Starting phenix.real_space_refine on Fri Feb 23 03:19:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb9_31875/02_2024/7vb9_31875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb9_31875/02_2024/7vb9_31875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb9_31875/02_2024/7vb9_31875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb9_31875/02_2024/7vb9_31875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb9_31875/02_2024/7vb9_31875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vb9_31875/02_2024/7vb9_31875_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 11 5.49 5 Mg 51 5.21 5 S 143 5.16 5 C 25539 2.51 5 N 5208 2.21 5 O 5520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 104": "OE1" <-> "OE2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "L ARG 231": "NH1" <-> "NH2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ARG 253": "NH1" <-> "NH2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H GLU 180": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 230": "OE1" <-> "OE2" Residue "H GLU 258": "OE1" <-> "OE2" Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "G TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 14": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "N TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "7 ARG 14": "NH1" <-> "NH2" Residue "8 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 53": "NH1" <-> "NH2" Residue "0 TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "l PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 217": "NH1" <-> "NH2" Residue "l ARG 231": "NH1" <-> "NH2" Residue "m ARG 87": "NH1" <-> "NH2" Residue "m GLU 95": "OE1" <-> "OE2" Residue "m ARG 136": "NH1" <-> "NH2" Residue "m ARG 253": "NH1" <-> "NH2" Residue "h TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 89": "NH1" <-> "NH2" Residue "h ARG 118": "NH1" <-> "NH2" Residue "h ARG 177": "NH1" <-> "NH2" Residue "h GLU 180": "OE1" <-> "OE2" Residue "h GLU 224": "OE1" <-> "OE2" Residue "h GLU 230": "OE1" <-> "OE2" Residue "h GLU 258": "OE1" <-> "OE2" Residue "a TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "b TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "e TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 14": "NH1" <-> "NH2" Residue "f TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 53": "NH1" <-> "NH2" Residue "g ASP 6": "OD1" <-> "OD2" Residue "g TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "j TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 14": "NH1" <-> "NH2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "n TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 14": "NH1" <-> "NH2" Residue "o TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "p TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 53": "NH1" <-> "NH2" Residue "r TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 14": "NH1" <-> "NH2" Residue "s ARG 53": "NH1" <-> "NH2" Residue "t TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 14": "NH1" <-> "NH2" Residue "u ARG 53": "NH1" <-> "NH2" Residue "v TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 15": "NH1" <-> "NH2" Residue "w ARG 53": "NH1" <-> "NH2" Residue "x TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 15": "NH1" <-> "NH2" Residue "y ARG 53": "NH1" <-> "NH2" Residue "z TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 53": "NH1" <-> "NH2" Residue "4 ARG 46": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "aa TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 14": "NH1" <-> "NH2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "ab TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36474 Number of models: 1 Model: "" Number of chains: 100 Chain: "L" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2132 Classifications: {'peptide': 268} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 254} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1972 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 362 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "N" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 500 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain: "l" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "h" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1972 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 236} Chain: "a" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "b" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "d" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "e" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "f" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "g" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "j" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "k" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "n" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "o" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "p" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 320 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "r" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "s" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "t" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "u" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "v" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "w" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "x" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "y" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "z" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 312 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Chain: "5" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 297 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "6" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "aa" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "ab" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "c" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 529 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "L" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 336 Unusual residues: {'BCL': 3, 'BPH': 2, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'BCL:plan_0002': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'BCL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 155 Unusual residues: {'BCL': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "8" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 312 Unusual residues: {'BCL': 2, 'BPH': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 319 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "h" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "a" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "b" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "r" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'SPO': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Chain: "aa" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ab" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.30, per 1000 atoms: 0.50 Number of scatterers: 36474 At special positions: 0 Unit cell: (217.895, 130.903, 121.789, 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 2 26.01 S 143 16.00 P 11 15.00 Mg 51 11.99 O 5520 8.00 N 5208 7.00 C 25539 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 - 3.50 Amino acid : False - 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=47, symmetry=0 Number of additional bonds: simple=47, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.15 Conformation dependent library (CDL) restraints added in 4.9 seconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 8 sheets defined 64.5% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 86 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.639A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 163 Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 228 through 249 Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.853A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 40 No H-bonds generated for 'chain 'M' and resid 37 through 40' Processing helix chain 'M' and resid 54 through 78 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 113 through 140 removed outlier: 3.513A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 4.393A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 4.102A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.963A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 259 Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'F' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR F 5 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'I' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR I 5 " --> pdb=" O SER I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 50 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain '7' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR 7 5 " --> pdb=" O SER 7 2 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 37 Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 2 through 9 removed outlier: 4.081A pdb=" N TYR 9 5 " --> pdb=" O SER 9 2 " (cutoff:3.500A) Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 51 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 15 through 54 removed outlier: 4.028A pdb=" N ALA C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 9 Processing helix chain 'l' and resid 32 through 56 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.672A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 4.247A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 171 through 198 removed outlier: 3.582A pdb=" N ALA l 176 " --> pdb=" O ALA l 172 " (cutoff:3.500A) Processing helix chain 'l' and resid 209 through 219 Processing helix chain 'l' and resid 226 through 249 Processing helix chain 'l' and resid 260 through 267 removed outlier: 4.073A pdb=" N TRP l 265 " --> pdb=" O ASP l 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP l 266 " --> pdb=" O TRP l 262 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL l 267 " --> pdb=" O TRP l 263 " (cutoff:3.500A) Processing helix chain 'm' and resid 37 through 40 No H-bonds generated for 'chain 'm' and resid 37 through 40' Processing helix chain 'm' and resid 54 through 78 Processing helix chain 'm' and resid 82 through 87 Processing helix chain 'm' and resid 99 through 101 No H-bonds generated for 'chain 'm' and resid 99 through 101' Processing helix chain 'm' and resid 113 through 140 removed outlier: 3.510A pdb=" N LEU m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 161 Processing helix chain 'm' and resid 163 through 168 Processing helix chain 'm' and resid 171 through 173 No H-bonds generated for 'chain 'm' and resid 171 through 173' Processing helix chain 'm' and resid 179 through 192 Processing helix chain 'm' and resid 196 through 198 No H-bonds generated for 'chain 'm' and resid 196 through 198' Processing helix chain 'm' and resid 200 through 225 Processing helix chain 'm' and resid 227 through 229 No H-bonds generated for 'chain 'm' and resid 227 through 229' Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 Processing helix chain 'm' and resid 264 through 286 removed outlier: 4.392A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 300 Processing helix chain 'h' and resid 12 through 36 Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 134 through 136 No H-bonds generated for 'chain 'h' and resid 134 through 136' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 215 removed outlier: 4.101A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 3.963A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 251 through 259 Processing helix chain 'a' and resid 4 through 9 Processing helix chain 'a' and resid 13 through 37 Processing helix chain 'a' and resid 43 through 50 Processing helix chain 'b' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 9 removed outlier: 4.081A pdb=" N TYR d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 37 Processing helix chain 'd' and resid 43 through 50 Processing helix chain 'e' and resid 14 through 45 Processing helix chain 'f' and resid 2 through 9 removed outlier: 4.083A pdb=" N TYR f 5 " --> pdb=" O SER f 2 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 37 Processing helix chain 'f' and resid 43 through 50 Processing helix chain 'g' and resid 14 through 45 Processing helix chain 'i' and resid 2 through 9 removed outlier: 4.081A pdb=" N TYR i 5 " --> pdb=" O SER i 2 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 37 Processing helix chain 'i' and resid 43 through 50 Processing helix chain 'j' and resid 14 through 45 Processing helix chain 'k' and resid 2 through 9 removed outlier: 4.081A pdb=" N TYR k 5 " --> pdb=" O SER k 2 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 37 Processing helix chain 'k' and resid 43 through 50 Processing helix chain 'n' and resid 14 through 45 Processing helix chain 'o' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR o 5 " --> pdb=" O SER o 2 " (cutoff:3.500A) Processing helix chain 'o' and resid 13 through 37 Processing helix chain 'o' and resid 43 through 50 Processing helix chain 'p' and resid 14 through 45 Processing helix chain 'q' and resid 2 through 9 removed outlier: 4.081A pdb=" N TYR q 5 " --> pdb=" O SER q 2 " (cutoff:3.500A) Processing helix chain 'q' and resid 13 through 37 Processing helix chain 'q' and resid 43 through 50 Processing helix chain 'r' and resid 14 through 45 Processing helix chain 's' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR s 5 " --> pdb=" O SER s 2 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 37 Processing helix chain 's' and resid 43 through 50 Processing helix chain 't' and resid 14 through 45 Processing helix chain 'u' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR u 5 " --> pdb=" O SER u 2 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 37 Processing helix chain 'u' and resid 43 through 50 Processing helix chain 'v' and resid 14 through 45 Processing helix chain 'w' and resid 13 through 37 Processing helix chain 'w' and resid 43 through 50 Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 14 through 37 Processing helix chain 'y' and resid 43 through 50 Processing helix chain 'z' and resid 14 through 45 Processing helix chain '5' and resid 14 through 37 Processing helix chain '5' and resid 43 through 50 Processing helix chain '4' and resid 14 through 45 Processing helix chain '6' and resid 2 through 9 removed outlier: 4.080A pdb=" N TYR 6 5 " --> pdb=" O SER 6 2 " (cutoff:3.500A) Processing helix chain '6' and resid 13 through 37 Processing helix chain 'aa' and resid 14 through 45 Processing helix chain 'Q' and resid 2 through 9 removed outlier: 4.082A pdb=" N TYR Q 5 " --> pdb=" O SER Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'ab' and resid 14 through 45 Processing helix chain 'c' and resid 10 through 12 No H-bonds generated for 'chain 'c' and resid 10 through 12' Processing helix chain 'c' and resid 15 through 54 removed outlier: 4.396A pdb=" N ALA c 24 " --> pdb=" O ARG c 20 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.475A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.870A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 196 through 198 removed outlier: 7.528A pdb=" N VAL H 205 " --> pdb=" O PRO H 152 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 154 " --> pdb=" O VAL H 205 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 66 removed outlier: 4.475A pdb=" N GLY h 71 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.869A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 196 through 198 removed outlier: 7.529A pdb=" N VAL h 205 " --> pdb=" O PRO h 152 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG h 154 " --> pdb=" O VAL h 205 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) 1867 hydrogen bonds defined for protein. 5376 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: 11.18 Time building geometry restraints manager: 15.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 9639 1.34 - 1.55: 27383 1.55 - 1.75: 385 1.75 - 1.96: 277 1.96 - 2.17: 204 Bond restraints: 37888 Sorted by residual: bond pdb=" C37 SPO t 102 " pdb=" C38 SPO t 102 " ideal model delta sigma weight residual 1.336 1.542 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C37 SPO p 102 " pdb=" C38 SPO p 102 " ideal model delta sigma weight residual 1.336 1.541 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C37 SPO b 101 " pdb=" C38 SPO b 101 " ideal model delta sigma weight residual 1.336 1.540 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C37 SPO 9 101 " pdb=" C38 SPO 9 101 " ideal model delta sigma weight residual 1.336 1.539 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C37 SPO D 102 " pdb=" C38 SPO D 102 " ideal model delta sigma weight residual 1.336 1.538 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 37883 not shown) Histogram of bond angle deviations from ideal: 84.69 - 100.12: 211 100.12 - 115.56: 24824 115.56 - 130.99: 26358 130.99 - 146.42: 579 146.42 - 161.85: 103 Bond angle restraints: 52075 Sorted by residual: angle pdb=" C16 BCL Q 602 " pdb=" C17 BCL Q 602 " pdb=" C18 BCL Q 602 " ideal model delta sigma weight residual 113.16 156.57 -43.41 5.53e+00 3.27e-02 6.17e+01 angle pdb=" C12 SPOab 102 " pdb=" C14 SPOab 102 " pdb=" C15 SPOab 102 " ideal model delta sigma weight residual 127.13 106.40 20.73 3.00e+00 1.11e-01 4.77e+01 angle pdb=" C10 SPO G 102 " pdb=" C9 SPO G 102 " pdb=" C7 SPO G 102 " ideal model delta sigma weight residual 127.14 106.85 20.29 3.00e+00 1.11e-01 4.58e+01 angle pdb=" C11 CDL m 406 " pdb=" CA5 CDL m 406 " pdb=" OA6 CDL m 406 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C17 SPO 0 101 " pdb=" C19 SPO 0 101 " pdb=" C20 SPO 0 101 " ideal model delta sigma weight residual 127.83 107.74 20.09 3.00e+00 1.11e-01 4.48e+01 ... (remaining 52070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 19469 35.71 - 71.42: 823 71.42 - 107.13: 78 107.13 - 142.83: 6 142.83 - 178.54: 2 Dihedral angle restraints: 20378 sinusoidal: 9386 harmonic: 10992 Sorted by residual: dihedral pdb=" C31 U10 l 303 " pdb=" C32 U10 l 303 " pdb=" C33 U10 l 303 " pdb=" C34 U10 l 303 " ideal model delta sinusoidal sigma weight residual -97.88 80.66 -178.54 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C37 U10 l 303 " pdb=" C38 U10 l 303 " pdb=" C39 U10 l 303 " pdb=" C41 U10 l 303 " ideal model delta sinusoidal sigma weight residual -5.63 -154.19 148.56 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C11 U10 l 303 " pdb=" C8 U10 l 303 " pdb=" C9 U10 l 303 " pdb=" C7 U10 l 303 " ideal model delta sinusoidal sigma weight residual -179.95 -52.13 -127.82 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 20375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4430 0.061 - 0.122: 649 0.122 - 0.183: 42 0.183 - 0.244: 7 0.244 - 0.304: 3 Chirality restraints: 5131 Sorted by residual: chirality pdb=" CG LEU c 19 " pdb=" CB LEU c 19 " pdb=" CD1 LEU c 19 " pdb=" CD2 LEU c 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU L 21 " pdb=" CB LEU L 21 " pdb=" CD1 LEU L 21 " pdb=" CD2 LEU L 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2C BPH l 302 " pdb=" C1C BPH l 302 " pdb=" C3C BPH l 302 " pdb=" CMC BPH l 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.53 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 5128 not shown) Planarity restraints: 6387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 SPO w 102 " 0.310 2.00e-02 2.50e+03 3.20e-01 1.28e+03 pdb=" C22 SPO w 102 " -0.275 2.00e-02 2.50e+03 pdb=" C23 SPO w 102 " -0.442 2.00e-02 2.50e+03 pdb=" C24 SPO w 102 " 0.026 2.00e-02 2.50e+03 pdb=" C25 SPO w 102 " 0.381 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 SPO 0 101 " 0.241 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C22 SPO 0 101 " -0.522 2.00e-02 2.50e+03 pdb=" C23 SPO 0 101 " 0.330 2.00e-02 2.50e+03 pdb=" C24 SPO 0 101 " -0.058 2.00e-02 2.50e+03 pdb=" C25 SPO 0 101 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 SPO 9 101 " 0.018 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C12 SPO 9 101 " 0.332 2.00e-02 2.50e+03 pdb=" C13 SPO 9 101 " -0.077 2.00e-02 2.50e+03 pdb=" C14 SPO 9 101 " -0.506 2.00e-02 2.50e+03 pdb=" C15 SPO 9 101 " 0.234 2.00e-02 2.50e+03 ... (remaining 6384 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 507 2.64 - 3.21: 31957 3.21 - 3.77: 57886 3.77 - 4.34: 82645 4.34 - 4.90: 134982 Nonbonded interactions: 307977 Sorted by model distance: nonbonded pdb=" C ILE 7 46 " pdb=" O LEU 6 44 " model vdw 2.077 3.270 nonbonded pdb=" OH TYR H 18 " pdb=" O14 PC1 H 602 " model vdw 2.118 2.440 nonbonded pdb=" O LEU 7 44 " pdb=" O TRP 6 43 " model vdw 2.141 3.040 nonbonded pdb=" O TRP 7 43 " pdb=" O LEU 6 44 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR a 38 " pdb=" O SER a 40 " model vdw 2.155 2.440 ... (remaining 307972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 12 through 49) selection = (chain '8' and resid 12 through 49) selection = (chain 'B' and resid 12 through 49) selection = (chain 'E' and resid 12 through 49) selection = (chain 'G' and resid 12 through 49) selection = (chain 'J' and resid 12 through 49) selection = (chain 'N' and resid 12 through 49) selection = (chain 'aa' and resid 12 through 49) selection = (chain 'ab' and resid 12 through 49) selection = (chain 'b' and resid 12 through 49) selection = (chain 'e' and resid 12 through 49) selection = (chain 'g' and resid 12 through 49) selection = (chain 'j' and resid 12 through 49) selection = (chain 'n' and resid 12 through 49) selection = (chain 'p' and resid 12 through 49) selection = (chain 'r' and resid 12 through 49) selection = (chain 't' and resid 12 through 49) selection = (chain 'x' and resid 12 through 49) } ncs_group { reference = (chain '4' and resid 13 through 48) selection = (chain 'v' and resid 13 through 48) selection = (chain 'z' and resid 13 through 48) } ncs_group { reference = chain '5' selection = (chain 'K' and (resid 13 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = (chain 'O' and (resid 13 through 54 or resid 101)) selection = (chain 'w' and (resid 13 through 54 or (resid 101 and (name NB or name ND or nam \ e C1A or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or \ name C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4 \ B or name C4C or name C4D or name CAA or name CAB or name CAC or name CAD or nam \ e CBA or name CBB or name CBC or name CBD or name CED or name CGA or name CGD or \ name CHA or name CHB or name CHC or name CHD or name CMA or name CMB or name CM \ C or name CMD or name NA or name NC or name O1A or name O1D or name O2A or name \ O2D or name OBB or name OBD or name MG )))) selection = chain 'y' } ncs_group { reference = chain '6' selection = chain '7' } ncs_group { reference = (chain '9' and resid 1 through 54) selection = (chain 'A' and resid 1 through 54) selection = (chain 'D' and resid 1 through 54) selection = (chain 'F' and resid 1 through 54) selection = (chain 'I' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'a' and resid 1 through 54) selection = (chain 'd' and resid 1 through 54) selection = (chain 'f' and resid 1 through 54) selection = (chain 'i' and resid 1 through 54) selection = (chain 'k' and resid 1 through 54) selection = (chain 'o' and resid 1 through 54) selection = (chain 'q' and resid 1 through 54) selection = (chain 's' and resid 1 through 54) selection = (chain 'u' and resid 1 through 54) } ncs_group { reference = (chain 'C' and (resid 6 through 69 or (resid 1201 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name \ C2F or name C2G or name C2H or name C2I or name C3 or name C31 or name C32 or na \ me C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 o \ r name C3A or name C3B or name C3C or name O11 or name O12 or name O13 or name O \ 14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 1202)) selection = (chain 'c' and (resid 6 through 69 or resid 1201 through 1202)) } ncs_group { reference = (chain 'H' and (resid 1 through 260 or resid 601)) selection = (chain 'h' and (resid 1 through 260 or (resid 301 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or na \ me C3C or name C3D or name C3E or name C3F or name C3G or name C3H or name O11 o \ r name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O \ 32 or name P )))) } ncs_group { reference = (chain 'L' and (resid 1 through 268 or resid 302 through 306)) selection = (chain 'l' and (resid 1 through 268 or (resid 301 and (name NB or name ND or nam \ e C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2A \ or name C2B or name C2C or name C2D or name C3 or name C3A or name C3B or name C \ 3C or name C3D or name C4 or name C4A or name C4B or name C4C or name C4D or nam \ e C5 or name C6 or name C7 or name C8 or name C9 or name CAA or name CAB or name \ CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CED or \ name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA \ or name CMB or name CMC or name CMD or name NA or name NC or name O1A or name O \ 1D or name O2A or name O2D or name OBB or name OBD or name MG )) or resid 302 or \ (resid 303 and (name C1 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C1M or \ name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 \ or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C \ 31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3M or na \ me C4 or name C4M or name C5 or name C6 or name C7 or name C8 or name C9 or name \ O2 or name O3 or name O4 or name O5 )) or (resid 304 and (name NB or name ND or \ name C1 or name C1A or name C1B or name C1C or name C1D or name C2 or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name CBA or name CBB or name CBC or name CBD or name CED \ or name CGA or name CGD or name CHA or name CHB or name CHC or name CHD or name \ CMA or name CMB or name CMC or name CMD or name NA or name NC or name O1A or nam \ e O1D or name O2A or name O2D or name OBB or name OBD or name MG )) or resid 305 \ )) } ncs_group { reference = (chain 'M' and resid 2 through 306) selection = (chain 'm' and resid 2 through 306) } 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=1.00 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: 1.830 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: 0.030 Extract box with map and model: 10.520 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 87.980 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.376 37888 Z= 0.977 Angle : 1.972 43.412 52075 Z= 0.692 Chirality : 0.043 0.304 5131 Planarity : 0.046 0.320 6387 Dihedral : 17.305 178.542 13314 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.01 % Allowed : 5.35 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.13), residues: 3704 helix: 2.55 (0.10), residues: 2342 sheet: 0.65 (0.82), residues: 44 loop : -0.31 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP l 263 HIS 0.007 0.001 HIS l 153 PHE 0.025 0.002 PHE c 7 TYR 0.013 0.001 TYR l 164 ARG 0.006 0.001 ARG s 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 756 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 73 TYR cc_start: 0.8025 (m-80) cc_final: 0.7768 (m-80) REVERT: L 193 LEU cc_start: 0.8535 (tp) cc_final: 0.8217 (tt) REVERT: L 248 MET cc_start: 0.8446 (mmm) cc_final: 0.8237 (mmp) REVERT: M 167 LEU cc_start: 0.8370 (mt) cc_final: 0.8074 (mt) REVERT: M 216 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8120 (t80) REVERT: H 46 ASP cc_start: 0.5723 (p0) cc_final: 0.5420 (p0) REVERT: H 62 LYS cc_start: 0.7579 (ptmt) cc_final: 0.7301 (mtpt) REVERT: H 124 ASP cc_start: 0.4951 (p0) cc_final: 0.4696 (p0) REVERT: H 255 MET cc_start: 0.5173 (mmt) cc_final: 0.4755 (ttm) REVERT: A 50 LYS cc_start: 0.6662 (tttt) cc_final: 0.6294 (ttmm) REVERT: A 52 ASN cc_start: 0.5732 (t0) cc_final: 0.5454 (t0) REVERT: D 33 LEU cc_start: 0.8369 (mt) cc_final: 0.8056 (mp) REVERT: F 8 TRP cc_start: 0.6489 (m100) cc_final: 0.5595 (m100) REVERT: G 25 MET cc_start: 0.6478 (mmm) cc_final: 0.5957 (mmm) REVERT: 9 10 ILE cc_start: 0.7845 (mm) cc_final: 0.7506 (mt) REVERT: 0 25 MET cc_start: 0.7164 (mmm) cc_final: 0.6905 (mmp) REVERT: l 213 ASP cc_start: 0.8608 (m-30) cc_final: 0.8281 (m-30) REVERT: m 15 PRO cc_start: 0.8185 (Cg_exo) cc_final: 0.7911 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8642 (tp) REVERT: h 12 LEU cc_start: 0.8893 (tp) cc_final: 0.8651 (tp) REVERT: h 103 ASP cc_start: 0.8395 (t0) cc_final: 0.8111 (t0) REVERT: h 185 ASP cc_start: 0.7021 (m-30) cc_final: 0.6537 (t0) REVERT: h 195 MET cc_start: 0.7934 (mmm) cc_final: 0.7657 (mmt) REVERT: h 255 MET cc_start: 0.3095 (mmt) cc_final: 0.2560 (ttp) REVERT: e 9 TYR cc_start: 0.7398 (m-10) cc_final: 0.7055 (m-80) REVERT: k 1 MET cc_start: 0.0757 (mpp) cc_final: 0.0488 (ppp) REVERT: n 24 TYR cc_start: 0.6960 (t80) cc_final: 0.6726 (t80) REVERT: o 20 GLN cc_start: 0.7235 (tt0) cc_final: 0.6934 (tt0) REVERT: p 44 ILE cc_start: 0.8366 (mm) cc_final: 0.8088 (mt) REVERT: r 43 TYR cc_start: 0.8237 (t80) cc_final: 0.7774 (t80) REVERT: t 14 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5787 (t0) REVERT: u 42 ASN cc_start: 0.7844 (t0) cc_final: 0.7417 (t0) REVERT: y 23 PHE cc_start: 0.3367 (OUTLIER) cc_final: 0.2939 (t80) REVERT: y 43 TRP cc_start: 0.5805 (p90) cc_final: 0.5565 (p90) REVERT: 5 23 PHE cc_start: 0.2986 (OUTLIER) cc_final: 0.1895 (t80) outliers start: 95 outliers final: 19 residues processed: 822 average time/residue: 0.4586 time to fit residues: 616.3436 Evaluate side-chains 577 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 553 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain d residue 47 SER Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain t residue 14 ASP Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain w residue 44 LEU Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain c residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.2980 chunk 272 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 282 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 210 optimal weight: 0.4980 chunk 326 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 237 GLN ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS I 20 GLN N 21 HIS ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN C 12 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 199 GLN d 20 GLN f 20 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 42 ASN j 21 HIS k 20 GLN o 20 GLN u 20 GLN y 20 GLN z 21 HIS Q 20 GLN c 8 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37888 Z= 0.157 Angle : 0.687 13.330 52075 Z= 0.271 Chirality : 0.037 0.178 5131 Planarity : 0.003 0.032 6387 Dihedral : 16.778 173.743 6664 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.09 % Allowed : 10.69 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.13), residues: 3704 helix: 2.57 (0.10), residues: 2459 sheet: 1.38 (0.77), residues: 62 loop : -0.38 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP z 48 HIS 0.013 0.001 HIS N 21 PHE 0.023 0.001 PHE k 23 TYR 0.013 0.001 TYR 0 24 ARG 0.007 0.000 ARG 7 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 600 time to evaluate : 4.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 193 LEU cc_start: 0.8348 (tp) cc_final: 0.8008 (tt) REVERT: H 118 ARG cc_start: 0.5329 (mtt180) cc_final: 0.4232 (mmt180) REVERT: H 255 MET cc_start: 0.5107 (mmt) cc_final: 0.4704 (ttm) REVERT: A 50 LYS cc_start: 0.6808 (tttt) cc_final: 0.6368 (ttmm) REVERT: A 52 ASN cc_start: 0.5908 (t0) cc_final: 0.5631 (t0) REVERT: B 43 TYR cc_start: 0.7304 (t80) cc_final: 0.7063 (t80) REVERT: D 8 TRP cc_start: 0.7586 (m100) cc_final: 0.7314 (m100) REVERT: D 33 LEU cc_start: 0.8412 (mt) cc_final: 0.8208 (mp) REVERT: F 8 TRP cc_start: 0.6422 (m100) cc_final: 0.5574 (m100) REVERT: F 9 MET cc_start: 0.5381 (mpp) cc_final: 0.4078 (mpp) REVERT: G 18 GLN cc_start: 0.6031 (pt0) cc_final: 0.5605 (pt0) REVERT: G 43 TYR cc_start: 0.6363 (t80) cc_final: 0.6034 (t80) REVERT: 7 9 MET cc_start: 0.7207 (mtm) cc_final: 0.6844 (mtt) REVERT: 9 10 ILE cc_start: 0.7599 (mm) cc_final: 0.7360 (mt) REVERT: 0 25 MET cc_start: 0.7234 (mmm) cc_final: 0.6832 (mmp) REVERT: C 20 ARG cc_start: 0.7053 (ttm170) cc_final: 0.5836 (tmt170) REVERT: l 202 LYS cc_start: 0.8008 (tttt) cc_final: 0.7573 (mtpt) REVERT: l 213 ASP cc_start: 0.8689 (m-30) cc_final: 0.8325 (m-30) REVERT: m 15 PRO cc_start: 0.8233 (Cg_exo) cc_final: 0.7993 (Cg_endo) REVERT: m 205 SER cc_start: 0.8562 (t) cc_final: 0.8300 (p) REVERT: m 214 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8726 (tp) REVERT: m 216 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8403 (t80) REVERT: h 185 ASP cc_start: 0.6961 (m-30) cc_final: 0.6498 (t0) REVERT: h 255 MET cc_start: 0.3124 (mmt) cc_final: 0.2578 (ttp) REVERT: e 9 TYR cc_start: 0.7303 (m-10) cc_final: 0.7000 (m-80) REVERT: j 25 MET cc_start: 0.7803 (mmt) cc_final: 0.7508 (mmt) REVERT: k 1 MET cc_start: 0.0708 (mpp) cc_final: -0.0641 (ttt) REVERT: o 9 MET cc_start: 0.7166 (mmm) cc_final: 0.6911 (mmm) REVERT: p 24 TYR cc_start: 0.7549 (t80) cc_final: 0.7257 (t80) REVERT: p 44 ILE cc_start: 0.8412 (mm) cc_final: 0.8130 (mt) REVERT: q 24 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7731 (mm) REVERT: s 6 LYS cc_start: 0.6799 (mtpt) cc_final: 0.6437 (tttt) REVERT: u 1 MET cc_start: 0.4109 (tpp) cc_final: 0.1615 (tmm) REVERT: w 41 TYR cc_start: 0.7076 (m-80) cc_final: 0.6804 (m-80) REVERT: x 44 ILE cc_start: 0.5683 (mm) cc_final: 0.5436 (mm) REVERT: y 23 PHE cc_start: 0.3387 (OUTLIER) cc_final: 0.3141 (t80) REVERT: y 43 TRP cc_start: 0.6010 (p90) cc_final: 0.5724 (p90) REVERT: z 45 TRP cc_start: 0.4287 (t60) cc_final: 0.3676 (t-100) REVERT: 5 23 PHE cc_start: 0.2736 (OUTLIER) cc_final: 0.1774 (t80) outliers start: 66 outliers final: 34 residues processed: 631 average time/residue: 0.4725 time to fit residues: 499.9504 Evaluate side-chains 577 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 538 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain e residue 14 ASP Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain j residue 28 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 27 MET Chi-restraints excluded: chain c residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 272 optimal weight: 8.9990 chunk 222 optimal weight: 0.0970 chunk 90 optimal weight: 9.9990 chunk 327 optimal weight: 0.9980 chunk 353 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 overall best weight: 3.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 HIS h 201 ASN s 20 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 37888 Z= 0.379 Angle : 0.850 15.154 52075 Z= 0.342 Chirality : 0.043 0.221 5131 Planarity : 0.005 0.068 6387 Dihedral : 16.821 169.724 6647 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.86 % Allowed : 12.31 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 3704 helix: 1.96 (0.10), residues: 2461 sheet: -0.44 (0.68), residues: 66 loop : -0.50 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 7 43 HIS 0.018 0.002 HIS m 182 PHE 0.042 0.002 PHE L 216 TYR 0.017 0.002 TYR l 67 ARG 0.005 0.001 ARG s 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 590 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 193 LEU cc_start: 0.8465 (tp) cc_final: 0.8221 (tt) REVERT: L 205 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5520 (mt-10) REVERT: L 248 MET cc_start: 0.8464 (tpp) cc_final: 0.8127 (tpt) REVERT: L 254 ILE cc_start: 0.5538 (OUTLIER) cc_final: 0.5142 (pt) REVERT: M 25 ASN cc_start: 0.5618 (t0) cc_final: 0.5147 (m110) REVERT: M 129 TRP cc_start: 0.7105 (t-100) cc_final: 0.6769 (t-100) REVERT: M 142 MET cc_start: 0.7526 (mtp) cc_final: 0.7297 (mtp) REVERT: M 216 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8206 (t80) REVERT: H 70 ARG cc_start: 0.6038 (mmt90) cc_final: 0.5725 (mmm160) REVERT: H 255 MET cc_start: 0.5362 (mmt) cc_final: 0.4781 (ttt) REVERT: A 50 LYS cc_start: 0.7793 (tttt) cc_final: 0.7096 (ttmm) REVERT: A 52 ASN cc_start: 0.6619 (t0) cc_final: 0.6278 (t0) REVERT: D 33 LEU cc_start: 0.8549 (mt) cc_final: 0.8221 (mp) REVERT: F 8 TRP cc_start: 0.6429 (m100) cc_final: 0.6003 (m100) REVERT: F 9 MET cc_start: 0.5363 (mpp) cc_final: 0.5110 (mmt) REVERT: J 15 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3794 (mm-30) REVERT: K 30 MET cc_start: 0.4775 (mmm) cc_final: 0.3294 (ppp) REVERT: 7 30 MET cc_start: 0.8181 (ptm) cc_final: 0.7977 (ttt) REVERT: 9 10 ILE cc_start: 0.7667 (mm) cc_final: 0.7310 (mt) REVERT: C 20 ARG cc_start: 0.7561 (ttm170) cc_final: 0.6351 (tmt170) REVERT: C 43 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8147 (mp) REVERT: l 202 LYS cc_start: 0.8095 (tttt) cc_final: 0.7784 (ptmt) REVERT: l 213 ASP cc_start: 0.8743 (m-30) cc_final: 0.8468 (m-30) REVERT: m 15 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.7951 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8569 (tp) REVERT: h 166 ASP cc_start: 0.7439 (t0) cc_final: 0.7148 (t0) REVERT: h 255 MET cc_start: 0.3620 (mmt) cc_final: 0.2771 (ttp) REVERT: e 9 TYR cc_start: 0.7706 (m-80) cc_final: 0.7454 (m-80) REVERT: f 27 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8823 (tp) REVERT: g 18 GLN cc_start: 0.7940 (mp10) cc_final: 0.7644 (mp10) REVERT: k 1 MET cc_start: 0.1564 (mpp) cc_final: 0.0384 (ttt) REVERT: k 47 SER cc_start: 0.8269 (t) cc_final: 0.7867 (p) REVERT: n 24 TYR cc_start: 0.6878 (t80) cc_final: 0.6649 (t80) REVERT: p 44 ILE cc_start: 0.8637 (mm) cc_final: 0.8313 (mt) REVERT: q 24 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7897 (mm) REVERT: s 6 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6495 (tttt) REVERT: t 19 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7203 (tm-30) REVERT: u 1 MET cc_start: 0.4546 (tpp) cc_final: 0.1605 (tmm) REVERT: u 45 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6455 (mt-10) REVERT: v 20 LEU cc_start: 0.6971 (tp) cc_final: 0.6769 (tp) REVERT: y 23 PHE cc_start: 0.3726 (OUTLIER) cc_final: 0.3393 (t80) REVERT: z 45 TRP cc_start: 0.4405 (t60) cc_final: 0.3702 (t-100) REVERT: 5 23 PHE cc_start: 0.2954 (OUTLIER) cc_final: 0.1927 (t80) REVERT: Q 20 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7964 (tt0) outliers start: 122 outliers final: 65 residues processed: 664 average time/residue: 0.4530 time to fit residues: 497.2632 Evaluate side-chains 627 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 551 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain K residue 23 PHE Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 14 ASP Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain p residue 34 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 347 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 20 ASN l 199 ASN ** m 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN c 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37888 Z= 0.165 Angle : 0.666 12.832 52075 Z= 0.264 Chirality : 0.037 0.182 5131 Planarity : 0.003 0.063 6387 Dihedral : 15.813 154.935 6646 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.56 % Allowed : 14.49 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.14), residues: 3704 helix: 2.39 (0.10), residues: 2469 sheet: 0.11 (0.63), residues: 86 loop : -0.32 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP l 271 HIS 0.013 0.001 HIS m 182 PHE 0.020 0.001 PHE L 216 TYR 0.018 0.001 TYR d 5 ARG 0.005 0.000 ARG l 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 579 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 193 LEU cc_start: 0.8344 (tp) cc_final: 0.8009 (tt) REVERT: L 248 MET cc_start: 0.8370 (tpp) cc_final: 0.8152 (tpt) REVERT: M 123 PHE cc_start: 0.7292 (t80) cc_final: 0.7047 (t80) REVERT: M 216 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7877 (t80) REVERT: H 70 ARG cc_start: 0.6040 (mmt90) cc_final: 0.5535 (mmm160) REVERT: H 118 ARG cc_start: 0.5425 (mtt180) cc_final: 0.4230 (mmt180) REVERT: H 255 MET cc_start: 0.5224 (mmt) cc_final: 0.4710 (ttt) REVERT: A 50 LYS cc_start: 0.7683 (tttt) cc_final: 0.7011 (ttmm) REVERT: A 52 ASN cc_start: 0.6667 (t0) cc_final: 0.6422 (t0) REVERT: D 8 TRP cc_start: 0.7545 (m100) cc_final: 0.7329 (m100) REVERT: D 33 LEU cc_start: 0.8447 (mt) cc_final: 0.8059 (mp) REVERT: F 8 TRP cc_start: 0.6404 (m100) cc_final: 0.5849 (m100) REVERT: F 9 MET cc_start: 0.5218 (mpp) cc_final: 0.5015 (mmt) REVERT: G 44 ILE cc_start: 0.7229 (mm) cc_final: 0.6990 (mm) REVERT: K 30 MET cc_start: 0.4772 (mmm) cc_final: 0.3370 (ppp) REVERT: C 20 ARG cc_start: 0.7322 (ttm170) cc_final: 0.6187 (tmt170) REVERT: l 202 LYS cc_start: 0.8049 (tttt) cc_final: 0.7822 (ptmt) REVERT: l 213 ASP cc_start: 0.8778 (m-30) cc_final: 0.8488 (m-30) REVERT: m 15 PRO cc_start: 0.8301 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: m 214 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8754 (tp) REVERT: m 216 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8532 (t80) REVERT: h 255 MET cc_start: 0.3367 (mmt) cc_final: 0.2720 (ttp) REVERT: e 9 TYR cc_start: 0.7499 (m-80) cc_final: 0.7208 (m-80) REVERT: g 18 GLN cc_start: 0.7998 (mp10) cc_final: 0.7616 (mp10) REVERT: k 1 MET cc_start: 0.1803 (mpp) cc_final: 0.0643 (ttt) REVERT: k 47 SER cc_start: 0.8222 (t) cc_final: 0.7790 (p) REVERT: p 44 ILE cc_start: 0.8443 (mm) cc_final: 0.8163 (mt) REVERT: q 24 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7941 (mm) REVERT: s 6 LYS cc_start: 0.6785 (mtpt) cc_final: 0.6438 (tttt) REVERT: u 1 MET cc_start: 0.4521 (tpp) cc_final: 0.1699 (tmm) REVERT: v 32 SER cc_start: 0.8340 (t) cc_final: 0.8108 (m) REVERT: y 23 PHE cc_start: 0.3837 (OUTLIER) cc_final: 0.3559 (t80) REVERT: z 45 TRP cc_start: 0.4487 (t60) cc_final: 0.3940 (t-100) REVERT: 5 23 PHE cc_start: 0.2997 (OUTLIER) cc_final: 0.2007 (t80) outliers start: 81 outliers final: 54 residues processed: 619 average time/residue: 0.4522 time to fit residues: 463.8785 Evaluate side-chains 608 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 548 time to evaluate : 4.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 36 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 274 VAL Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain i residue 37 SER Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain j residue 42 VAL Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 296 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37888 Z= 0.237 Angle : 0.724 13.124 52075 Z= 0.288 Chirality : 0.039 0.229 5131 Planarity : 0.004 0.050 6387 Dihedral : 15.673 142.977 6642 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.32 % Allowed : 14.68 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.14), residues: 3704 helix: 2.25 (0.10), residues: 2471 sheet: 0.01 (0.64), residues: 86 loop : -0.34 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP x 48 HIS 0.016 0.002 HIS m 182 PHE 0.025 0.001 PHE L 216 TYR 0.017 0.001 TYR 0 24 ARG 0.006 0.000 ARG l 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 555 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 254 ILE cc_start: 0.5498 (OUTLIER) cc_final: 0.5099 (pt) REVERT: M 25 ASN cc_start: 0.5315 (t0) cc_final: 0.4829 (m-40) REVERT: M 129 TRP cc_start: 0.7135 (t-100) cc_final: 0.6864 (t-100) REVERT: M 216 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7966 (t80) REVERT: H 70 ARG cc_start: 0.6052 (mmt90) cc_final: 0.5616 (mmm160) REVERT: H 120 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5845 (mt) REVERT: H 255 MET cc_start: 0.5261 (mmt) cc_final: 0.4778 (ttt) REVERT: A 50 LYS cc_start: 0.7661 (tttt) cc_final: 0.6991 (ttmm) REVERT: A 52 ASN cc_start: 0.6798 (t0) cc_final: 0.6545 (t0) REVERT: D 33 LEU cc_start: 0.8469 (mt) cc_final: 0.8098 (mp) REVERT: F 8 TRP cc_start: 0.6338 (m100) cc_final: 0.5901 (m100) REVERT: G 44 ILE cc_start: 0.7263 (mm) cc_final: 0.7014 (mm) REVERT: J 15 GLU cc_start: 0.4003 (OUTLIER) cc_final: 0.3719 (mm-30) REVERT: 7 26 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 20 ARG cc_start: 0.7434 (ttm170) cc_final: 0.6304 (tmt170) REVERT: l 202 LYS cc_start: 0.8081 (tttt) cc_final: 0.7855 (ptmt) REVERT: l 213 ASP cc_start: 0.8721 (m-30) cc_final: 0.8431 (m-30) REVERT: m 15 PRO cc_start: 0.8290 (Cg_exo) cc_final: 0.8052 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8724 (tp) REVERT: m 216 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (t80) REVERT: h 12 LEU cc_start: 0.8826 (tp) cc_final: 0.8610 (tp) REVERT: h 255 MET cc_start: 0.3376 (mmt) cc_final: 0.2721 (ttp) REVERT: f 27 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8795 (tp) REVERT: g 18 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: k 1 MET cc_start: 0.1886 (mpp) cc_final: 0.0326 (mtp) REVERT: k 47 SER cc_start: 0.8309 (t) cc_final: 0.7982 (p) REVERT: n 34 VAL cc_start: 0.8044 (t) cc_final: 0.7832 (t) REVERT: p 44 ILE cc_start: 0.8474 (mm) cc_final: 0.8198 (mt) REVERT: q 24 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7880 (mm) REVERT: s 6 LYS cc_start: 0.6914 (mtpt) cc_final: 0.6484 (tttt) REVERT: u 1 MET cc_start: 0.4695 (tpp) cc_final: 0.1736 (tmm) REVERT: u 26 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7983 (tp) REVERT: v 44 ILE cc_start: 0.8011 (mm) cc_final: 0.7799 (mt) REVERT: x 13 THR cc_start: 0.5797 (p) cc_final: 0.5241 (t) REVERT: y 23 PHE cc_start: 0.3790 (OUTLIER) cc_final: 0.3555 (t80) REVERT: z 45 TRP cc_start: 0.4529 (t60) cc_final: 0.3913 (t-100) REVERT: 5 23 PHE cc_start: 0.2978 (OUTLIER) cc_final: 0.1976 (t80) outliers start: 105 outliers final: 68 residues processed: 615 average time/residue: 0.4834 time to fit residues: 496.6488 Evaluate side-chains 623 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 542 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 185 ASP Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 19 GLU Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain x residue 39 HIS Chi-restraints excluded: chain y residue 23 PHE Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain 6 residue 26 LEU Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 20 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37888 Z= 0.248 Angle : 0.723 13.230 52075 Z= 0.289 Chirality : 0.039 0.231 5131 Planarity : 0.004 0.042 6387 Dihedral : 15.626 138.898 6642 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 3.20 % Allowed : 15.22 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.14), residues: 3704 helix: 2.18 (0.10), residues: 2459 sheet: -0.02 (0.63), residues: 86 loop : -0.19 (0.19), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP s 8 HIS 0.016 0.002 HIS m 182 PHE 0.029 0.001 PHE L 216 TYR 0.033 0.001 TYR L 169 ARG 0.007 0.000 ARG z 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 557 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 25 ASN cc_start: 0.5278 (t0) cc_final: 0.4760 (m-40) REVERT: M 129 TRP cc_start: 0.7183 (t-100) cc_final: 0.6928 (t-100) REVERT: M 216 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.8138 (t80) REVERT: M 228 ARG cc_start: 0.7696 (ptp-170) cc_final: 0.7409 (ptp-170) REVERT: H 70 ARG cc_start: 0.6000 (mmt90) cc_final: 0.5461 (mmm160) REVERT: H 118 ARG cc_start: 0.5302 (mtt180) cc_final: 0.4146 (mmt180) REVERT: H 120 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5811 (mt) REVERT: H 255 MET cc_start: 0.5260 (mmt) cc_final: 0.4803 (ttt) REVERT: A 50 LYS cc_start: 0.7760 (tttt) cc_final: 0.7065 (ttmm) REVERT: A 52 ASN cc_start: 0.6777 (t0) cc_final: 0.6549 (t0) REVERT: D 33 LEU cc_start: 0.8458 (mt) cc_final: 0.8078 (mp) REVERT: F 8 TRP cc_start: 0.6123 (m100) cc_final: 0.5693 (m100) REVERT: G 18 GLN cc_start: 0.6121 (pt0) cc_final: 0.5653 (pt0) REVERT: G 29 TRP cc_start: 0.7263 (m100) cc_final: 0.7007 (m100) REVERT: G 44 ILE cc_start: 0.7286 (mm) cc_final: 0.7050 (mm) REVERT: I 45 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5670 (mm-30) REVERT: 7 10 ILE cc_start: 0.7424 (mm) cc_final: 0.7211 (mt) REVERT: 7 26 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8358 (mt) REVERT: C 20 ARG cc_start: 0.7493 (ttm170) cc_final: 0.6305 (tmt170) REVERT: l 202 LYS cc_start: 0.8064 (tttt) cc_final: 0.7842 (ptmt) REVERT: l 213 ASP cc_start: 0.8718 (m-30) cc_final: 0.8418 (m-30) REVERT: m 15 PRO cc_start: 0.8285 (Cg_exo) cc_final: 0.8061 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8737 (tp) REVERT: m 216 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8543 (t80) REVERT: h 12 LEU cc_start: 0.8867 (tp) cc_final: 0.8644 (tp) REVERT: h 80 SER cc_start: 0.5976 (OUTLIER) cc_final: 0.5593 (m) REVERT: h 255 MET cc_start: 0.3636 (mmt) cc_final: 0.2843 (ttp) REVERT: g 18 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: k 33 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8070 (mm) REVERT: k 47 SER cc_start: 0.8327 (t) cc_final: 0.8034 (p) REVERT: o 9 MET cc_start: 0.7450 (mmm) cc_final: 0.7091 (tpt) REVERT: p 44 ILE cc_start: 0.8456 (mm) cc_final: 0.8178 (mt) REVERT: q 24 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7872 (mm) REVERT: s 8 TRP cc_start: 0.7626 (m100) cc_final: 0.7412 (m100) REVERT: u 1 MET cc_start: 0.4931 (tpp) cc_final: 0.1913 (tmm) REVERT: u 26 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8041 (tp) REVERT: v 44 ILE cc_start: 0.8044 (mm) cc_final: 0.7821 (mt) REVERT: x 13 THR cc_start: 0.5857 (p) cc_final: 0.5291 (t) REVERT: z 46 ARG cc_start: 0.4180 (tmt170) cc_final: 0.3742 (mpt180) REVERT: 5 23 PHE cc_start: 0.2807 (OUTLIER) cc_final: 0.1970 (t80) outliers start: 101 outliers final: 65 residues processed: 609 average time/residue: 0.4462 time to fit residues: 448.6207 Evaluate side-chains 621 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 545 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 185 ASP Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain h residue 201 ASN Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 19 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 18 GLN Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 34 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain x residue 39 HIS Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 50 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 254 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 346 optimal weight: 0.4980 chunk 217 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 0.0050 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN 0 18 GLN l 199 ASN Q 20 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37888 Z= 0.228 Angle : 0.707 13.407 52075 Z= 0.284 Chirality : 0.038 0.265 5131 Planarity : 0.004 0.033 6387 Dihedral : 15.450 138.655 6640 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.23 % Allowed : 15.41 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.14), residues: 3704 helix: 2.21 (0.10), residues: 2459 sheet: -0.04 (0.62), residues: 88 loop : -0.18 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP x 48 HIS 0.019 0.002 HIS N 39 PHE 0.032 0.001 PHE L 216 TYR 0.016 0.001 TYR 0 24 ARG 0.006 0.000 ARG l 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 558 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 254 ILE cc_start: 0.5437 (OUTLIER) cc_final: 0.5053 (pt) REVERT: M 25 ASN cc_start: 0.5401 (t0) cc_final: 0.4808 (m-40) REVERT: M 129 TRP cc_start: 0.7179 (t-100) cc_final: 0.6969 (t-100) REVERT: M 216 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.7915 (t80) REVERT: H 37 ARG cc_start: 0.8319 (mmt-90) cc_final: 0.8023 (mmt-90) REVERT: H 70 ARG cc_start: 0.6063 (mmt90) cc_final: 0.5439 (mmm160) REVERT: H 118 ARG cc_start: 0.5251 (mtt180) cc_final: 0.4123 (mmt180) REVERT: H 255 MET cc_start: 0.5290 (mmt) cc_final: 0.4860 (ttt) REVERT: A 50 LYS cc_start: 0.7793 (tttt) cc_final: 0.7112 (ttmm) REVERT: A 52 ASN cc_start: 0.6794 (t0) cc_final: 0.6564 (t0) REVERT: D 33 LEU cc_start: 0.8469 (mt) cc_final: 0.8083 (mp) REVERT: F 8 TRP cc_start: 0.5988 (m100) cc_final: 0.5735 (m100) REVERT: F 45 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6256 (mm-30) REVERT: G 18 GLN cc_start: 0.6235 (pt0) cc_final: 0.5697 (pt0) REVERT: G 44 ILE cc_start: 0.7294 (mm) cc_final: 0.7060 (mm) REVERT: J 15 GLU cc_start: 0.3774 (OUTLIER) cc_final: 0.3499 (mm-30) REVERT: 7 26 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8371 (mt) REVERT: C 20 ARG cc_start: 0.7583 (ttm170) cc_final: 0.6391 (tmt170) REVERT: l 202 LYS cc_start: 0.8100 (tttt) cc_final: 0.7858 (ptmt) REVERT: l 213 ASP cc_start: 0.8749 (m-30) cc_final: 0.8465 (m-30) REVERT: m 15 PRO cc_start: 0.8286 (Cg_exo) cc_final: 0.8075 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8746 (tp) REVERT: m 216 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8584 (t80) REVERT: h 255 MET cc_start: 0.3500 (mmt) cc_final: 0.2804 (ttp) REVERT: k 33 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8089 (mm) REVERT: k 47 SER cc_start: 0.8320 (t) cc_final: 0.8037 (p) REVERT: o 9 MET cc_start: 0.7491 (mmm) cc_final: 0.7149 (tpt) REVERT: p 44 ILE cc_start: 0.8409 (mm) cc_final: 0.8127 (mt) REVERT: q 24 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7831 (mm) REVERT: u 1 MET cc_start: 0.4915 (tpp) cc_final: 0.1891 (tmm) REVERT: u 26 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8042 (tp) REVERT: v 32 SER cc_start: 0.8333 (t) cc_final: 0.8086 (m) REVERT: v 44 ILE cc_start: 0.8019 (mm) cc_final: 0.7784 (mt) REVERT: x 13 THR cc_start: 0.5878 (p) cc_final: 0.5310 (t) REVERT: z 46 ARG cc_start: 0.4276 (tmt170) cc_final: 0.3672 (mpt180) REVERT: 5 23 PHE cc_start: 0.2793 (OUTLIER) cc_final: 0.2001 (t80) outliers start: 102 outliers final: 72 residues processed: 610 average time/residue: 0.4516 time to fit residues: 454.7270 Evaluate side-chains 632 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 550 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain 7 residue 26 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 27 LEU Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 35 ASN Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 185 ASP Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain h residue 201 ASN Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 19 GLU Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain s residue 34 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 44 ILE Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 6 ILE Chi-restraints excluded: chain c residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 220 optimal weight: 0.0770 chunk 236 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 266 HIS M 299 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN l 199 ASN ** h 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 20 GLN ** y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 37888 Z= 0.428 Angle : 0.881 16.244 52075 Z= 0.357 Chirality : 0.044 0.306 5131 Planarity : 0.005 0.085 6387 Dihedral : 16.076 143.314 6640 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.76 % Allowed : 15.47 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.14), residues: 3704 helix: 1.66 (0.10), residues: 2449 sheet: -0.61 (0.69), residues: 66 loop : -0.20 (0.19), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP s 8 HIS 0.019 0.002 HIS m 182 PHE 0.034 0.002 PHE L 216 TYR 0.018 0.002 TYR m 134 ARG 0.006 0.001 ARG l 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 568 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 254 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.5163 (pt) REVERT: M 25 ASN cc_start: 0.5461 (t0) cc_final: 0.5016 (m110) REVERT: M 129 TRP cc_start: 0.7347 (t-100) cc_final: 0.7131 (t-100) REVERT: M 195 ASN cc_start: 0.7516 (m-40) cc_final: 0.6939 (m110) REVERT: M 216 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8204 (t80) REVERT: H 70 ARG cc_start: 0.6045 (mmt90) cc_final: 0.5531 (mmm160) REVERT: H 83 ARG cc_start: 0.6171 (ptm160) cc_final: 0.5852 (ptm-80) REVERT: H 120 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5879 (mt) REVERT: H 219 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6689 (mt) REVERT: H 255 MET cc_start: 0.5453 (mmt) cc_final: 0.4960 (ttt) REVERT: A 50 LYS cc_start: 0.7796 (tttt) cc_final: 0.7090 (ttmm) REVERT: A 52 ASN cc_start: 0.6857 (t0) cc_final: 0.6571 (t0) REVERT: D 33 LEU cc_start: 0.8490 (mt) cc_final: 0.8083 (mp) REVERT: F 45 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6228 (mm-30) REVERT: G 44 ILE cc_start: 0.7406 (mm) cc_final: 0.7161 (mm) REVERT: J 15 GLU cc_start: 0.3717 (OUTLIER) cc_final: 0.3421 (mm-30) REVERT: J 25 MET cc_start: 0.6521 (mmm) cc_final: 0.6304 (mmt) REVERT: C 20 ARG cc_start: 0.7783 (ttm170) cc_final: 0.6538 (tmt170) REVERT: l 202 LYS cc_start: 0.8114 (tttt) cc_final: 0.7844 (ptmt) REVERT: l 213 ASP cc_start: 0.8767 (m-30) cc_final: 0.8490 (m-30) REVERT: m 15 PRO cc_start: 0.8264 (Cg_exo) cc_final: 0.7983 (Cg_endo) REVERT: m 214 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8563 (tp) REVERT: h 255 MET cc_start: 0.3739 (mmt) cc_final: 0.3021 (ttp) REVERT: b 15 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6932 (mm-30) REVERT: d 26 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8559 (mp) REVERT: f 27 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8760 (tp) REVERT: k 33 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8098 (mm) REVERT: k 47 SER cc_start: 0.8353 (t) cc_final: 0.8064 (p) REVERT: o 15 ARG cc_start: 0.5356 (mtp180) cc_final: 0.4788 (mtp85) REVERT: p 44 ILE cc_start: 0.8564 (mm) cc_final: 0.8253 (mt) REVERT: q 24 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7930 (mm) REVERT: r 20 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6306 (mp) REVERT: s 8 TRP cc_start: 0.7649 (m100) cc_final: 0.7443 (m100) REVERT: u 1 MET cc_start: 0.5182 (tpp) cc_final: 0.2448 (tmm) REVERT: u 16 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7341 (t) REVERT: u 26 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8139 (tt) REVERT: y 33 LEU cc_start: 0.7091 (mt) cc_final: 0.6516 (tp) REVERT: z 46 ARG cc_start: 0.4276 (tmt170) cc_final: 0.3657 (mpt180) REVERT: 5 23 PHE cc_start: 0.2919 (OUTLIER) cc_final: 0.2077 (t80) outliers start: 119 outliers final: 79 residues processed: 624 average time/residue: 0.4688 time to fit residues: 483.9822 Evaluate side-chains 645 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 552 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 20 LEU Chi-restraints excluded: chain 9 residue 2 SER Chi-restraints excluded: chain 9 residue 27 LEU Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 25 MET Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 260 VAL Chi-restraints excluded: chain m residue 12 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 80 SER Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 185 ASP Chi-restraints excluded: chain h residue 188 THR Chi-restraints excluded: chain h residue 201 ASN Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain e residue 42 VAL Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LEU Chi-restraints excluded: chain f residue 54 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 9 MET Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain o residue 54 VAL Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 34 ILE Chi-restraints excluded: chain r residue 20 LEU Chi-restraints excluded: chain r residue 26 SER Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain u residue 16 VAL Chi-restraints excluded: chain u residue 26 LEU Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain x residue 39 HIS Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain aa residue 40 LEU Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 9.9990 chunk 332 optimal weight: 0.5980 chunk 303 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 292 optimal weight: 0.9980 chunk 305 optimal weight: 0.8980 chunk 322 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN l 199 ASN ** y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37888 Z= 0.193 Angle : 0.690 13.584 52075 Z= 0.279 Chirality : 0.038 0.208 5131 Planarity : 0.003 0.038 6387 Dihedral : 15.274 144.492 6640 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.40 % Allowed : 16.93 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3704 helix: 2.10 (0.10), residues: 2460 sheet: -0.12 (0.62), residues: 88 loop : -0.21 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP x 48 HIS 0.014 0.001 HIS m 182 PHE 0.022 0.001 PHE A 23 TYR 0.018 0.001 TYR d 5 ARG 0.006 0.000 ARG l 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 568 time to evaluate : 3.453 Fit side-chains revert: symmetry clash REVERT: M 25 ASN cc_start: 0.5477 (t0) cc_final: 0.4945 (m-40) REVERT: M 216 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8016 (t80) REVERT: H 70 ARG cc_start: 0.6071 (mmt90) cc_final: 0.5405 (mmm160) REVERT: H 83 ARG cc_start: 0.6161 (ptm160) cc_final: 0.5925 (ptm-80) REVERT: H 118 ARG cc_start: 0.5241 (mtt180) cc_final: 0.4087 (mmt180) REVERT: H 255 MET cc_start: 0.5451 (mmt) cc_final: 0.4984 (ttt) REVERT: A 50 LYS cc_start: 0.7688 (tttt) cc_final: 0.7102 (ttmm) REVERT: A 52 ASN cc_start: 0.6842 (t0) cc_final: 0.6562 (t0) REVERT: D 33 LEU cc_start: 0.8427 (mt) cc_final: 0.8043 (mp) REVERT: F 8 TRP cc_start: 0.6252 (m100) cc_final: 0.5887 (m100) REVERT: G 44 ILE cc_start: 0.7308 (mm) cc_final: 0.7092 (mm) REVERT: 0 14 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7551 (t0) REVERT: C 20 ARG cc_start: 0.7558 (ttm170) cc_final: 0.6350 (tmt170) REVERT: C 28 MET cc_start: 0.6596 (ttt) cc_final: 0.6230 (ttt) REVERT: l 202 LYS cc_start: 0.8096 (tttt) cc_final: 0.7851 (ptmt) REVERT: l 213 ASP cc_start: 0.8771 (m-30) cc_final: 0.8484 (m-30) REVERT: m 15 PRO cc_start: 0.8314 (Cg_exo) cc_final: 0.8107 (Cg_endo) REVERT: m 214 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8732 (tp) REVERT: m 216 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8586 (t80) REVERT: h 255 MET cc_start: 0.3520 (mmt) cc_final: 0.2932 (ttp) REVERT: k 33 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8082 (mm) REVERT: k 47 SER cc_start: 0.8246 (t) cc_final: 0.7987 (p) REVERT: p 44 ILE cc_start: 0.8437 (mm) cc_final: 0.8156 (mt) REVERT: q 24 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7827 (mm) REVERT: u 1 MET cc_start: 0.5086 (tpp) cc_final: 0.2293 (tmm) REVERT: v 32 SER cc_start: 0.8498 (t) cc_final: 0.8234 (m) REVERT: v 44 ILE cc_start: 0.8025 (mm) cc_final: 0.7742 (mt) REVERT: x 13 THR cc_start: 0.5750 (p) cc_final: 0.5160 (t) REVERT: z 45 TRP cc_start: 0.4449 (t60) cc_final: 0.4210 (t60) REVERT: z 46 ARG cc_start: 0.4289 (tmt170) cc_final: 0.3772 (mpt180) REVERT: 5 23 PHE cc_start: 0.2931 (OUTLIER) cc_final: 0.2098 (t80) outliers start: 76 outliers final: 57 residues processed: 606 average time/residue: 0.4560 time to fit residues: 456.1951 Evaluate side-chains 611 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 547 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain 9 residue 27 LEU Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 220 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 111 GLU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 10 ILE Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain ab residue 14 ASP Chi-restraints excluded: chain c residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.9990 chunk 341 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 chunk 358 optimal weight: 0.5980 chunk 330 optimal weight: 0.5980 chunk 285 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN 9 52 ASN l 199 ASN ** y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 20 GLN c 66 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37888 Z= 0.153 Angle : 0.636 12.593 52075 Z= 0.260 Chirality : 0.037 0.203 5131 Planarity : 0.003 0.035 6387 Dihedral : 14.769 141.245 6640 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.96 % Allowed : 17.49 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.14), residues: 3704 helix: 2.35 (0.10), residues: 2470 sheet: 0.02 (0.63), residues: 88 loop : 0.01 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP s 8 HIS 0.011 0.001 HIS m 182 PHE 0.024 0.001 PHE L 216 TYR 0.017 0.001 TYR d 5 ARG 0.007 0.000 ARG l 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 562 time to evaluate : 3.693 Fit side-chains revert: symmetry clash REVERT: M 216 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7662 (t80) REVERT: H 7 PHE cc_start: 0.7871 (p90) cc_final: 0.7526 (p90) REVERT: H 120 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5815 (mt) REVERT: H 255 MET cc_start: 0.5355 (mmt) cc_final: 0.4988 (ttt) REVERT: A 50 LYS cc_start: 0.7606 (tttt) cc_final: 0.7085 (ttmm) REVERT: A 52 ASN cc_start: 0.6658 (t0) cc_final: 0.6393 (t0) REVERT: D 33 LEU cc_start: 0.8305 (mt) cc_final: 0.7926 (mp) REVERT: F 8 TRP cc_start: 0.5962 (m100) cc_final: 0.5548 (m100) REVERT: G 43 TYR cc_start: 0.6403 (t80) cc_final: 0.6093 (t80) REVERT: G 44 ILE cc_start: 0.7276 (mm) cc_final: 0.7060 (mm) REVERT: 0 14 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7485 (t0) REVERT: C 20 ARG cc_start: 0.7332 (ttm170) cc_final: 0.6117 (tmt170) REVERT: l 202 LYS cc_start: 0.8099 (tttt) cc_final: 0.7853 (ptmt) REVERT: l 213 ASP cc_start: 0.8766 (m-30) cc_final: 0.8457 (m-30) REVERT: m 214 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8707 (tp) REVERT: m 216 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8488 (t80) REVERT: h 218 THR cc_start: 0.7844 (p) cc_final: 0.7503 (t) REVERT: h 255 MET cc_start: 0.3402 (mmt) cc_final: 0.2795 (ttp) REVERT: k 47 SER cc_start: 0.8238 (t) cc_final: 0.7985 (p) REVERT: n 34 VAL cc_start: 0.7938 (t) cc_final: 0.7715 (t) REVERT: p 44 ILE cc_start: 0.8368 (mm) cc_final: 0.8094 (mt) REVERT: q 24 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7820 (mm) REVERT: r 20 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6271 (mp) REVERT: u 1 MET cc_start: 0.5101 (tpp) cc_final: 0.2229 (tmm) REVERT: v 32 SER cc_start: 0.8429 (t) cc_final: 0.8192 (m) REVERT: v 44 ILE cc_start: 0.7887 (mm) cc_final: 0.7606 (mt) REVERT: y 33 LEU cc_start: 0.7007 (mt) cc_final: 0.6422 (tp) REVERT: z 45 TRP cc_start: 0.4341 (t60) cc_final: 0.4088 (t60) REVERT: z 46 ARG cc_start: 0.4282 (tmt170) cc_final: 0.3807 (mpt180) REVERT: 5 23 PHE cc_start: 0.3188 (OUTLIER) cc_final: 0.2323 (t80) REVERT: 6 45 GLU cc_start: 0.5762 (mp0) cc_final: 0.5301 (mp0) REVERT: Q 20 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7990 (tt0) outliers start: 62 outliers final: 44 residues processed: 596 average time/residue: 0.4611 time to fit residues: 454.1482 Evaluate side-chains 604 residues out of total 3161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 551 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 182 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain A residue 9 MET Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 9 residue 27 LEU Chi-restraints excluded: chain 0 residue 14 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain l residue 132 VAL Chi-restraints excluded: chain l residue 235 LEU Chi-restraints excluded: chain l residue 237 SER Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 32 VAL Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 214 LEU Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 118 ARG Chi-restraints excluded: chain h residue 143 SER Chi-restraints excluded: chain h residue 241 LEU Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain d residue 10 ILE Chi-restraints excluded: chain e residue 13 THR Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 19 GLU Chi-restraints excluded: chain j residue 40 LEU Chi-restraints excluded: chain k residue 37 SER Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain r residue 20 LEU Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain s residue 7 ILE Chi-restraints excluded: chain t residue 32 SER Chi-restraints excluded: chain w residue 34 ILE Chi-restraints excluded: chain w residue 40 SER Chi-restraints excluded: chain 5 residue 23 PHE Chi-restraints excluded: chain aa residue 10 THR Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain c residue 50 VAL Chi-restraints excluded: chain c residue 66 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN 0 16 GLN l 199 ASN t 16 GLN ** y 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.175487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.144714 restraints weight = 45919.107| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.12 r_work: 0.3250 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 37888 Z= 0.240 Angle : 0.785 59.144 52075 Z= 0.389 Chirality : 0.043 1.358 5131 Planarity : 0.004 0.106 6387 Dihedral : 14.776 141.278 6640 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 2.06 % Allowed : 17.43 % Favored : 80.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.14), residues: 3704 helix: 2.33 (0.10), residues: 2470 sheet: 0.04 (0.63), residues: 88 loop : 0.01 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP H 114 HIS 0.031 0.001 HIS G 39 PHE 0.021 0.001 PHE L 123 TYR 0.016 0.001 TYR d 5 ARG 0.048 0.001 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9118.13 seconds wall clock time: 164 minutes 57.54 seconds (9897.54 seconds total)