.78 ( 3333) Misc. bond : bond 0.00252 / 0.17 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: M 218 MET cc_start: 0.9517 (mtp) cc_final: 0.9256 (mtp) REVERT: L 83 GLU cc_start: 0.8769 (mp0) cc_final: 0.8414 (mp0) REVERT: L 175 MET cc_start: 0.9402 (mtm) cc_final: 0.9119 (mtt) REVERT: H 202 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5990 (p90) REVERT: 5 38 PHE cc_start: 0.8688 (m-80) cc_final: 0.8480 (m-80) REVERT: 6 11 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7827 (tp30) REVERT: 4 27 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7635 (mt) REVERT: Y 11 ARG cc_start: 0.7646 (tmm160) cc_final: 0.7276 (ttm-80) REVERT: Z 15 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8535 (mmtt) REVERT: Z 20 ILE cc_start: 0.8814 (mm) cc_final: 0.8606 (tp) REVERT: V 3 ARG cc_start: 0.8249 (mpp80) cc_final: 0.8007 (mpp80) REVERT: A 3 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7437 (mtm-85) REVERT: A 4 ILE cc_start: 0.8674 (tp) cc_final: 0.8325 (tt) REVERT: A 12 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7941 (mpt-90) outliers start: 38 outliers final: 20 residues processed: 277 average time/residue: 0.6692 time to fit residues: 212.3651 Evaluate side-chains 269 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 84 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 18 HIS Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain X residue 27 LEU Chi-restraints excluded: chain U residue 13 GLU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 79 optimal weight: 0.0010 chunk 109 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.077308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057924 restraints weight = 184492.217| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.60 r_work: 0.2806 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23746 Z= 0.135 Angle : 0.733 12.895 32531 Z= 0.295 Chirality : 0.039 0.194 3391 Planarity : 0.005 0.075 3711 Dihedral : 20.394 179.973 4302 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.79 % Allowed : 18.32 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.56 (0.18), residues: 2164 helix: 2.41 (0.13), residues: 1340 sheet: -1.21 (0.85), residues: 32 loop : -1.40 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 45 TYR 0.010 0.001 TYR M 38 PHE 0.032 0.001 PHE X 25 TRP 0.023 0.001 TRP 3 2 HIS 0.008 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (23716) covalent geometry : angle 0.73289 / 0.29 (32531) hydrogen bonds : bond 0.04063 / 2.65 ( 1146) hydrogen bonds : angle 3.82492 / 2.74 ( 3333) Misc. bond : bond 0.00213 / 0.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: M 65 PHE cc_start: 0.8195 (m-80) cc_final: 0.7825 (t80) REVERT: M 218 MET cc_start: 0.9511 (mtp) cc_final: 0.9234 (mtp) REVERT: L 83 GLU cc_start: 0.8776 (mp0) cc_final: 0.8453 (mp0) REVERT: L 175 MET cc_start: 0.9388 (mtm) cc_final: 0.9096 (mtt) REVERT: H 202 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5916 (p90) REVERT: 5 38 PHE cc_start: 0.8726 (m-80) cc_final: 0.8514 (m-80) REVERT: 6 11 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7851 (tp30) REVERT: 4 11 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7650 (mm-30) REVERT: 4 27 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7585 (mt) REVERT: Z 15 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8139 (mptp) REVERT: Z 20 ILE cc_start: 0.8821 (mm) cc_final: 0.8594 (tp) REVERT: A 4 ILE cc_start: 0.8656 (tp) cc_final: 0.8291 (tt) REVERT: A 12 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7953 (mpt-90) REVERT: N 11 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7604 (ttp-110) outliers start: 33 outliers final: 18 residues processed: 275 average time/residue: 0.6689 time to fit residues: 210.5858 Evaluate side-chains 264 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 18 HIS Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain X residue 27 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 15 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN H 11 GLN H 146 ASN ** 4 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057389 restraints weight = 166051.962| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.49 r_work: 0.2795 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23746 Z= 0.159 Angle : 0.759 13.292 32531 Z= 0.310 Chirality : 0.040 0.221 3391 Planarity : 0.005 0.075 3711 Dihedral : 20.335 179.984 4302 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.63 % Allowed : 18.91 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.49 (0.18), residues: 2164 helix: 2.38 (0.13), residues: 1337 sheet: -1.15 (0.84), residues: 32 loop : -1.48 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG V 45 TYR 0.012 0.001 TYR M 198 PHE 0.034 0.001 PHE X 25 TRP 0.016 0.001 TRP 3 2 HIS 0.007 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (23716) covalent geometry : angle 0.75911 / 0.31 (32531) hydrogen bonds : bond 0.04233 / 2.75 ( 1146) hydrogen bonds : angle 3.86171 / 2.76 ( 3333) Misc. bond : bond 0.00260 / 0.17 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: M 65 PHE cc_start: 0.8215 (m-80) cc_final: 0.7808 (t80) REVERT: M 218 MET cc_start: 0.9527 (mtp) cc_final: 0.9257 (mtp) REVERT: L 83 GLU cc_start: 0.8793 (mp0) cc_final: 0.8458 (mp0) REVERT: L 175 MET cc_start: 0.9404 (mtm) cc_final: 0.9104 (mtt) REVERT: H 181 GLU cc_start: 0.8045 (tp30) cc_final: 0.7803 (tp30) REVERT: H 202 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5911 (p90) REVERT: 5 38 PHE cc_start: 0.8691 (m-80) cc_final: 0.8452 (m-80) REVERT: 6 11 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7856 (tp30) REVERT: 4 15 LYS cc_start: 0.6600 (ptpp) cc_final: 0.6220 (ptpp) REVERT: Y 11 ARG cc_start: 0.7660 (tmm160) cc_final: 0.7318 (ttm-80) REVERT: Z 15 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8261 (mmmt) REVERT: Z 20 ILE cc_start: 0.8813 (mm) cc_final: 0.8591 (tp) REVERT: A 4 ILE cc_start: 0.8695 (tp) cc_final: 0.8373 (tt) REVERT: A 12 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7957 (mpt-90) REVERT: N 11 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7531 (ttp-110) outliers start: 30 outliers final: 22 residues processed: 264 average time/residue: 0.6814 time to fit residues: 205.4350 Evaluate side-chains 268 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 84 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 10 SER Chi-restraints excluded: chain 4 residue 18 HIS Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain X residue 27 LEU Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain K residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 183 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN M 10 GLN ** 4 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057474 restraints weight = 206396.546| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.74 r_work: 0.2791 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23746 Z= 0.146 Angle : 0.754 12.941 32531 Z= 0.308 Chirality : 0.040 0.342 3391 Planarity : 0.005 0.076 3711 Dihedral : 20.201 179.985 4302 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.68 % Allowed : 19.02 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.53 (0.18), residues: 2164 helix: 2.41 (0.13), residues: 1336 sheet: -1.08 (0.85), residues: 32 loop : -1.45 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 45 TYR 0.012 0.001 TYR M 198 PHE 0.037 0.001 PHE 4 25 TRP 0.017 0.001 TRP 3 5 HIS 0.010 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (23716) covalent geometry : angle 0.75414 / 0.31 (32531) hydrogen bonds : bond 0.04137 / 2.69 ( 1146) hydrogen bonds : angle 3.85340 / 2.76 ( 3333) Misc. bond : bond 0.00229 / 0.15 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4328 Ramachandran restraints generated. 2164 Oldfield, 0 Emsley, 2164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 65 PHE cc_start: 0.8222 (m-80) cc_final: 0.7835 (t80) REVERT: M 218 MET cc_start: 0.9518 (mtp) cc_final: 0.9242 (mtp) REVERT: L 83 GLU cc_start: 0.8774 (mp0) cc_final: 0.8453 (mp0) REVERT: L 175 MET cc_start: 0.9407 (mtm) cc_final: 0.9057 (mtt) REVERT: H 202 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5926 (p90) REVERT: 5 38 PHE cc_start: 0.8695 (m-80) cc_final: 0.8446 (m-80) REVERT: 6 11 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7781 (tp30) REVERT: Z 15 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8267 (mmmt) REVERT: Z 20 ILE cc_start: 0.8823 (mm) cc_final: 0.8595 (tp) REVERT: A 11 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8346 (mtt90) REVERT: A 12 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7984 (mpt-90) REVERT: N 11 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7524 (ttp-110) REVERT: F 15 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8863 (mptm) outliers start: 31 outliers final: 24 residues processed: 262 average time/residue: 0.6886 time to fit residues: 206.1178 Evaluate side-chains 267 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 84 VAL Chi-restraints excluded: chain M residue 79 VAL Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 185 SER Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 202 PHE Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 2 residue 9 LEU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 6 residue 33 VAL Chi-restraints excluded: chain 4 residue 18 HIS Chi-restraints excluded: chain 4 residue 50 THR Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 16 LEU Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain X residue 27 LEU Chi-restraints excluded: chain A residue 3 ARG Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain F residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 103 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 174 optimal weight: 0.0970 chunk 154 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 chunk 6 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.078142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058789 restraints weight = 176119.962| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.58 r_work: 0.2833 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23746 Z= 0.125 Angle : 0.730 12.352 32531 Z= 0.299 Chirality : 0.039 0.258 3391 Planarity : 0.005 0.074 3711 Dihedral : 19.920 179.986 4302 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.41 % Allowed : 19.40 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.71 (0.18), residues: 2164 helix: 2.59 (0.13), residues: 1322 sheet: -0.97 (0.86), residues: 32 loop : -1.36 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG V 45 TYR 0.010 0.001 TYR M 18 PHE 0.036 0.001 PHE 4 25 TRP 0.020 0.001 TRP 3 2 HIS 0.008 0.001 HIS 4 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (23716) covalent geometry : angle 0.73035 / 0.30 (32531) hydrogen bonds : bond 0.03935 / 2.56 ( 1146) hydrogen bonds : angle 3.80124 / 2.72 ( 3333) Misc. bond : bond 0.00171 / 0.12 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7798.94 seconds wall clock time: 133 minutes 51.77 seconds (8031.77 seconds total)