Starting phenix.real_space_refine on Wed Sep 25 13:55:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/09_2024/7sca_25031.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/09_2024/7sca_25031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/09_2024/7sca_25031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/09_2024/7sca_25031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/09_2024/7sca_25031.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sca_25031/09_2024/7sca_25031.cif" } resolution = 2.1 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= 0.001 sd= 0.174 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: 4 Type Number sf(0) Gaussians S 191 5.16 5 C 33993 2.51 5 N 9391 2.21 5 O 11862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 188 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55437 Number of models: 1 Model: "" Number of chains: 116 Chain: "AA" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AB" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AC" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AD" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AE" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AF" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AG" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AH" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AI" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AJ" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AK" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AL" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AM" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AN" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AO" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AP" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AQ" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AR" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AS" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AT" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AU" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AV" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "AW" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AX" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1269 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AY" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "AZ" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BA" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BB" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BC" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BD" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BE" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BF" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BG" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BH" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BI" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1240 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "BJ" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1270 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain: "BK" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1617 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "BL" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 275} Chain: "BM" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2122 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 260} Chain breaks: 2 Chain: "BN" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "AA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AG" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AK" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AM" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AO" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AQ" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AS" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AU" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AW" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AY" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BA" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BF" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BG" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BI" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AA" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "AB" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "AC" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "AD" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "AE" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "AF" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "AG" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "AH" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "AI" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "AJ" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "AK" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "AL" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "AM" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "AN" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "AO" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "AP" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "AQ" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "AR" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "AS" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "AT" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "AU" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "AV" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "AW" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "AX" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "AY" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "AZ" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "BA" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "BB" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "BC" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "BD" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "BE" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "BF" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "BG" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "BH" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "BI" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "BJ" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "BK" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "BL" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "BM" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "BN" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 24.57, per 1000 atoms: 0.44 Number of scatterers: 55437 At special positions: 0 Unit cell: (126, 127.05, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 191 16.00 O 11862 8.00 N 9391 7.00 C 33993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=54, symmetry=0 Number of additional bonds: simple=54, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.61 Conformation dependent library (CDL) restraints added in 5.3 seconds 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12588 Finding SS restraints... Secondary structure from input PDB file: 377 helices and 3 sheets defined 82.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 15 Processing helix chain 'AA' and resid 20 through 47 removed outlier: 4.499A pdb=" N ASNAA 35 " --> pdb=" O LEUAA 31 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALAAA 36 " --> pdb=" O ARGAA 32 " (cutoff:3.500A) Processing helix chain 'AA' and resid 47 through 63 Processing helix chain 'AA' and resid 64 through 69 removed outlier: 3.586A pdb=" N GLNAA 68 " --> pdb=" O PROAA 64 " (cutoff:3.500A) Processing helix chain 'AA' and resid 77 through 102 Processing helix chain 'AA' and resid 104 through 111 Processing helix chain 'AA' and resid 114 through 123 Processing helix chain 'AA' and resid 125 through 140 removed outlier: 4.198A pdb=" N TYRAA 129 " --> pdb=" O SERAA 125 " (cutoff:3.500A) Processing helix chain 'AA' and resid 143 through 162 Processing helix chain 'AB' and resid 3 through 16 removed outlier: 3.928A pdb=" N VALAB 8 " --> pdb=" O VALAB 4 " (cutoff:3.500A) Processing helix chain 'AB' and resid 20 through 47 removed outlier: 4.394A pdb=" N ASNAB 35 " --> pdb=" O VALAB 31 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYSAB 36 " --> pdb=" O ALAAB 32 " (cutoff:3.500A) Processing helix chain 'AB' and resid 47 through 62 Processing helix chain 'AB' and resid 63 through 67 removed outlier: 3.569A pdb=" N LEUAB 66 " --> pdb=" O GLNAB 63 " (cutoff:3.500A) Processing helix chain 'AB' and resid 75 through 100 Processing helix chain 'AB' and resid 102 through 109 Processing helix chain 'AB' and resid 112 through 121 Processing helix chain 'AB' and resid 123 through 143 Processing helix chain 'AB' and resid 153 through 172 Processing helix chain 'AC' and resid 3 through 15 Processing helix chain 'AC' and resid 20 through 47 removed outlier: 4.236A pdb=" N ASNAC 35 " --> pdb=" O LEUAC 31 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALAAC 36 " --> pdb=" O ARGAC 32 " (cutoff:3.500A) Processing helix chain 'AC' and resid 47 through 63 Processing helix chain 'AC' and resid 64 through 69 removed outlier: 3.933A pdb=" N GLNAC 68 " --> pdb=" O PROAC 64 " (cutoff:3.500A) Processing helix chain 'AC' and resid 77 through 102 Processing helix chain 'AC' and resid 104 through 111 Processing helix chain 'AC' and resid 114 through 122 Processing helix chain 'AC' and resid 125 through 140 removed outlier: 4.033A pdb=" N TYRAC 129 " --> pdb=" O SERAC 125 " (cutoff:3.500A) Processing helix chain 'AC' and resid 144 through 162 Processing helix chain 'AD' and resid 3 through 16 removed outlier: 3.884A pdb=" N VALAD 8 " --> pdb=" O VALAD 4 " (cutoff:3.500A) Processing helix chain 'AD' and resid 20 through 33 Processing helix chain 'AD' and resid 33 through 47 Processing helix chain 'AD' and resid 47 through 63 Processing helix chain 'AD' and resid 64 through 67 Processing helix chain 'AD' and resid 75 through 100 Processing helix chain 'AD' and resid 102 through 109 Processing helix chain 'AD' and resid 112 through 121 Processing helix chain 'AD' and resid 123 through 143 Processing helix chain 'AD' and resid 153 through 172 Processing helix chain 'AE' and resid 3 through 15 Processing helix chain 'AE' and resid 20 through 47 removed outlier: 4.283A pdb=" N ASNAE 35 " --> pdb=" O LEUAE 31 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALAAE 36 " --> pdb=" O ARGAE 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASNAE 47 " --> pdb=" O ALAAE 43 " (cutoff:3.500A) Processing helix chain 'AE' and resid 47 through 63 Processing helix chain 'AE' and resid 64 through 68 Processing helix chain 'AE' and resid 77 through 102 Processing helix chain 'AE' and resid 104 through 111 Processing helix chain 'AE' and resid 114 through 123 Processing helix chain 'AE' and resid 125 through 140 removed outlier: 4.151A pdb=" N TYRAE 129 " --> pdb=" O SERAE 125 " (cutoff:3.500A) Processing helix chain 'AE' and resid 143 through 162 Processing helix chain 'AF' and resid 3 through 16 removed outlier: 3.999A pdb=" N VALAF 8 " --> pdb=" O VALAF 4 " (cutoff:3.500A) Processing helix chain 'AF' and resid 20 through 33 Processing helix chain 'AF' and resid 33 through 47 Processing helix chain 'AF' and resid 47 through 62 Processing helix chain 'AF' and resid 63 through 67 removed outlier: 3.530A pdb=" N LEUAF 66 " --> pdb=" O GLNAF 63 " (cutoff:3.500A) Processing helix chain 'AF' and resid 75 through 100 Processing helix chain 'AF' and resid 102 through 109 Processing helix chain 'AF' and resid 112 through 121 Processing helix chain 'AF' and resid 123 through 143 Processing helix chain 'AF' and resid 153 through 172 Processing helix chain 'AG' and resid 3 through 15 Processing helix chain 'AG' and resid 20 through 47 removed outlier: 4.380A pdb=" N ASNAG 35 " --> pdb=" O LEUAG 31 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALAAG 36 " --> pdb=" O ARGAG 32 " (cutoff:3.500A) Processing helix chain 'AG' and resid 47 through 63 Processing helix chain 'AG' and resid 64 through 68 removed outlier: 3.601A pdb=" N GLNAG 68 " --> pdb=" O TYRAG 65 " (cutoff:3.500A) Processing helix chain 'AG' and resid 77 through 102 Processing helix chain 'AG' and resid 104 through 111 Processing helix chain 'AG' and resid 114 through 122 Processing helix chain 'AG' and resid 125 through 140 removed outlier: 3.996A pdb=" N TYRAG 129 " --> pdb=" O SERAG 125 " (cutoff:3.500A) Processing helix chain 'AG' and resid 143 through 162 removed outlier: 3.721A pdb=" N ARGAG 147 " --> pdb=" O SERAG 143 " (cutoff:3.500A) Processing helix chain 'AH' and resid 3 through 16 removed outlier: 3.963A pdb=" N VALAH 8 " --> pdb=" O VALAH 4 " (cutoff:3.500A) Processing helix chain 'AH' and resid 20 through 33 Processing helix chain 'AH' and resid 33 through 47 removed outlier: 3.581A pdb=" N ASNAH 47 " --> pdb=" O ARGAH 43 " (cutoff:3.500A) Processing helix chain 'AH' and resid 47 through 63 Processing helix chain 'AH' and resid 75 through 100 Processing helix chain 'AH' and resid 102 through 109 Processing helix chain 'AH' and resid 112 through 121 Processing helix chain 'AH' and resid 123 through 143 Processing helix chain 'AH' and resid 153 through 172 Processing helix chain 'AI' and resid 3 through 15 Processing helix chain 'AI' and resid 20 through 47 removed outlier: 4.228A pdb=" N ASNAI 35 " --> pdb=" O LEUAI 31 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALAAI 36 " --> pdb=" O ARGAI 32 " (cutoff:3.500A) Processing helix chain 'AI' and resid 47 through 63 Processing helix chain 'AI' and resid 64 through 69 removed outlier: 3.803A pdb=" N GLNAI 68 " --> pdb=" O PROAI 64 " (cutoff:3.500A) Processing helix chain 'AI' and resid 77 through 102 Processing helix chain 'AI' and resid 104 through 111 Processing helix chain 'AI' and resid 114 through 122 Processing helix chain 'AI' and resid 125 through 140 removed outlier: 3.993A pdb=" N TYRAI 129 " --> pdb=" O SERAI 125 " (cutoff:3.500A) Processing helix chain 'AI' and resid 143 through 162 Processing helix chain 'AJ' and resid 3 through 16 removed outlier: 4.160A pdb=" N VALAJ 8 " --> pdb=" O VALAJ 4 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 20 through 33 Processing helix chain 'AJ' and resid 33 through 47 Processing helix chain 'AJ' and resid 47 through 63 Processing helix chain 'AJ' and resid 75 through 100 Processing helix chain 'AJ' and resid 102 through 108 Processing helix chain 'AJ' and resid 112 through 121 Processing helix chain 'AJ' and resid 123 through 143 Processing helix chain 'AJ' and resid 153 through 172 Processing helix chain 'AK' and resid 3 through 15 Processing helix chain 'AK' and resid 20 through 47 removed outlier: 4.668A pdb=" N ASNAK 35 " --> pdb=" O LEUAK 31 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALAAK 36 " --> pdb=" O ARGAK 32 " (cutoff:3.500A) Processing helix chain 'AK' and resid 47 through 63 Processing helix chain 'AK' and resid 64 through 68 Processing helix chain 'AK' and resid 77 through 102 Processing helix chain 'AK' and resid 104 through 111 Processing helix chain 'AK' and resid 114 through 122 Processing helix chain 'AK' and resid 125 through 140 removed outlier: 3.999A pdb=" N TYRAK 129 " --> pdb=" O SERAK 125 " (cutoff:3.500A) Processing helix chain 'AK' and resid 143 through 162 Processing helix chain 'AL' and resid 3 through 16 removed outlier: 4.004A pdb=" N VALAL 8 " --> pdb=" O VALAL 4 " (cutoff:3.500A) Processing helix chain 'AL' and resid 20 through 33 Processing helix chain 'AL' and resid 33 through 47 Processing helix chain 'AL' and resid 47 through 63 Processing helix chain 'AL' and resid 63 through 68 removed outlier: 4.320A pdb=" N ILEAL 67 " --> pdb=" O GLNAL 63 " (cutoff:3.500A) Processing helix chain 'AL' and resid 75 through 100 Processing helix chain 'AL' and resid 102 through 109 Processing helix chain 'AL' and resid 112 through 121 Processing helix chain 'AL' and resid 123 through 143 Processing helix chain 'AL' and resid 153 through 172 Processing helix chain 'AM' and resid 3 through 15 Processing helix chain 'AM' and resid 20 through 47 removed outlier: 4.617A pdb=" N ASNAM 35 " --> pdb=" O LEUAM 31 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALAAM 36 " --> pdb=" O ARGAM 32 " (cutoff:3.500A) Processing helix chain 'AM' and resid 47 through 63 Processing helix chain 'AM' and resid 64 through 68 Processing helix chain 'AM' and resid 77 through 102 Processing helix chain 'AM' and resid 104 through 111 Processing helix chain 'AM' and resid 114 through 122 Processing helix chain 'AM' and resid 125 through 140 removed outlier: 4.020A pdb=" N TYRAM 129 " --> pdb=" O SERAM 125 " (cutoff:3.500A) Processing helix chain 'AM' and resid 143 through 162 Processing helix chain 'AN' and resid 3 through 16 removed outlier: 3.803A pdb=" N VALAN 8 " --> pdb=" O VALAN 4 " (cutoff:3.500A) Processing helix chain 'AN' and resid 20 through 33 Processing helix chain 'AN' and resid 33 through 47 Processing helix chain 'AN' and resid 47 through 63 Processing helix chain 'AN' and resid 64 through 67 Processing helix chain 'AN' and resid 75 through 100 Processing helix chain 'AN' and resid 102 through 109 Processing helix chain 'AN' and resid 112 through 121 Processing helix chain 'AN' and resid 123 through 143 Processing helix chain 'AN' and resid 153 through 172 Processing helix chain 'AO' and resid 3 through 15 Processing helix chain 'AO' and resid 20 through 47 removed outlier: 4.308A pdb=" N ASNAO 35 " --> pdb=" O LEUAO 31 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALAAO 36 " --> pdb=" O ARGAO 32 " (cutoff:3.500A) Processing helix chain 'AO' and resid 47 through 63 Processing helix chain 'AO' and resid 64 through 68 Processing helix chain 'AO' and resid 77 through 102 Processing helix chain 'AO' and resid 104 through 111 Processing helix chain 'AO' and resid 114 through 122 Processing helix chain 'AO' and resid 125 through 140 removed outlier: 3.916A pdb=" N TYRAO 129 " --> pdb=" O SERAO 125 " (cutoff:3.500A) Processing helix chain 'AO' and resid 143 through 162 Processing helix chain 'AP' and resid 3 through 16 removed outlier: 4.112A pdb=" N VALAP 8 " --> pdb=" O VALAP 4 " (cutoff:3.500A) Processing helix chain 'AP' and resid 20 through 33 Processing helix chain 'AP' and resid 33 through 47 Processing helix chain 'AP' and resid 47 through 63 Processing helix chain 'AP' and resid 75 through 100 Processing helix chain 'AP' and resid 102 through 109 Processing helix chain 'AP' and resid 112 through 121 Processing helix chain 'AP' and resid 123 through 143 Processing helix chain 'AP' and resid 153 through 172 Processing helix chain 'AQ' and resid 3 through 15 Processing helix chain 'AQ' and resid 20 through 47 removed outlier: 4.454A pdb=" N ASNAQ 35 " --> pdb=" O LEUAQ 31 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALAAQ 36 " --> pdb=" O ARGAQ 32 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 47 through 63 Processing helix chain 'AQ' and resid 64 through 68 Processing helix chain 'AQ' and resid 77 through 102 Processing helix chain 'AQ' and resid 104 through 111 Processing helix chain 'AQ' and resid 114 through 122 Processing helix chain 'AQ' and resid 125 through 140 removed outlier: 4.106A pdb=" N TYRAQ 129 " --> pdb=" O SERAQ 125 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 144 through 162 Processing helix chain 'AR' and resid 3 through 16 removed outlier: 3.706A pdb=" N VALAR 8 " --> pdb=" O VALAR 4 " (cutoff:3.500A) Processing helix chain 'AR' and resid 20 through 47 removed outlier: 4.512A pdb=" N ASNAR 35 " --> pdb=" O VALAR 31 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYSAR 36 " --> pdb=" O ALAAR 32 " (cutoff:3.500A) Processing helix chain 'AR' and resid 47 through 63 Processing helix chain 'AR' and resid 64 through 67 Processing helix chain 'AR' and resid 75 through 100 Processing helix chain 'AR' and resid 102 through 109 Processing helix chain 'AR' and resid 112 through 121 Processing helix chain 'AR' and resid 123 through 143 Processing helix chain 'AR' and resid 153 through 172 removed outlier: 3.509A pdb=" N ALAAR 172 " --> pdb=" O ALAAR 168 " (cutoff:3.500A) Processing helix chain 'AS' and resid 3 through 15 Processing helix chain 'AS' and resid 20 through 47 removed outlier: 4.569A pdb=" N ASNAS 35 " --> pdb=" O LEUAS 31 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALAAS 36 " --> pdb=" O ARGAS 32 " (cutoff:3.500A) Processing helix chain 'AS' and resid 47 through 63 Processing helix chain 'AS' and resid 64 through 68 Processing helix chain 'AS' and resid 77 through 102 Processing helix chain 'AS' and resid 104 through 111 Processing helix chain 'AS' and resid 114 through 122 Processing helix chain 'AS' and resid 125 through 140 removed outlier: 3.926A pdb=" N TYRAS 129 " --> pdb=" O SERAS 125 " (cutoff:3.500A) Processing helix chain 'AS' and resid 143 through 162 Processing helix chain 'AT' and resid 3 through 16 removed outlier: 4.092A pdb=" N VALAT 8 " --> pdb=" O VALAT 4 " (cutoff:3.500A) Processing helix chain 'AT' and resid 20 through 33 Processing helix chain 'AT' and resid 33 through 47 Processing helix chain 'AT' and resid 47 through 63 Processing helix chain 'AT' and resid 64 through 67 Processing helix chain 'AT' and resid 75 through 100 Processing helix chain 'AT' and resid 102 through 109 Processing helix chain 'AT' and resid 112 through 121 Processing helix chain 'AT' and resid 123 through 144 Processing helix chain 'AT' and resid 153 through 172 removed outlier: 3.565A pdb=" N VALAT 171 " --> pdb=" O ALAAT 167 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAT 172 " --> pdb=" O ALAAT 168 " (cutoff:3.500A) Processing helix chain 'AU' and resid 3 through 15 Processing helix chain 'AU' and resid 20 through 47 removed outlier: 4.376A pdb=" N ASNAU 35 " --> pdb=" O LEUAU 31 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALAAU 36 " --> pdb=" O ARGAU 32 " (cutoff:3.500A) Processing helix chain 'AU' and resid 47 through 63 Processing helix chain 'AU' and resid 64 through 68 Processing helix chain 'AU' and resid 77 through 102 Processing helix chain 'AU' and resid 104 through 111 Processing helix chain 'AU' and resid 114 through 122 Processing helix chain 'AU' and resid 125 through 140 removed outlier: 4.101A pdb=" N TYRAU 129 " --> pdb=" O SERAU 125 " (cutoff:3.500A) Processing helix chain 'AU' and resid 143 through 162 Processing helix chain 'AV' and resid 3 through 16 removed outlier: 3.815A pdb=" N VALAV 8 " --> pdb=" O VALAV 4 " (cutoff:3.500A) Processing helix chain 'AV' and resid 20 through 33 Processing helix chain 'AV' and resid 33 through 47 Processing helix chain 'AV' and resid 47 through 63 Processing helix chain 'AV' and resid 64 through 67 Processing helix chain 'AV' and resid 75 through 100 Processing helix chain 'AV' and resid 102 through 109 Processing helix chain 'AV' and resid 112 through 121 Processing helix chain 'AV' and resid 123 through 143 Processing helix chain 'AV' and resid 153 through 172 removed outlier: 3.529A pdb=" N VALAV 171 " --> pdb=" O ALAAV 167 " (cutoff:3.500A) Processing helix chain 'AW' and resid 3 through 16 Processing helix chain 'AW' and resid 20 through 47 removed outlier: 4.525A pdb=" N ASNAW 35 " --> pdb=" O LEUAW 31 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALAAW 36 " --> pdb=" O ARGAW 32 " (cutoff:3.500A) Processing helix chain 'AW' and resid 47 through 63 Processing helix chain 'AW' and resid 64 through 69 Processing helix chain 'AW' and resid 77 through 102 Processing helix chain 'AW' and resid 104 through 111 Processing helix chain 'AW' and resid 114 through 123 Processing helix chain 'AW' and resid 125 through 140 removed outlier: 3.976A pdb=" N TYRAW 129 " --> pdb=" O SERAW 125 " (cutoff:3.500A) Processing helix chain 'AW' and resid 144 through 162 Processing helix chain 'AX' and resid 3 through 14 removed outlier: 3.831A pdb=" N VALAX 8 " --> pdb=" O VALAX 4 " (cutoff:3.500A) Processing helix chain 'AX' and resid 20 through 33 Processing helix chain 'AX' and resid 33 through 47 removed outlier: 3.519A pdb=" N ASNAX 47 " --> pdb=" O ARGAX 43 " (cutoff:3.500A) Processing helix chain 'AX' and resid 47 through 63 Processing helix chain 'AX' and resid 64 through 67 Processing helix chain 'AX' and resid 75 through 100 Processing helix chain 'AX' and resid 102 through 109 Processing helix chain 'AX' and resid 112 through 121 Processing helix chain 'AX' and resid 123 through 143 removed outlier: 3.818A pdb=" N ASPAX 140 " --> pdb=" O GLUAX 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILEAX 141 " --> pdb=" O ALAAX 137 " (cutoff:3.500A) Processing helix chain 'AX' and resid 153 through 172 Processing helix chain 'AY' and resid 3 through 15 Processing helix chain 'AY' and resid 20 through 47 removed outlier: 4.453A pdb=" N ASNAY 35 " --> pdb=" O LEUAY 31 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALAAY 36 " --> pdb=" O ARGAY 32 " (cutoff:3.500A) Processing helix chain 'AY' and resid 47 through 63 Processing helix chain 'AY' and resid 64 through 68 Processing helix chain 'AY' and resid 77 through 102 Processing helix chain 'AY' and resid 104 through 111 Processing helix chain 'AY' and resid 114 through 122 Processing helix chain 'AY' and resid 125 through 140 removed outlier: 4.128A pdb=" N TYRAY 129 " --> pdb=" O SERAY 125 " (cutoff:3.500A) Processing helix chain 'AY' and resid 143 through 162 Processing helix chain 'AZ' and resid 3 through 16 removed outlier: 3.726A pdb=" N VALAZ 8 " --> pdb=" O VALAZ 4 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 20 through 33 Processing helix chain 'AZ' and resid 33 through 47 Processing helix chain 'AZ' and resid 47 through 63 Processing helix chain 'AZ' and resid 75 through 100 Processing helix chain 'AZ' and resid 102 through 109 Processing helix chain 'AZ' and resid 112 through 121 Processing helix chain 'AZ' and resid 123 through 143 Processing helix chain 'AZ' and resid 153 through 172 removed outlier: 3.510A pdb=" N ALAAZ 172 " --> pdb=" O ALAAZ 168 " (cutoff:3.500A) Processing helix chain 'BA' and resid 3 through 16 Processing helix chain 'BA' and resid 20 through 47 removed outlier: 4.353A pdb=" N ASNBA 35 " --> pdb=" O LEUBA 31 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALABA 36 " --> pdb=" O ARGBA 32 " (cutoff:3.500A) Processing helix chain 'BA' and resid 47 through 63 Processing helix chain 'BA' and resid 64 through 68 Processing helix chain 'BA' and resid 77 through 102 Processing helix chain 'BA' and resid 104 through 111 Processing helix chain 'BA' and resid 114 through 122 Processing helix chain 'BA' and resid 125 through 140 removed outlier: 3.961A pdb=" N TYRBA 129 " --> pdb=" O SERBA 125 " (cutoff:3.500A) Processing helix chain 'BA' and resid 143 through 162 Processing helix chain 'BB' and resid 3 through 16 removed outlier: 3.598A pdb=" N VALBB 8 " --> pdb=" O VALBB 4 " (cutoff:3.500A) Processing helix chain 'BB' and resid 20 through 33 Processing helix chain 'BB' and resid 33 through 47 Processing helix chain 'BB' and resid 47 through 63 Processing helix chain 'BB' and resid 64 through 67 Processing helix chain 'BB' and resid 75 through 100 Processing helix chain 'BB' and resid 102 through 109 Processing helix chain 'BB' and resid 112 through 121 Processing helix chain 'BB' and resid 123 through 143 Processing helix chain 'BB' and resid 153 through 172 Processing helix chain 'BC' and resid 3 through 16 Processing helix chain 'BC' and resid 20 through 47 removed outlier: 4.263A pdb=" N ASNBC 35 " --> pdb=" O LEUBC 31 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALABC 36 " --> pdb=" O ARGBC 32 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASNBC 47 " --> pdb=" O ALABC 43 " (cutoff:3.500A) Processing helix chain 'BC' and resid 47 through 63 Processing helix chain 'BC' and resid 64 through 69 Processing helix chain 'BC' and resid 77 through 102 Processing helix chain 'BC' and resid 104 through 111 Processing helix chain 'BC' and resid 114 through 122 Processing helix chain 'BC' and resid 125 through 140 removed outlier: 4.012A pdb=" N TYRBC 129 " --> pdb=" O SERBC 125 " (cutoff:3.500A) Processing helix chain 'BC' and resid 144 through 162 Processing helix chain 'BD' and resid 3 through 15 removed outlier: 3.741A pdb=" N VALBD 8 " --> pdb=" O VALBD 4 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARGBD 15 " --> pdb=" O GLNBD 11 " (cutoff:3.500A) Processing helix chain 'BD' and resid 20 through 33 Processing helix chain 'BD' and resid 33 through 47 Processing helix chain 'BD' and resid 47 through 63 Processing helix chain 'BD' and resid 63 through 68 removed outlier: 4.281A pdb=" N ILEBD 67 " --> pdb=" O GLNBD 63 " (cutoff:3.500A) Processing helix chain 'BD' and resid 75 through 100 Processing helix chain 'BD' and resid 102 through 109 Processing helix chain 'BD' and resid 112 through 121 Processing helix chain 'BD' and resid 123 through 143 Processing helix chain 'BD' and resid 153 through 172 Processing helix chain 'BE' and resid 3 through 15 Processing helix chain 'BE' and resid 20 through 47 removed outlier: 4.271A pdb=" N ASNBE 35 " --> pdb=" O LEUBE 31 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALABE 36 " --> pdb=" O ARGBE 32 " (cutoff:3.500A) Processing helix chain 'BE' and resid 47 through 63 Processing helix chain 'BE' and resid 64 through 68 Processing helix chain 'BE' and resid 77 through 102 Processing helix chain 'BE' and resid 104 through 111 Processing helix chain 'BE' and resid 114 through 122 Processing helix chain 'BE' and resid 125 through 140 removed outlier: 3.969A pdb=" N TYRBE 129 " --> pdb=" O SERBE 125 " (cutoff:3.500A) Processing helix chain 'BE' and resid 143 through 162 removed outlier: 3.661A pdb=" N ARGBE 147 " --> pdb=" O SERBE 143 " (cutoff:3.500A) Processing helix chain 'BF' and resid 3 through 16 removed outlier: 3.922A pdb=" N VALBF 8 " --> pdb=" O VALBF 4 " (cutoff:3.500A) Processing helix chain 'BF' and resid 20 through 33 Processing helix chain 'BF' and resid 33 through 46 Processing helix chain 'BF' and resid 47 through 63 Processing helix chain 'BF' and resid 64 through 67 Processing helix chain 'BF' and resid 75 through 100 Processing helix chain 'BF' and resid 102 through 109 Processing helix chain 'BF' and resid 112 through 121 Processing helix chain 'BF' and resid 123 through 144 Processing helix chain 'BF' and resid 153 through 172 Processing helix chain 'BG' and resid 3 through 15 removed outlier: 3.676A pdb=" N GLNBG 15 " --> pdb=" O THRBG 11 " (cutoff:3.500A) Processing helix chain 'BG' and resid 20 through 47 removed outlier: 4.363A pdb=" N ASNBG 35 " --> pdb=" O LEUBG 31 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ALABG 36 " --> pdb=" O ARGBG 32 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASNBG 47 " --> pdb=" O ALABG 43 " (cutoff:3.500A) Processing helix chain 'BG' and resid 47 through 63 Processing helix chain 'BG' and resid 64 through 68 Processing helix chain 'BG' and resid 77 through 102 Processing helix chain 'BG' and resid 104 through 111 Processing helix chain 'BG' and resid 114 through 122 removed outlier: 3.819A pdb=" N ILEBG 118 " --> pdb=" O GLYBG 114 " (cutoff:3.500A) Processing helix chain 'BG' and resid 125 through 140 removed outlier: 3.921A pdb=" N TYRBG 129 " --> pdb=" O SERBG 125 " (cutoff:3.500A) Processing helix chain 'BG' and resid 144 through 162 Processing helix chain 'BH' and resid 3 through 16 removed outlier: 3.948A pdb=" N VALBH 8 " --> pdb=" O VALBH 4 " (cutoff:3.500A) Processing helix chain 'BH' and resid 20 through 33 removed outlier: 3.559A pdb=" N GLUBH 33 " --> pdb=" O ALABH 29 " (cutoff:3.500A) Processing helix chain 'BH' and resid 33 through 47 Processing helix chain 'BH' and resid 47 through 63 Processing helix chain 'BH' and resid 64 through 67 Processing helix chain 'BH' and resid 75 through 100 Processing helix chain 'BH' and resid 102 through 109 Processing helix chain 'BH' and resid 112 through 121 Processing helix chain 'BH' and resid 123 through 143 Processing helix chain 'BH' and resid 153 through 172 removed outlier: 3.668A pdb=" N VALBH 171 " --> pdb=" O ALABH 167 " (cutoff:3.500A) Processing helix chain 'BI' and resid 3 through 15 Processing helix chain 'BI' and resid 20 through 47 removed outlier: 4.387A pdb=" N ASNBI 35 " --> pdb=" O LEUBI 31 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALABI 36 " --> pdb=" O ARGBI 32 " (cutoff:3.500A) Processing helix chain 'BI' and resid 47 through 63 Processing helix chain 'BI' and resid 64 through 68 Processing helix chain 'BI' and resid 77 through 102 Processing helix chain 'BI' and resid 104 through 111 Processing helix chain 'BI' and resid 114 through 122 Processing helix chain 'BI' and resid 125 through 140 removed outlier: 4.164A pdb=" N TYRBI 129 " --> pdb=" O SERBI 125 " (cutoff:3.500A) Processing helix chain 'BI' and resid 143 through 162 Processing helix chain 'BJ' and resid 3 through 16 removed outlier: 3.542A pdb=" N VALBJ 8 " --> pdb=" O VALBJ 4 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 20 through 33 Processing helix chain 'BJ' and resid 33 through 47 removed outlier: 3.502A pdb=" N ASNBJ 47 " --> pdb=" O ARGBJ 43 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 47 through 63 Processing helix chain 'BJ' and resid 64 through 67 Processing helix chain 'BJ' and resid 75 through 100 Processing helix chain 'BJ' and resid 102 through 109 Processing helix chain 'BJ' and resid 112 through 121 Processing helix chain 'BJ' and resid 123 through 143 Processing helix chain 'BJ' and resid 153 through 172 removed outlier: 3.541A pdb=" N VALBJ 171 " --> pdb=" O ALABJ 167 " (cutoff:3.500A) Processing helix chain 'BK' and resid 38 through 55 Processing helix chain 'BK' and resid 63 through 72 Processing helix chain 'BK' and resid 76 through 87 Processing helix chain 'BK' and resid 87 through 94 Processing helix chain 'BK' and resid 100 through 105 Processing helix chain 'BK' and resid 107 through 112 Processing helix chain 'BK' and resid 118 through 133 removed outlier: 3.637A pdb=" N LYSBK 122 " --> pdb=" O SERBK 118 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILEBK 127 " --> pdb=" O ILEBK 123 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VALBK 128 " --> pdb=" O ALABK 124 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VALBK 129 " --> pdb=" O TRPBK 125 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALABK 130 " --> pdb=" O SERBK 126 " (cutoff:3.500A) Processing helix chain 'BK' and resid 133 through 143 Processing helix chain 'BK' and resid 144 through 151 Processing helix chain 'BK' and resid 173 through 178 Processing helix chain 'BK' and resid 182 through 190 Processing helix chain 'BL' and resid 12 through 17 removed outlier: 3.795A pdb=" N GLUBL 17 " --> pdb=" O ALABL 13 " (cutoff:3.500A) Processing helix chain 'BL' and resid 28 through 44 Processing helix chain 'BL' and resid 50 through 54 Processing helix chain 'BL' and resid 55 through 64 Processing helix chain 'BL' and resid 68 through 79 Processing helix chain 'BL' and resid 79 through 87 Processing helix chain 'BL' and resid 91 through 104 Processing helix chain 'BL' and resid 110 through 125 removed outlier: 3.808A pdb=" N VALBL 114 " --> pdb=" O SERBL 110 " (cutoff:3.500A) Processing helix chain 'BL' and resid 125 through 135 Processing helix chain 'BL' and resid 136 through 143 Processing helix chain 'BL' and resid 160 through 171 removed outlier: 3.602A pdb=" N PHEBL 164 " --> pdb=" O ARGBL 160 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHEBL 168 " --> pdb=" O PHEBL 164 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGBL 169 " --> pdb=" O THRBL 165 " (cutoff:3.500A) Processing helix chain 'BL' and resid 189 through 196 Processing helix chain 'BL' and resid 229 through 233 Processing helix chain 'BL' and resid 267 through 278 Processing helix chain 'BM' and resid 3 through 11 removed outlier: 4.091A pdb=" N ARGBM 9 " --> pdb=" O VALBM 5 " (cutoff:3.500A) Processing helix chain 'BM' and resid 12 through 17 Processing helix chain 'BM' and resid 28 through 44 Processing helix chain 'BM' and resid 50 through 54 Processing helix chain 'BM' and resid 55 through 64 Processing helix chain 'BM' and resid 68 through 79 Processing helix chain 'BM' and resid 79 through 87 Processing helix chain 'BM' and resid 91 through 104 Processing helix chain 'BM' and resid 111 through 116 Processing helix chain 'BM' and resid 118 through 135 removed outlier: 8.129A pdb=" N TYRBM 126 " --> pdb=" O HISBM 122 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLUBM 127 " --> pdb=" O GLNBM 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALABM 128 " --> pdb=" O GLYBM 124 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYRBM 133 " --> pdb=" O GLUBM 129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILEBM 134 " --> pdb=" O ILEBM 130 " (cutoff:3.500A) Processing helix chain 'BM' and resid 136 through 143 Processing helix chain 'BM' and resid 162 through 172 removed outlier: 3.792A pdb=" N SERBM 166 " --> pdb=" O THRBM 162 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHEBM 169 " --> pdb=" O PHEBM 165 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLNBM 170 " --> pdb=" O SERBM 166 " (cutoff:3.500A) Processing helix chain 'BM' and resid 190 through 196 Processing helix chain 'BM' and resid 252 through 263 Processing helix chain 'BN' and resid 30 through 34 removed outlier: 3.852A pdb=" N GLUBN 34 " --> pdb=" O ASPBN 31 " (cutoff:3.500A) Processing helix chain 'BN' and resid 54 through 65 removed outlier: 3.575A pdb=" N ARGBN 60 " --> pdb=" O ASNBN 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'BL' and resid 259 through 264 removed outlier: 7.233A pdb=" N LEUBL 238 " --> pdb=" O PROBL 287 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARGBL 240 " --> pdb=" O ILEBL 285 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILEBL 285 " --> pdb=" O ARGBL 240 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLUBL 242 " --> pdb=" O ALABL 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'BM' and resid 243 through 249 removed outlier: 7.223A pdb=" N METBM 222 " --> pdb=" O LEUBM 272 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEUBM 272 " --> pdb=" O METBM 222 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGBM 224 " --> pdb=" O ILEBM 270 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILEBM 270 " --> pdb=" O ARGBM 224 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLNBM 226 " --> pdb=" O THRBM 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BN' and resid 46 through 51 removed outlier: 3.743A pdb=" N ASNBN 71 " --> pdb=" O GLUBN 23 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SERBN 25 " --> pdb=" O ILEBN 69 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ILEBN 69 " --> pdb=" O SERBN 25 " (cutoff:3.500A) 4065 hydrogen bonds defined for protein. 12051 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: 20.52 Time building geometry restraints manager: 12.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9472 1.31 - 1.44: 14772 1.44 - 1.57: 30485 1.57 - 1.69: 10 1.69 - 1.82: 291 Bond restraints: 55030 Sorted by residual: bond pdb=" CG1 ILEAW 118 " pdb=" CD1 ILEAW 118 " ideal model delta sigma weight residual 1.513 1.345 0.168 3.90e-02 6.57e+02 1.85e+01 bond pdb=" CB GLNAU 15 " pdb=" CG GLNAU 15 " ideal model delta sigma weight residual 1.520 1.398 0.122 3.00e-02 1.11e+03 1.64e+01 bond pdb=" CB METAD 134 " pdb=" CG METAD 134 " ideal model delta sigma weight residual 1.520 1.403 0.117 3.00e-02 1.11e+03 1.52e+01 bond pdb=" SD METAD 134 " pdb=" CE METAD 134 " ideal model delta sigma weight residual 1.791 1.695 0.096 2.50e-02 1.60e+03 1.46e+01 bond pdb=" CG1 ILEBE 118 " pdb=" CD1 ILEBE 118 " ideal model delta sigma weight residual 1.513 1.377 0.136 3.90e-02 6.57e+02 1.21e+01 ... (remaining 55025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 73371 3.36 - 6.73: 1285 6.73 - 10.09: 156 10.09 - 13.46: 33 13.46 - 16.82: 9 Bond angle restraints: 74854 Sorted by residual: angle pdb=" CD ARGBI 120 " pdb=" NE ARGBI 120 " pdb=" CZ ARGBI 120 " ideal model delta sigma weight residual 124.40 109.36 15.04 1.40e+00 5.10e-01 1.15e+02 angle pdb=" C ARGBD 114 " pdb=" CA ARGBD 114 " pdb=" CB ARGBD 114 " ideal model delta sigma weight residual 110.88 98.27 12.61 1.57e+00 4.06e-01 6.45e+01 angle pdb=" CG LYSBC 134 " pdb=" CD LYSBC 134 " pdb=" CE LYSBC 134 " ideal model delta sigma weight residual 111.30 96.67 14.63 2.30e+00 1.89e-01 4.05e+01 angle pdb=" CA GLNBM 259 " pdb=" CB GLNBM 259 " pdb=" CG GLNBM 259 " ideal model delta sigma weight residual 114.10 126.80 -12.70 2.00e+00 2.50e-01 4.04e+01 angle pdb=" N GLNAU 15 " pdb=" CA GLNAU 15 " pdb=" CB GLNAU 15 " ideal model delta sigma weight residual 110.44 100.98 9.46 1.53e+00 4.27e-01 3.82e+01 ... (remaining 74849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.56: 30987 18.56 - 37.12: 2253 37.12 - 55.68: 427 55.68 - 74.25: 243 74.25 - 92.81: 66 Dihedral angle restraints: 33976 sinusoidal: 14260 harmonic: 19716 Sorted by residual: dihedral pdb=" C ARGBD 114 " pdb=" N ARGBD 114 " pdb=" CA ARGBD 114 " pdb=" CB ARGBD 114 " ideal model delta harmonic sigma weight residual -122.60 -106.42 -16.18 0 2.50e+00 1.60e-01 4.19e+01 dihedral pdb=" C GLNAQ 68 " pdb=" N GLNAQ 68 " pdb=" CA GLNAQ 68 " pdb=" CB GLNAQ 68 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" N GLNAQ 68 " pdb=" C GLNAQ 68 " pdb=" CA GLNAQ 68 " pdb=" CB GLNAQ 68 " ideal model delta harmonic sigma weight residual 122.80 134.99 -12.19 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 33973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 7347 0.107 - 0.215: 780 0.215 - 0.322: 41 0.322 - 0.430: 10 0.430 - 0.537: 3 Chirality restraints: 8181 Sorted by residual: chirality pdb=" CA GLNAQ 68 " pdb=" N GLNAQ 68 " pdb=" C GLNAQ 68 " pdb=" CB GLNAQ 68 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CB ILEAM 118 " pdb=" CA ILEAM 118 " pdb=" CG1 ILEAM 118 " pdb=" CG2 ILEAM 118 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CB VALBK 17 " pdb=" CA VALBK 17 " pdb=" CG1 VALBK 17 " pdb=" CG2 VALBK 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 8178 not shown) Planarity restraints: 9805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYCBF 201 " 0.081 2.00e-02 2.50e+03 2.64e-01 1.56e+03 pdb=" OB CYCBF 201 " 0.143 2.00e-02 2.50e+03 pdb=" C1B CYCBF 201 " -0.071 2.00e-02 2.50e+03 pdb=" C2B CYCBF 201 " 0.134 2.00e-02 2.50e+03 pdb=" C3B CYCBF 201 " 0.106 2.00e-02 2.50e+03 pdb=" C4B CYCBF 201 " 0.123 2.00e-02 2.50e+03 pdb=" CAB CYCBF 201 " -0.522 2.00e-02 2.50e+03 pdb=" CHB CYCBF 201 " -0.369 2.00e-02 2.50e+03 pdb=" CMB CYCBF 201 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAX 201 " -0.100 2.00e-02 2.50e+03 1.92e-01 8.28e+02 pdb=" OB CYCAX 201 " 0.205 2.00e-02 2.50e+03 pdb=" C1B CYCAX 201 " -0.046 2.00e-02 2.50e+03 pdb=" C2B CYCAX 201 " 0.121 2.00e-02 2.50e+03 pdb=" C3B CYCAX 201 " 0.145 2.00e-02 2.50e+03 pdb=" C4B CYCAX 201 " 0.025 2.00e-02 2.50e+03 pdb=" CAB CYCAX 201 " -0.397 2.00e-02 2.50e+03 pdb=" CHB CYCAX 201 " -0.179 2.00e-02 2.50e+03 pdb=" CMB CYCAX 201 " 0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAE 201 " 0.090 2.00e-02 2.50e+03 1.45e-01 4.72e+02 pdb=" OB CYCAE 201 " 0.037 2.00e-02 2.50e+03 pdb=" C1B CYCAE 201 " -0.057 2.00e-02 2.50e+03 pdb=" C2B CYCAE 201 " 0.058 2.00e-02 2.50e+03 pdb=" C3B CYCAE 201 " 0.087 2.00e-02 2.50e+03 pdb=" C4B CYCAE 201 " 0.079 2.00e-02 2.50e+03 pdb=" CAB CYCAE 201 " -0.277 2.00e-02 2.50e+03 pdb=" CHB CYCAE 201 " -0.210 2.00e-02 2.50e+03 pdb=" CMB CYCAE 201 " 0.194 2.00e-02 2.50e+03 ... (remaining 9802 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1373 2.63 - 3.19: 52414 3.19 - 3.76: 107085 3.76 - 4.33: 141920 4.33 - 4.90: 223377 Nonbonded interactions: 526169 Sorted by model distance: nonbonded pdb=" NH1 ARGBD 114 " pdb=" O ALABD 172 " model vdw 2.057 3.120 nonbonded pdb=" O1D CYCBD 201 " pdb=" O HOHBD 301 " model vdw 2.165 3.040 nonbonded pdb=" O SERBL 177 " pdb=" OG SERBL 177 " model vdw 2.174 3.040 nonbonded pdb=" OG SERAN 76 " pdb=" O ALAAO 113 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASNBA 47 " pdb=" OG SERBA 50 " model vdw 2.189 3.040 ... (remaining 526164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' selection = chain 'BA' selection = chain 'BC' selection = chain 'BE' selection = chain 'BG' selection = chain 'BI' } ncs_group { reference = (chain 'AB' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AD' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AF' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AH' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AJ' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AL' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AN' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AP' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AR' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AT' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'AV' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = chain 'AX' selection = (chain 'AZ' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BB' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BD' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BF' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BH' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) selection = (chain 'BJ' and (resid 1 through 10 or (resid 11 and (name N or name CA or name \ C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 12 through \ 172 or resid 201 through 202)) } 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: 2.570 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: 0.040 Extract box with map and model: 1.490 Check model and map are aligned: 0.330 Set scattering table: 0.380 Process input model: 96.800 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.730 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.011 0.168 55030 Z= 0.717 Angle : 1.136 16.822 74854 Z= 0.594 Chirality : 0.068 0.537 8181 Planarity : 0.012 0.264 9805 Dihedral : 14.951 92.808 21388 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.99 % Favored : 98.99 % Rotamer: Outliers : 0.78 % Allowed : 1.70 % Favored : 97.52 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.10), residues: 6752 helix: 1.93 (0.07), residues: 5195 sheet: 1.04 (0.53), residues: 55 loop : -0.20 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRPBG 128 HIS 0.018 0.007 HISAK 140 PHE 0.037 0.004 PHEAM 63 TYR 0.055 0.004 TYRBN 75 ARG 0.087 0.003 ARGAX 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 955 time to evaluate : 4.647 Fit side-chains TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7432 (ttp80) REVERT: AD 156 ILE cc_start: 0.8389 (tp) cc_final: 0.8175 (tp) REVERT: AF 15 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7107 (mtp180) REVERT: AF 17 GLU cc_start: 0.7895 (pt0) cc_final: 0.7678 (pt0) REVERT: AF 39 ASP cc_start: 0.8253 (m-30) cc_final: 0.8029 (m-30) REVERT: AG 42 LYS cc_start: 0.8204 (ttpm) cc_final: 0.7909 (ttpt) REVERT: AJ 30 THR cc_start: 0.8809 (m) cc_final: 0.8581 (m) REVERT: AK 35 ASN cc_start: 0.8199 (m-40) cc_final: 0.7904 (m110) REVERT: AN 79 MET cc_start: 0.9170 (tpp) cc_final: 0.8950 (tpp) REVERT: AT 134 MET cc_start: 0.8980 (mtm) cc_final: 0.8544 (mtp) REVERT: AY 42 LYS cc_start: 0.8192 (tttp) cc_final: 0.7987 (tppt) REVERT: BB 25 ASP cc_start: 0.6704 (m-30) cc_final: 0.6386 (m-30) REVERT: BB 156 ILE cc_start: 0.8227 (mm) cc_final: 0.7878 (mm) REVERT: BD 25 ASP cc_start: 0.7365 (p0) cc_final: 0.7137 (p0) REVERT: BD 30 THR cc_start: 0.8825 (m) cc_final: 0.8592 (m) REVERT: BH 133 LYS cc_start: 0.8553 (mttp) cc_final: 0.8171 (mttp) REVERT: BI 39 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7350 (mm-40) REVERT: BJ 79 MET cc_start: 0.8946 (tpp) cc_final: 0.8708 (tpp) REVERT: BK 42 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8118 (tpt) REVERT: BN 48 ILE cc_start: 0.8555 (mt) cc_final: 0.8226 (mm) outliers start: 41 outliers final: 8 residues processed: 968 average time/residue: 1.6986 time to fit residues: 1997.1425 Evaluate side-chains 870 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 860 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AO residue 120 ARG Chi-restraints excluded: chain AW residue 1 MET Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 42 LYS Chi-restraints excluded: chain BK residue 42 MET Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 569 optimal weight: 1.9990 chunk 510 optimal weight: 0.8980 chunk 283 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 528 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 321 optimal weight: 0.9990 chunk 393 optimal weight: 0.0570 chunk 612 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 39 GLN AE 68 GLN AF 68 GLN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 111 ASN AI 49 GLN AJ 68 GLN AL 35 ASN AL 68 GLN AM 68 GLN AN 111 ASN AO 78 GLN ** AQ 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 39 GLN AR 111 ASN AS 15 GLN AS 68 GLN AT 132 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 39 GLN AW 47 ASN AW 68 GLN AW 78 GLN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN ** AZ 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AZ 132 GLN BA 49 GLN BA 61 ASN BA 78 GLN BC 49 GLN BC 57 GLN BC 78 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 68 GLN BF 132 GLN BG 53 ASN BI 47 ASN BI 53 ASN BJ 11 GLN BL 89 ASN ** BM 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 12 ASN BN 14 GLN BN 71 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 55030 Z= 0.178 Angle : 0.614 10.085 74854 Z= 0.305 Chirality : 0.037 0.158 8181 Planarity : 0.004 0.064 9805 Dihedral : 10.222 84.178 10023 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.74 % Allowed : 4.92 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.10), residues: 6752 helix: 2.25 (0.07), residues: 5190 sheet: 0.96 (0.56), residues: 55 loop : -0.15 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPBM 146 HIS 0.005 0.002 HISBA 140 PHE 0.015 0.001 PHEBL 168 TYR 0.021 0.001 TYRBN 75 ARG 0.009 0.001 ARGAX 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 999 time to evaluate : 4.489 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7521 (ttp80) REVERT: AB 39 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: AD 156 ILE cc_start: 0.8402 (tp) cc_final: 0.8187 (tp) REVERT: AF 15 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7097 (mtp180) REVERT: AG 42 LYS cc_start: 0.8103 (ttpm) cc_final: 0.7879 (ttpt) REVERT: AG 50 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8124 (p) REVERT: AG 120 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7399 (ttp-110) REVERT: AK 35 ASN cc_start: 0.8169 (m-40) cc_final: 0.7959 (m110) REVERT: AL 65 GLN cc_start: 0.7641 (pm20) cc_final: 0.7376 (pp30) REVERT: AL 115 GLU cc_start: 0.7454 (pm20) cc_final: 0.7198 (pm20) REVERT: AN 65 GLN cc_start: 0.7750 (pt0) cc_final: 0.7359 (tp40) REVERT: AP 132 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: AT 134 MET cc_start: 0.8970 (mtm) cc_final: 0.8518 (mtm) REVERT: AU 109 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7224 (tp30) REVERT: AZ 65 GLN cc_start: 0.7913 (pm20) cc_final: 0.7553 (pm20) REVERT: BA 42 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7912 (tttt) REVERT: BB 156 ILE cc_start: 0.8155 (mm) cc_final: 0.7858 (mm) REVERT: BE 155 ASP cc_start: 0.8018 (m-30) cc_final: 0.7789 (m-30) REVERT: BF 39 ASP cc_start: 0.7357 (p0) cc_final: 0.6923 (p0) REVERT: BH 133 LYS cc_start: 0.8456 (mttp) cc_final: 0.8151 (mttp) REVERT: BI 139 ASN cc_start: 0.8626 (m-40) cc_final: 0.8375 (m110) REVERT: BJ 134 MET cc_start: 0.8590 (mtm) cc_final: 0.8187 (mtm) REVERT: BJ 159 GLU cc_start: 0.8619 (tt0) cc_final: 0.8166 (tt0) REVERT: BL 84 LYS cc_start: 0.7881 (pttp) cc_final: 0.7678 (ttpp) REVERT: BM 96 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7958 (mt) REVERT: BN 48 ILE cc_start: 0.8530 (mt) cc_final: 0.8259 (mp) outliers start: 39 outliers final: 11 residues processed: 1010 average time/residue: 1.7734 time to fit residues: 2161.0617 Evaluate side-chains 907 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 891 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 39 ASP Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 15 GLN Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BM residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 509 optimal weight: 4.9990 chunk 416 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 613 optimal weight: 3.9990 chunk 662 optimal weight: 0.8980 chunk 546 optimal weight: 1.9990 chunk 608 optimal weight: 1.9990 chunk 209 optimal weight: 0.6980 chunk 491 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 39 GLN AE 78 GLN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 111 ASN AJ 68 GLN AK 47 ASN AL 35 ASN AL 132 GLN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 78 GLN AQ 15 GLN AQ 39 GLN AR 111 ASN AS 68 GLN AT 132 GLN ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 39 GLN AU 47 ASN AU 49 GLN AW 47 ASN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 68 GLN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BC 139 ASN BD 68 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 68 GLN BF 132 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN ** BM 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 14 GLN BN 71 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 55030 Z= 0.187 Angle : 0.588 10.162 74854 Z= 0.291 Chirality : 0.038 0.146 8181 Planarity : 0.004 0.053 9805 Dihedral : 10.181 84.812 10002 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.23 % Allowed : 7.48 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.10), residues: 6752 helix: 2.37 (0.07), residues: 5198 sheet: 0.95 (0.57), residues: 55 loop : -0.09 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAM 128 HIS 0.007 0.002 HISBA 140 PHE 0.012 0.001 PHEBL 91 TYR 0.017 0.001 TYRBN 75 ARG 0.006 0.000 ARGAG 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 954 time to evaluate : 4.507 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7481 (ttp80) REVERT: AC 39 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.7122 (mm110) REVERT: AD 86 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7432 (mmm) REVERT: AD 156 ILE cc_start: 0.8326 (tp) cc_final: 0.8124 (tp) REVERT: AG 120 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7504 (ttp-110) REVERT: AL 65 GLN cc_start: 0.7697 (pm20) cc_final: 0.7418 (pp30) REVERT: AL 115 GLU cc_start: 0.7502 (pm20) cc_final: 0.7243 (pm20) REVERT: AN 65 GLN cc_start: 0.7838 (pt0) cc_final: 0.7455 (tp40) REVERT: AP 132 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: AQ 62 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8105 (ttmt) REVERT: AT 134 MET cc_start: 0.8993 (mtm) cc_final: 0.8331 (mtm) REVERT: AU 109 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7242 (tp30) REVERT: AV 106 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: AY 70 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6760 (mp10) REVERT: AZ 65 GLN cc_start: 0.7950 (pm20) cc_final: 0.7561 (pm20) REVERT: AZ 136 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7281 (mt-10) REVERT: BA 42 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7905 (tttt) REVERT: BA 49 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: BA 53 ASN cc_start: 0.7441 (m110) cc_final: 0.7034 (m110) REVERT: BB 156 ILE cc_start: 0.8177 (mm) cc_final: 0.7916 (mm) REVERT: BC 68 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6684 (mt0) REVERT: BC 117 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: BE 79 ARG cc_start: 0.7577 (ttt-90) cc_final: 0.7341 (ttt-90) REVERT: BH 133 LYS cc_start: 0.8470 (mttp) cc_final: 0.8270 (mttm) REVERT: BH 166 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: BI 139 ASN cc_start: 0.8611 (m-40) cc_final: 0.8373 (m110) REVERT: BJ 134 MET cc_start: 0.8643 (mtm) cc_final: 0.8309 (mtm) REVERT: BJ 159 GLU cc_start: 0.8628 (tt0) cc_final: 0.8344 (tt0) REVERT: BK 122 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7873 (mtmt) REVERT: BK 187 ARG cc_start: 0.7152 (ptp90) cc_final: 0.6637 (ttp-110) REVERT: BL 84 LYS cc_start: 0.7995 (pttp) cc_final: 0.7759 (ttpp) REVERT: BM 258 GLN cc_start: 0.7939 (mt0) cc_final: 0.7649 (mt0) REVERT: BN 48 ILE cc_start: 0.8538 (mt) cc_final: 0.8194 (mm) REVERT: BN 55 MET cc_start: 0.8509 (mtp) cc_final: 0.8031 (mtp) REVERT: BN 62 ILE cc_start: 0.8196 (mt) cc_final: 0.7963 (mt) outliers start: 65 outliers final: 21 residues processed: 973 average time/residue: 1.7488 time to fit residues: 2058.5441 Evaluate side-chains 927 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 896 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AD residue 86 MET Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AF residue 133 LYS Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 106 GLU Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 70 GLN Chi-restraints excluded: chain BA residue 49 GLN Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BC residue 117 GLU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BM residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 4.9990 chunk 461 optimal weight: 6.9990 chunk 318 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 411 optimal weight: 4.9990 chunk 615 optimal weight: 3.9990 chunk 651 optimal weight: 20.0000 chunk 321 optimal weight: 0.9990 chunk 583 optimal weight: 4.9990 chunk 175 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 39 GLN AE 78 GLN AF 72 ASN AF 111 ASN ** AH 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 68 GLN AL 35 ASN AM 47 ASN AM 68 GLN AN 111 ASN AO 78 GLN AQ 39 GLN AR 68 GLN AR 111 ASN AS 68 GLN AT 132 GLN AU 39 GLN AU 47 ASN AU 49 GLN AW 47 ASN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 68 GLN AZ 132 GLN BA 61 ASN BC 49 GLN BC 78 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 39 GLN BF 132 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 263 GLN BN 14 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 55030 Z= 0.204 Angle : 0.593 10.018 74854 Z= 0.294 Chirality : 0.038 0.221 8181 Planarity : 0.004 0.055 9805 Dihedral : 10.214 86.615 10002 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.53 % Allowed : 8.35 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.10), residues: 6752 helix: 2.40 (0.07), residues: 5204 sheet: 0.78 (0.57), residues: 55 loop : -0.03 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAM 128 HIS 0.007 0.003 HISBA 140 PHE 0.012 0.002 PHEAP 98 TYR 0.016 0.001 TYRAX 92 ARG 0.007 0.000 ARGBM 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 925 time to evaluate : 4.468 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7463 (ttp80) REVERT: AA 109 GLU cc_start: 0.8216 (tp30) cc_final: 0.7964 (tp30) REVERT: AB 39 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: AC 39 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7104 (mm110) REVERT: AE 117 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: AF 106 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: AG 120 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7610 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.6750 (mp10) REVERT: AN 65 GLN cc_start: 0.7885 (pt0) cc_final: 0.7460 (tp40) REVERT: AO 120 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8041 (ttm110) REVERT: AP 132 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: AQ 62 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8142 (ttmt) REVERT: AT 134 MET cc_start: 0.9011 (mtm) cc_final: 0.8517 (mtm) REVERT: AU 109 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: AV 106 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: AW 78 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8090 (tp-100) REVERT: AY 42 LYS cc_start: 0.8233 (tttp) cc_final: 0.7920 (tppt) REVERT: AY 70 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: AY 78 GLN cc_start: 0.8489 (tp40) cc_final: 0.8269 (tp-100) REVERT: AY 109 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: AZ 65 GLN cc_start: 0.7980 (pm20) cc_final: 0.7685 (pm20) REVERT: BA 42 LYS cc_start: 0.8137 (ttpp) cc_final: 0.7910 (tttt) REVERT: BA 49 GLN cc_start: 0.7122 (pm20) cc_final: 0.6695 (pm20) REVERT: BA 53 ASN cc_start: 0.7444 (m110) cc_final: 0.7041 (m110) REVERT: BB 156 ILE cc_start: 0.8260 (mm) cc_final: 0.8024 (mm) REVERT: BC 68 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6685 (mt0) REVERT: BE 79 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.7344 (ttt-90) REVERT: BF 144 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6924 (OUTLIER) REVERT: BG 77 ASP cc_start: 0.6921 (p0) cc_final: 0.6683 (p0) REVERT: BI 139 ASN cc_start: 0.8613 (m-40) cc_final: 0.8371 (m110) REVERT: BJ 77 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.6535 (tmm160) REVERT: BJ 134 MET cc_start: 0.8665 (mtm) cc_final: 0.8394 (mtm) REVERT: BJ 159 GLU cc_start: 0.8636 (tt0) cc_final: 0.8351 (tt0) REVERT: BK 42 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: BK 122 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: BK 177 LYS cc_start: 0.8686 (tttm) cc_final: 0.8456 (tttp) REVERT: BK 187 ARG cc_start: 0.7269 (ptp90) cc_final: 0.6702 (ttp-110) REVERT: BL 84 LYS cc_start: 0.8076 (pttp) cc_final: 0.7807 (ttpp) REVERT: BL 273 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6715 (mp-120) REVERT: BN 1 MET cc_start: 0.6842 (tpp) cc_final: 0.6585 (mmt) REVERT: BN 48 ILE cc_start: 0.8546 (mt) cc_final: 0.8258 (mp) REVERT: BN 55 MET cc_start: 0.8606 (mtp) cc_final: 0.8082 (mtp) outliers start: 81 outliers final: 36 residues processed: 959 average time/residue: 1.8787 time to fit residues: 2187.0653 Evaluate side-chains 940 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 888 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 39 ASP Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 117 GLU Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AF residue 133 LYS Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AK residue 35 ASN Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AN residue 1 MET Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AO residue 120 ARG Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 106 GLU Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 70 GLN Chi-restraints excluded: chain AY residue 109 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BI residue 143 SER Chi-restraints excluded: chain BJ residue 77 ARG Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 42 MET Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 273 GLN Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BN residue 39 ASP Chi-restraints excluded: chain BN residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 485 optimal weight: 0.6980 chunk 268 optimal weight: 4.9990 chunk 555 optimal weight: 5.9990 chunk 450 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 chunk 584 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 15 GLN AE 39 GLN AE 78 GLN AF 68 GLN AF 111 ASN AG 53 ASN AH 72 ASN AI 78 GLN AJ 68 GLN AK 39 GLN AL 35 ASN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 78 GLN AQ 39 GLN AQ 68 GLN AR 68 GLN AR 111 ASN AS 15 GLN AS 68 GLN AT 132 GLN AU 49 GLN AW 47 ASN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AZ 132 GLN BA 61 ASN BB 35 ASN BC 49 GLN BC 78 GLN BC 139 ASN BD 65 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 39 GLN BG 49 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 122 HIS BM 263 GLN BN 14 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 55030 Z= 0.249 Angle : 0.628 9.988 74854 Z= 0.313 Chirality : 0.040 0.191 8181 Planarity : 0.004 0.054 9805 Dihedral : 10.329 88.403 10002 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.76 % Allowed : 9.02 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.10), residues: 6752 helix: 2.34 (0.07), residues: 5204 sheet: 0.68 (0.56), residues: 55 loop : -0.01 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRPAM 128 HIS 0.007 0.003 HISBA 140 PHE 0.014 0.002 PHEAX 98 TYR 0.018 0.002 TYRAX 92 ARG 0.006 0.001 ARGBJ 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 915 time to evaluate : 4.490 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7435 (ttp80) REVERT: AA 109 GLU cc_start: 0.8263 (tp30) cc_final: 0.8019 (tp30) REVERT: AC 1 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.5990 (mpp) REVERT: AC 39 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7107 (mm110) REVERT: AD 86 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7423 (mtp) REVERT: AF 106 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: AG 2 LYS cc_start: 0.8074 (tttp) cc_final: 0.7825 (tttm) REVERT: AG 120 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7395 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: AI 39 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7457 (tm-30) REVERT: AM 109 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: AN 65 GLN cc_start: 0.7945 (pt0) cc_final: 0.7464 (tp40) REVERT: AP 3 ASP cc_start: 0.8370 (p0) cc_final: 0.8161 (p0) REVERT: AP 132 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: AQ 159 ASN cc_start: 0.8474 (m-40) cc_final: 0.8216 (m-40) REVERT: AT 134 MET cc_start: 0.9021 (mtm) cc_final: 0.8507 (mtm) REVERT: AU 109 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: AW 78 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8255 (tp-100) REVERT: AY 109 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: AZ 65 GLN cc_start: 0.8007 (pm20) cc_final: 0.7710 (pm20) REVERT: BA 42 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7898 (tttt) REVERT: BA 145 ASP cc_start: 0.8018 (m-30) cc_final: 0.7794 (m-30) REVERT: BB 156 ILE cc_start: 0.8283 (mm) cc_final: 0.8055 (mm) REVERT: BC 68 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6708 (mt0) REVERT: BD 30 THR cc_start: 0.8700 (m) cc_final: 0.8490 (m) REVERT: BE 79 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.7389 (ttt-90) REVERT: BE 155 ASP cc_start: 0.8018 (m-30) cc_final: 0.7796 (m-30) REVERT: BG 15 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: BJ 134 MET cc_start: 0.8693 (mtm) cc_final: 0.8436 (mtm) REVERT: BJ 159 GLU cc_start: 0.8639 (tt0) cc_final: 0.8366 (tt0) REVERT: BK 122 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: BL 84 LYS cc_start: 0.8122 (pttp) cc_final: 0.7838 (ttpp) REVERT: BM 50 MET cc_start: 0.8456 (mmp) cc_final: 0.8073 (mmt) REVERT: BN 1 MET cc_start: 0.6907 (tpp) cc_final: 0.6586 (mmt) REVERT: BN 48 ILE cc_start: 0.8565 (mt) cc_final: 0.8256 (mp) outliers start: 93 outliers final: 40 residues processed: 954 average time/residue: 1.9078 time to fit residues: 2223.1813 Evaluate side-chains 932 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 880 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AD residue 86 MET Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 1 MET Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 109 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BI residue 143 SER Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BK residue 155 THR Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BN residue 39 ASP Chi-restraints excluded: chain BN residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 1.9990 chunk 586 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 382 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 652 optimal weight: 0.8980 chunk 541 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AE 15 GLN AE 39 GLN AE 68 GLN AF 68 GLN AF 111 ASN AG 53 ASN AJ 68 GLN AK 49 GLN AL 35 ASN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 78 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 132 GLN AW 47 ASN AW 78 GLN AW 139 ASN AX 65 GLN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 132 GLN BA 49 GLN BA 53 ASN BA 61 ASN BC 49 GLN BC 78 GLN BD 72 ASN BE 39 GLN BF 132 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 263 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 55030 Z= 0.245 Angle : 0.626 11.969 74854 Z= 0.311 Chirality : 0.040 0.188 8181 Planarity : 0.004 0.055 9805 Dihedral : 10.379 89.642 10002 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.78 % Allowed : 9.70 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.10), residues: 6752 helix: 2.31 (0.07), residues: 5204 sheet: 0.77 (0.57), residues: 50 loop : -0.03 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPBM 146 HIS 0.007 0.003 HISAK 140 PHE 0.014 0.002 PHEBF 98 TYR 0.017 0.002 TYRBG 90 ARG 0.007 0.001 ARGAB 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 906 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7434 (ttp80) REVERT: AA 137 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8115 (ttmt) REVERT: AC 1 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.5870 (mpp) REVERT: AC 39 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7118 (mm110) REVERT: AD 86 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7438 (mtp) REVERT: AF 106 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: AG 120 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7400 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: AI 39 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7396 (tm-30) REVERT: AI 137 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8374 (ttpt) REVERT: AJ 166 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7850 (ttp-170) REVERT: AM 109 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: AN 65 GLN cc_start: 0.7942 (pt0) cc_final: 0.7467 (tp40) REVERT: AP 132 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: AQ 159 ASN cc_start: 0.8472 (m-40) cc_final: 0.8226 (m-40) REVERT: AT 134 MET cc_start: 0.9005 (mtm) cc_final: 0.8485 (mtm) REVERT: AU 109 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: AY 78 GLN cc_start: 0.8510 (tp40) cc_final: 0.8274 (tp-100) REVERT: AY 109 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: AZ 65 GLN cc_start: 0.7993 (pm20) cc_final: 0.7661 (pm20) REVERT: BA 42 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7900 (tttt) REVERT: BA 145 ASP cc_start: 0.8009 (m-30) cc_final: 0.7792 (m-30) REVERT: BB 25 ASP cc_start: 0.6588 (m-30) cc_final: 0.6344 (m-30) REVERT: BB 156 ILE cc_start: 0.8281 (mm) cc_final: 0.8054 (mm) REVERT: BC 61 ASN cc_start: 0.8462 (m-40) cc_final: 0.8257 (m110) REVERT: BC 68 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6701 (mt0) REVERT: BC 117 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: BD 30 THR cc_start: 0.8711 (m) cc_final: 0.8506 (m) REVERT: BD 107 ASP cc_start: 0.7856 (m-30) cc_final: 0.7644 (m-30) REVERT: BE 79 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.7378 (ttt-90) REVERT: BG 15 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: BG 77 ASP cc_start: 0.6843 (p0) cc_final: 0.6611 (p0) REVERT: BH 17 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: BI 139 ASN cc_start: 0.8626 (m-40) cc_final: 0.8405 (m110) REVERT: BJ 134 MET cc_start: 0.8696 (mtm) cc_final: 0.8356 (mtm) REVERT: BJ 159 GLU cc_start: 0.8624 (tt0) cc_final: 0.8398 (tt0) REVERT: BK 122 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7891 (mtmt) REVERT: BL 84 LYS cc_start: 0.8127 (pttp) cc_final: 0.7843 (ttpp) REVERT: BM 50 MET cc_start: 0.8443 (mmp) cc_final: 0.8084 (mmt) REVERT: BN 1 MET cc_start: 0.6951 (tpp) cc_final: 0.6608 (mmt) REVERT: BN 48 ILE cc_start: 0.8543 (mt) cc_final: 0.8233 (mp) outliers start: 94 outliers final: 45 residues processed: 945 average time/residue: 1.7738 time to fit residues: 2022.0809 Evaluate side-chains 933 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 872 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 50 SER Chi-restraints excluded: chain AA residue 137 LYS Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AD residue 86 MET Chi-restraints excluded: chain AE residue 10 SER Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AI residue 137 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AM residue 109 GLU Chi-restraints excluded: chain AN residue 1 MET Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 33 GLU Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AR residue 22 SER Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AW residue 1 MET Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AY residue 109 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BC residue 117 GLU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 141 ILE Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BH residue 17 GLU Chi-restraints excluded: chain BH residue 141 ILE Chi-restraints excluded: chain BI residue 143 SER Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BK residue 155 THR Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BM residue 47 ASP Chi-restraints excluded: chain BN residue 39 ASP Chi-restraints excluded: chain BN residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 371 optimal weight: 0.9990 chunk 476 optimal weight: 8.9990 chunk 368 optimal weight: 8.9990 chunk 548 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 649 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 396 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 39 GLN AE 68 GLN AE 78 GLN AF 111 ASN AG 53 ASN AJ 68 GLN AK 49 GLN AL 35 ASN AL 132 GLN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 78 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 132 GLN AV 68 GLN AW 47 ASN AW 78 GLN AW 139 ASN AX 65 GLN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BC 139 ASN BD 65 GLN BE 39 GLN BF 132 GLN BG 15 GLN BG 53 ASN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 55030 Z= 0.166 Angle : 0.567 9.973 74854 Z= 0.281 Chirality : 0.037 0.227 8181 Planarity : 0.004 0.061 9805 Dihedral : 10.257 86.438 10002 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.34 % Allowed : 10.45 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.10), residues: 6752 helix: 2.49 (0.07), residues: 5204 sheet: 0.58 (0.56), residues: 55 loop : -0.01 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.006 0.002 HISBE 140 PHE 0.012 0.001 PHEBL 91 TYR 0.020 0.001 TYRBH 92 ARG 0.012 0.000 ARGAN 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 909 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7471 (ttp80) REVERT: AC 1 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.5902 (mpp) REVERT: AC 39 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7130 (mm110) REVERT: AD 86 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7555 (mtp) REVERT: AF 106 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: AG 120 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7385 (ttp-110) REVERT: AH 132 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: AI 39 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7377 (tm-30) REVERT: AJ 166 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7888 (ttp-170) REVERT: AL 132 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7376 (mm110) REVERT: AL 136 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: AN 65 GLN cc_start: 0.7794 (pt0) cc_final: 0.7420 (tp40) REVERT: AQ 159 ASN cc_start: 0.8419 (m-40) cc_final: 0.8162 (m-40) REVERT: AT 134 MET cc_start: 0.8965 (mtm) cc_final: 0.8384 (mtm) REVERT: AU 109 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: AZ 65 GLN cc_start: 0.7970 (pm20) cc_final: 0.7651 (pm20) REVERT: BA 145 ASP cc_start: 0.8001 (m-30) cc_final: 0.7793 (m-30) REVERT: BB 156 ILE cc_start: 0.8231 (mm) cc_final: 0.8006 (mm) REVERT: BD 107 ASP cc_start: 0.7813 (m-30) cc_final: 0.7592 (m-30) REVERT: BE 79 ARG cc_start: 0.7624 (ttt-90) cc_final: 0.7347 (ttt-90) REVERT: BE 147 ARG cc_start: 0.8064 (tmm160) cc_final: 0.7825 (ttp-170) REVERT: BG 77 ASP cc_start: 0.6820 (p0) cc_final: 0.6589 (p0) REVERT: BH 166 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: BI 139 ASN cc_start: 0.8596 (m-40) cc_final: 0.8374 (m110) REVERT: BJ 77 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6568 (tmm160) REVERT: BJ 134 MET cc_start: 0.8664 (mtm) cc_final: 0.8373 (mtm) REVERT: BJ 159 GLU cc_start: 0.8607 (tt0) cc_final: 0.8393 (tt0) REVERT: BK 122 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7883 (mtmt) REVERT: BK 187 ARG cc_start: 0.7255 (ptp90) cc_final: 0.6724 (ttp-110) REVERT: BL 167 MET cc_start: 0.7288 (tpt) cc_final: 0.6878 (tpp) REVERT: BM 50 MET cc_start: 0.8402 (mmp) cc_final: 0.8088 (mmt) REVERT: BN 48 ILE cc_start: 0.8523 (mt) cc_final: 0.8163 (mm) outliers start: 71 outliers final: 33 residues processed: 938 average time/residue: 1.8669 time to fit residues: 2130.0761 Evaluate side-chains 907 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 865 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AD residue 86 MET Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 33 GLU Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BJ residue 77 ARG Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BN residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 0.8980 chunk 259 optimal weight: 0.6980 chunk 387 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 chunk 442 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 510 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 68 GLN AF 111 ASN AG 53 ASN AJ 68 GLN AK 49 GLN AK 78 GLN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AQ 15 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 132 GLN AU 49 GLN AW 47 ASN AW 78 GLN AW 139 ASN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AY 78 GLN AZ 68 GLN AZ 132 GLN ** BA 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 61 ASN BC 49 GLN BC 78 GLN BD 65 GLN BE 39 GLN BF 132 GLN BG 53 ASN BI 15 GLN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55030 Z= 0.191 Angle : 0.585 9.971 74854 Z= 0.291 Chirality : 0.038 0.232 8181 Planarity : 0.004 0.053 9805 Dihedral : 10.238 87.099 10000 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.34 % Allowed : 10.81 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.10), residues: 6752 helix: 2.45 (0.07), residues: 5215 sheet: 0.79 (0.59), residues: 50 loop : 0.06 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.006 0.002 HISBA 140 PHE 0.012 0.002 PHEBF 98 TYR 0.019 0.001 TYRBH 92 ARG 0.010 0.000 ARGBM 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 892 time to evaluate : 4.508 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7473 (ttp80) REVERT: AC 1 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.5890 (mpp) REVERT: AC 39 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7122 (mm110) REVERT: AD 86 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7534 (mtp) REVERT: AF 106 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: AH 132 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6998 (mp10) REVERT: AI 39 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7372 (tm-30) REVERT: AJ 166 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7893 (ttp-170) REVERT: AN 33 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7219 (pp20) REVERT: AN 65 GLN cc_start: 0.7881 (pt0) cc_final: 0.7507 (tp40) REVERT: AP 132 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: AQ 62 LYS cc_start: 0.8439 (tttm) cc_final: 0.8218 (tttp) REVERT: AQ 159 ASN cc_start: 0.8432 (m-40) cc_final: 0.8167 (m-40) REVERT: AT 134 MET cc_start: 0.8969 (mtm) cc_final: 0.8374 (mtm) REVERT: AU 109 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7219 (tp30) REVERT: AW 78 GLN cc_start: 0.8203 (tp40) cc_final: 0.7896 (tp-100) REVERT: AY 78 GLN cc_start: 0.8475 (tp40) cc_final: 0.8236 (tp-100) REVERT: AZ 17 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: AZ 65 GLN cc_start: 0.7979 (pm20) cc_final: 0.7656 (pm20) REVERT: BA 145 ASP cc_start: 0.8005 (m-30) cc_final: 0.7786 (m-30) REVERT: BB 156 ILE cc_start: 0.8247 (mm) cc_final: 0.8019 (mm) REVERT: BC 61 ASN cc_start: 0.8447 (m-40) cc_final: 0.8218 (m110) REVERT: BD 107 ASP cc_start: 0.7825 (m-30) cc_final: 0.7573 (m-30) REVERT: BE 79 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.7371 (ttt-90) REVERT: BF 144 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6679 (t70) REVERT: BG 77 ASP cc_start: 0.6834 (p0) cc_final: 0.6587 (p0) REVERT: BH 17 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: BI 139 ASN cc_start: 0.8616 (m-40) cc_final: 0.8387 (m110) REVERT: BJ 77 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6488 (tmm160) REVERT: BJ 134 MET cc_start: 0.8666 (mtm) cc_final: 0.8378 (mtm) REVERT: BJ 159 GLU cc_start: 0.8608 (tt0) cc_final: 0.8408 (tt0) REVERT: BK 122 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7880 (mtmt) REVERT: BK 187 ARG cc_start: 0.7268 (ptp90) cc_final: 0.6744 (ttp-110) REVERT: BM 50 MET cc_start: 0.8410 (mmp) cc_final: 0.8102 (mmt) REVERT: BM 158 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7469 (ttp-170) outliers start: 71 outliers final: 41 residues processed: 927 average time/residue: 1.7852 time to fit residues: 1992.3389 Evaluate side-chains 923 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 870 time to evaluate : 4.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AD residue 86 MET Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 33 GLU Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AQ residue 120 ARG Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain AX residue 136 GLU Chi-restraints excluded: chain AZ residue 17 GLU Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BC residue 68 GLN Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 8 VAL Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BG residue 14 SER Chi-restraints excluded: chain BH residue 17 GLU Chi-restraints excluded: chain BJ residue 77 ARG Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BL residue 29 LEU Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BN residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 9.9990 chunk 622 optimal weight: 0.9990 chunk 567 optimal weight: 0.8980 chunk 605 optimal weight: 0.9990 chunk 364 optimal weight: 0.7980 chunk 263 optimal weight: 0.7980 chunk 475 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 547 optimal weight: 0.9980 chunk 572 optimal weight: 6.9990 chunk 603 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 GLN AC 78 GLN AE 15 GLN AE 68 GLN AF 111 ASN AG 53 ASN AJ 68 GLN AK 49 GLN AL 35 ASN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AO 78 GLN AQ 39 GLN AQ 68 GLN AR 111 ASN AS 68 GLN AT 132 GLN AU 49 GLN AW 47 ASN AW 139 ASN AX 65 GLN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AZ 68 GLN AZ 132 GLN ** BA 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 61 ASN BC 49 GLN BC 78 GLN BC 139 ASN BD 65 GLN BE 39 GLN BF 132 GLN BG 49 GLN BG 53 ASN BI 15 GLN BI 53 ASN BJ 11 GLN BL 89 ASN BM 8 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55030 Z= 0.170 Angle : 0.571 9.943 74854 Z= 0.284 Chirality : 0.037 0.197 8181 Planarity : 0.004 0.059 9805 Dihedral : 10.209 86.616 10000 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.21 % Allowed : 11.23 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.10), residues: 6752 helix: 2.49 (0.07), residues: 5215 sheet: 0.81 (0.62), residues: 50 loop : 0.06 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPBM 146 HIS 0.006 0.002 HISAG 140 PHE 0.012 0.001 PHEBL 91 TYR 0.019 0.001 TYRBG 90 ARG 0.008 0.000 ARGBM 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 895 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7493 (ttp80) REVERT: AC 1 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.5887 (mpp) REVERT: AC 39 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7119 (mm110) REVERT: AD 150 ARG cc_start: 0.7324 (mmm160) cc_final: 0.7040 (mmm160) REVERT: AF 106 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: AH 132 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: AI 39 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7411 (tm-30) REVERT: AJ 166 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7891 (ttp-170) REVERT: AL 65 GLN cc_start: 0.7763 (pm20) cc_final: 0.7511 (pp30) REVERT: AN 33 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7140 (pp20) REVERT: AN 65 GLN cc_start: 0.7814 (pt0) cc_final: 0.7478 (tp40) REVERT: AP 132 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: AQ 120 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7098 (ttm110) REVERT: AQ 159 ASN cc_start: 0.8414 (m-40) cc_final: 0.8148 (m-40) REVERT: AT 134 MET cc_start: 0.8957 (mtm) cc_final: 0.8430 (mtm) REVERT: AU 109 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7193 (tp30) REVERT: AX 134 MET cc_start: 0.8542 (mtm) cc_final: 0.8323 (mtm) REVERT: AZ 65 GLN cc_start: 0.7971 (pm20) cc_final: 0.7651 (pm20) REVERT: BA 145 ASP cc_start: 0.8003 (m-30) cc_final: 0.7789 (m-30) REVERT: BB 156 ILE cc_start: 0.8240 (mm) cc_final: 0.8016 (mm) REVERT: BD 77 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7691 (ttp80) REVERT: BD 107 ASP cc_start: 0.7841 (m-30) cc_final: 0.7595 (m-30) REVERT: BE 79 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7360 (ttt-90) REVERT: BF 144 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6819 (t70) REVERT: BG 77 ASP cc_start: 0.6829 (p0) cc_final: 0.6566 (p0) REVERT: BH 17 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6774 (pm20) REVERT: BI 139 ASN cc_start: 0.8600 (m-40) cc_final: 0.8375 (m110) REVERT: BJ 77 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.6511 (tmm160) REVERT: BJ 134 MET cc_start: 0.8657 (mtm) cc_final: 0.8379 (mtm) REVERT: BK 122 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7876 (mtmt) REVERT: BK 187 ARG cc_start: 0.7227 (ptp90) cc_final: 0.6725 (ttp-110) REVERT: BL 167 MET cc_start: 0.7312 (tpt) cc_final: 0.6844 (tpp) REVERT: BM 50 MET cc_start: 0.8396 (mmp) cc_final: 0.8088 (mmt) REVERT: BN 64 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7491 (mtm110) outliers start: 64 outliers final: 35 residues processed: 923 average time/residue: 1.7812 time to fit residues: 1981.6201 Evaluate side-chains 913 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 866 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AK residue 1 MET Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 33 GLU Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AQ residue 68 GLN Chi-restraints excluded: chain AQ residue 120 ARG Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 8 VAL Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BH residue 17 GLU Chi-restraints excluded: chain BJ residue 77 ARG Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BN residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 4.9990 chunk 640 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 445 optimal weight: 4.9990 chunk 671 optimal weight: 7.9990 chunk 618 optimal weight: 4.9990 chunk 534 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 413 optimal weight: 0.9990 chunk 327 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 78 GLN AE 15 GLN AE 68 GLN AE 78 GLN AF 68 GLN AF 111 ASN AG 53 ASN AJ 68 GLN AJ 143 ASN AK 49 GLN AK 78 GLN AL 47 ASN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AQ 39 GLN AQ 68 GLN AQ 70 GLN AR 111 ASN AS 68 GLN AT 132 GLN AU 49 GLN AW 47 ASN AW 139 ASN AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AZ 132 GLN BA 49 GLN BA 61 ASN BC 49 GLN BC 78 GLN BC 139 ASN BD 65 GLN BE 39 GLN BF 132 GLN BG 49 GLN BG 53 ASN BI 15 GLN BI 53 ASN BJ 11 GLN BJ 47 ASN BK 56 HIS BK 72 ASN BK 74 GLN BL 89 ASN BM 8 GLN BM 263 GLN BN 17 ASN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 55030 Z= 0.387 Angle : 0.738 9.985 74854 Z= 0.372 Chirality : 0.047 0.537 8181 Planarity : 0.005 0.075 9805 Dihedral : 10.518 87.697 10000 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.27 % Allowed : 11.40 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.10), residues: 6752 helix: 2.08 (0.07), residues: 5211 sheet: 0.69 (0.60), residues: 50 loop : -0.01 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRPAS 128 HIS 0.010 0.003 HISBA 140 PHE 0.022 0.003 PHEAX 98 TYR 0.033 0.003 TYRBH 92 ARG 0.019 0.001 ARGBM 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13504 Ramachandran restraints generated. 6752 Oldfield, 0 Emsley, 6752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 889 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 79 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7396 (ttp80) REVERT: AC 1 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.5888 (mpp) REVERT: AD 150 ARG cc_start: 0.7408 (mmm160) cc_final: 0.7099 (mmm160) REVERT: AF 106 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: AH 132 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: AI 39 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7338 (tm-30) REVERT: AI 137 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8400 (ttpt) REVERT: AP 3 ASP cc_start: 0.8395 (p0) cc_final: 0.8171 (p0) REVERT: AP 132 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: AQ 62 LYS cc_start: 0.8388 (tttm) cc_final: 0.8142 (ttmt) REVERT: AT 68 GLN cc_start: 0.8246 (pt0) cc_final: 0.8032 (pt0) REVERT: AT 86 MET cc_start: 0.8042 (mmm) cc_final: 0.7837 (mmm) REVERT: AT 134 MET cc_start: 0.8995 (mtm) cc_final: 0.8437 (mtm) REVERT: AU 109 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: AX 136 GLU cc_start: 0.6987 (pt0) cc_final: 0.6699 (pp20) REVERT: AZ 65 GLN cc_start: 0.8016 (pm20) cc_final: 0.7670 (pm20) REVERT: BA 145 ASP cc_start: 0.8014 (m-30) cc_final: 0.7782 (m-30) REVERT: BC 61 ASN cc_start: 0.8432 (m-40) cc_final: 0.8225 (m110) REVERT: BE 79 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7326 (ttt-90) REVERT: BF 144 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6824 (t70) REVERT: BH 166 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: BI 47 ASN cc_start: 0.7653 (t0) cc_final: 0.7332 (t0) REVERT: BJ 134 MET cc_start: 0.8719 (mtm) cc_final: 0.8338 (mtm) REVERT: BK 122 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7962 (mtmt) REVERT: BM 50 MET cc_start: 0.8388 (mmp) cc_final: 0.8110 (mmt) REVERT: BN 64 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (mtm110) outliers start: 67 outliers final: 38 residues processed: 917 average time/residue: 1.7833 time to fit residues: 1970.9151 Evaluate side-chains 931 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 884 time to evaluate : 4.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 21 SER Chi-restraints excluded: chain AB residue 22 SER Chi-restraints excluded: chain AB residue 86 MET Chi-restraints excluded: chain AC residue 1 MET Chi-restraints excluded: chain AC residue 39 GLN Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 118 ILE Chi-restraints excluded: chain AF residue 106 GLU Chi-restraints excluded: chain AF residue 136 GLU Chi-restraints excluded: chain AF residue 171 VAL Chi-restraints excluded: chain AG residue 39 GLN Chi-restraints excluded: chain AG residue 50 SER Chi-restraints excluded: chain AH residue 132 GLN Chi-restraints excluded: chain AI residue 62 LYS Chi-restraints excluded: chain AI residue 137 LYS Chi-restraints excluded: chain AJ residue 8 VAL Chi-restraints excluded: chain AJ residue 22 SER Chi-restraints excluded: chain AJ residue 86 MET Chi-restraints excluded: chain AL residue 9 VAL Chi-restraints excluded: chain AL residue 22 SER Chi-restraints excluded: chain AL residue 136 GLU Chi-restraints excluded: chain AM residue 1 MET Chi-restraints excluded: chain AP residue 33 GLU Chi-restraints excluded: chain AP residue 132 GLN Chi-restraints excluded: chain AP residue 136 GLU Chi-restraints excluded: chain AP residue 156 ILE Chi-restraints excluded: chain AQ residue 120 ARG Chi-restraints excluded: chain AT residue 8 VAL Chi-restraints excluded: chain AU residue 1 MET Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AV residue 141 ILE Chi-restraints excluded: chain AX residue 22 SER Chi-restraints excluded: chain BB residue 141 ILE Chi-restraints excluded: chain BD residue 8 VAL Chi-restraints excluded: chain BD residue 65 GLN Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BF residue 144 ASP Chi-restraints excluded: chain BF residue 152 ASP Chi-restraints excluded: chain BI residue 143 SER Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 122 LYS Chi-restraints excluded: chain BL residue 47 ASP Chi-restraints excluded: chain BL residue 157 VAL Chi-restraints excluded: chain BL residue 161 THR Chi-restraints excluded: chain BM residue 28 THR Chi-restraints excluded: chain BN residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 9.9990 chunk 569 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 493 optimal weight: 10.0000 chunk 78 optimal weight: 0.0020 chunk 148 optimal weight: 1.9990 chunk 535 optimal weight: 0.0570 chunk 224 optimal weight: 3.9990 chunk 549 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 78 GLN AE 15 GLN AE 68 GLN AF 68 GLN AF 111 ASN AG 53 ASN AJ 68 GLN AK 49 GLN AK 78 GLN AM 47 ASN ** AM 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 68 GLN AN 111 ASN AQ 15 GLN AQ 39 GLN AQ 68 GLN AQ 159 ASN AR 111 ASN AS 68 GLN AT 132 GLN AU 49 GLN AW 47 ASN AW 139 ASN ** AX 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AX 146 ASN AY 39 GLN AY 47 ASN AY 53 ASN AZ 132 GLN BA 49 GLN BA 61 ASN BD 65 GLN BE 39 GLN BF 132 GLN BG 49 GLN BG 53 ASN BI 15 GLN BI 53 ASN BJ 11 GLN BK 72 ASN BK 74 GLN BL 89 ASN BM 8 GLN BM 258 GLN ** BN 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122717 restraints weight = 57196.999| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 0.73 r_work: 0.3402 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55030 Z= 0.198 Angle : 0.610 9.971 74854 Z= 0.304 Chirality : 0.039 0.389 8181 Planarity : 0.004 0.060 9805 Dihedral : 10.389 87.342 10000 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.16 % Allowed : 11.82 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.10), residues: 6752 helix: 2.32 (0.07), residues: 5215 sheet: 0.68 (0.60), residues: 50 loop : 0.03 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAM 128 HIS 0.006 0.002 HISBA 140 PHE 0.011 0.002 PHEBF 98 TYR 0.025 0.001 TYRBG 90 ARG 0.008 0.000 ARGAR 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26315.56 seconds wall clock time: 450 minutes 18.84 seconds (27018.84 seconds total)