Starting phenix.real_space_refine on Wed Sep 25 18:53:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/09_2024/7sc8_25029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/09_2024/7sc8_25029.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/7sc8_25029/09_2024/7sc8_25029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/09_2024/7sc8_25029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/09_2024/7sc8_25029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc8_25029/09_2024/7sc8_25029.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= 0.002 sd= 0.034 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 13209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56784 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "AB" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "AC" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "AD" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "AE" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "AF" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "AG" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "AH" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "AI" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "AJ" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "AK" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "AL" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "AM" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "AN" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "AO" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "AP" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "AQ" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "AR" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "AS" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "AT" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "AU" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "AV" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "AW" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "AX" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "AY" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "AZ" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "BA" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "BB" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "BC" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "BD" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "BE" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "BF" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "BG" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "BH" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "BI" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "BJ" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "BK" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "BL" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "BM" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "BN" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 27.63, per 1000 atoms: 0.49 Number of scatterers: 56784 At special positions: 0 Unit cell: (127.05, 128.1, 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 13209 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: 11.87 Conformation dependent library (CDL) restraints added in 5.4 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: 380 helices and 3 sheets defined 82.8% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 15 Processing helix chain 'AA' and resid 20 through 47 removed outlier: 4.316A pdb=" N ASNAA 35 " --> pdb=" O LEUAA 31 " (cutoff:3.500A) removed outlier: 4.961A 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: 3.594A 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 122 Processing helix chain 'AA' and resid 125 through 140 removed outlier: 4.219A 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: 3.971A pdb=" N VALAB 8 " --> pdb=" O VALAB 4 " (cutoff:3.500A) Processing helix chain 'AB' and resid 20 through 47 removed outlier: 4.523A pdb=" N ASNAB 35 " --> pdb=" O VALAB 31 " (cutoff:3.500A) removed outlier: 5.256A 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: 3.660A 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: 4.296A pdb=" N ASNAC 35 " --> pdb=" O LEUAC 31 " (cutoff:3.500A) removed outlier: 5.206A 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: 3.731A 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: 4.065A pdb=" N TYRAC 129 " --> pdb=" O SERAC 125 " (cutoff:3.500A) Processing helix chain 'AC' and resid 143 through 162 removed outlier: 3.596A pdb=" N ARGAC 147 " --> pdb=" O SERAC 143 " (cutoff:3.500A) Processing helix chain 'AD' and resid 3 through 16 removed outlier: 3.853A 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 removed outlier: 3.591A pdb=" N GLNAE 15 " --> pdb=" O THRAE 11 " (cutoff:3.500A) Processing helix chain 'AE' and resid 20 through 47 removed outlier: 4.328A pdb=" N ASNAE 35 " --> pdb=" O LEUAE 31 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALAAE 36 " --> pdb=" O ARGAE 32 " (cutoff:3.500A) removed outlier: 3.821A 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 122 Processing helix chain 'AE' and resid 125 through 140 removed outlier: 4.205A 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: 4.037A 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: 3.512A 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: 4.394A pdb=" N ASNAG 35 " --> pdb=" O LEUAG 31 " (cutoff:3.500A) removed outlier: 5.169A 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: 3.555A 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: 4.070A pdb=" N TYRAG 129 " --> pdb=" O SERAG 125 " (cutoff:3.500A) Processing helix chain 'AG' and resid 144 through 162 Processing helix chain 'AH' and resid 3 through 16 removed outlier: 3.946A 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: 3.508A 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: 4.178A pdb=" N ASNAI 35 " --> pdb=" O LEUAI 31 " (cutoff:3.500A) removed outlier: 5.002A 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 68 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: 4.037A 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: 4.272A 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 removed outlier: 3.525A pdb=" N GLUAJ 106 " --> pdb=" O ALAAJ 102 " (cutoff:3.500A) 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 removed outlier: 3.683A pdb=" N VALAJ 171 " --> pdb=" O ALAAJ 167 " (cutoff:3.500A) Processing helix chain 'AK' and resid 3 through 16 Processing helix chain 'AK' and resid 20 through 47 removed outlier: 4.493A pdb=" N ASNAK 35 " --> pdb=" O LEUAK 31 " (cutoff:3.500A) removed outlier: 5.383A 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: 4.045A 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 14 removed outlier: 4.050A 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: 4.352A 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: 4.485A pdb=" N ASNAM 35 " --> pdb=" O LEUAM 31 " (cutoff:3.500A) removed outlier: 5.128A 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 69 removed outlier: 3.720A pdb=" N GLNAM 68 " --> pdb=" O PROAM 64 " (cutoff:3.500A) 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 15 removed outlier: 3.825A 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: 4.385A pdb=" N ASNAO 35 " --> pdb=" O LEUAO 31 " (cutoff:3.500A) removed outlier: 5.137A 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: 3.977A 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: 4.122A 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 64 through 67 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: 4.461A pdb=" N ASNAQ 35 " --> pdb=" O LEUAQ 31 " (cutoff:3.500A) removed outlier: 5.136A 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: 4.218A pdb=" N TYRAQ 129 " --> pdb=" O SERAQ 125 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 143 through 162 removed outlier: 3.529A pdb=" N ARGAQ 147 " --> pdb=" O SERAQ 143 " (cutoff:3.500A) Processing helix chain 'AR' and resid 3 through 16 removed outlier: 3.800A pdb=" N VALAR 8 " --> pdb=" O VALAR 4 " (cutoff:3.500A) Processing helix chain 'AR' and resid 20 through 33 Processing helix chain 'AR' and resid 33 through 47 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 Processing helix chain 'AS' and resid 3 through 15 Processing helix chain 'AS' and resid 20 through 47 removed outlier: 4.475A pdb=" N ASNAS 35 " --> pdb=" O LEUAS 31 " (cutoff:3.500A) removed outlier: 5.121A 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: 4.006A 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: 4.057A 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 143 Processing helix chain 'AT' and resid 153 through 172 removed outlier: 3.577A pdb=" N VALAT 171 " --> pdb=" O ALAAT 167 " (cutoff:3.500A) removed outlier: 3.724A 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: 4.403A pdb=" N ASNAU 35 " --> pdb=" O LEUAU 31 " (cutoff:3.500A) removed outlier: 5.132A 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: 4.143A 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: 3.835A 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 63 through 68 removed outlier: 4.267A pdb=" N ILEAV 67 " --> pdb=" O GLNAV 63 " (cutoff:3.500A) Processing helix chain 'AV' and resid 75 through 100 Processing helix chain 'AV' and resid 102 through 108 removed outlier: 3.583A pdb=" N GLUAV 106 " --> pdb=" O ALAAV 102 " (cutoff:3.500A) 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: 3.651A pdb=" N VALAV 171 " --> pdb=" O ALAAV 167 " (cutoff:3.500A) Processing helix chain 'AW' and resid 3 through 15 Processing helix chain 'AW' and resid 20 through 47 removed outlier: 4.612A pdb=" N ASNAW 35 " --> pdb=" O LEUAW 31 " (cutoff:3.500A) removed outlier: 5.282A 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 removed outlier: 3.508A pdb=" N GLNAW 68 " --> pdb=" O PROAW 64 " (cutoff:3.500A) 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: 3.964A pdb=" N TYRAW 129 " --> pdb=" O SERAW 125 " (cutoff:3.500A) Processing helix chain 'AW' and resid 143 through 162 Processing helix chain 'AX' and resid 3 through 14 removed outlier: 3.810A 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 Processing helix chain 'AX' and resid 47 through 63 Processing helix chain 'AX' and resid 63 through 68 removed outlier: 4.327A pdb=" N ILEAX 67 " --> pdb=" O GLNAX 63 " (cutoff:3.500A) 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: 3.693A pdb=" N ASPAX 140 " --> pdb=" O GLUAX 136 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILEAX 141 " --> pdb=" O ALAAX 137 " (cutoff:3.500A) Processing helix chain 'AX' and resid 153 through 172 removed outlier: 3.517A pdb=" N VALAX 171 " --> pdb=" O ALAAX 167 " (cutoff:3.500A) Processing helix chain 'AY' and resid 3 through 15 Processing helix chain 'AY' and resid 20 through 47 removed outlier: 4.472A pdb=" N ASNAY 35 " --> pdb=" O LEUAY 31 " (cutoff:3.500A) removed outlier: 5.057A 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: 4.052A 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: 3.967A 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 Processing helix chain 'BA' and resid 3 through 15 Processing helix chain 'BA' and resid 20 through 47 removed outlier: 4.349A pdb=" N ASNBA 35 " --> pdb=" O LEUBA 31 " (cutoff:3.500A) removed outlier: 5.189A 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: 4.054A 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: 3.897A 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: 4.306A pdb=" N ASNBC 35 " --> pdb=" O LEUBC 31 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALABC 36 " --> pdb=" O ARGBC 32 " (cutoff:3.500A) removed outlier: 3.644A 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 removed outlier: 3.586A pdb=" N GLNBC 68 " --> pdb=" O PROBC 64 " (cutoff:3.500A) 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: 4.057A pdb=" N TYRBC 129 " --> pdb=" O SERBC 125 " (cutoff:3.500A) Processing helix chain 'BC' and resid 143 through 162 removed outlier: 3.532A pdb=" N ARGBC 147 " --> pdb=" O SERBC 143 " (cutoff:3.500A) Processing helix chain 'BD' and resid 3 through 16 removed outlier: 3.775A pdb=" N VALBD 8 " --> pdb=" O VALBD 4 " (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 64 through 67 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: 4.331A pdb=" N ASNBE 35 " --> pdb=" O LEUBE 31 " (cutoff:3.500A) removed outlier: 4.995A 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: 4.015A pdb=" N TYRBE 129 " --> pdb=" O SERBE 125 " (cutoff:3.500A) Processing helix chain 'BE' and resid 144 through 162 Processing helix chain 'BF' and resid 3 through 16 removed outlier: 4.020A 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 47 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: 3.589A pdb=" N GLNBG 15 " --> pdb=" O THRBG 11 " (cutoff:3.500A) Processing helix chain 'BG' and resid 20 through 47 removed outlier: 4.400A pdb=" N ASNBG 35 " --> pdb=" O LEUBG 31 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALABG 36 " --> pdb=" O ARGBG 32 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.525A pdb=" N ILEBG 118 " --> pdb=" O GLYBG 114 " (cutoff:3.500A) Processing helix chain 'BG' and resid 125 through 140 removed outlier: 4.026A pdb=" N TYRBG 129 " --> pdb=" O SERBG 125 " (cutoff:3.500A) Processing helix chain 'BG' and resid 143 through 162 removed outlier: 3.541A pdb=" N ARGBG 147 " --> pdb=" O SERBG 143 " (cutoff:3.500A) Processing helix chain 'BH' and resid 3 through 16 removed outlier: 4.133A pdb=" N VALBH 8 " --> pdb=" O VALBH 4 " (cutoff:3.500A) Processing helix chain 'BH' and resid 20 through 33 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: 3.821A 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: 4.305A pdb=" N ASNBI 35 " --> pdb=" O LEUBI 31 " (cutoff:3.500A) removed outlier: 5.046A 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 123 Processing helix chain 'BI' and resid 125 through 140 removed outlier: 4.147A 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: 3.590A 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 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: 3.629A 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: 3.576A pdb=" N LYSBK 122 " --> pdb=" O SERBK 118 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILEBK 127 " --> pdb=" O ILEBK 123 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VALBK 128 " --> pdb=" O ALABK 124 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VALBK 129 " --> pdb=" O TRPBK 125 " (cutoff:3.500A) removed outlier: 4.531A 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: 3.824A 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: 3.874A 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: 3.710A pdb=" N PHEBL 164 " --> pdb=" O ARGBL 160 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHEBL 168 " --> pdb=" O PHEBL 164 " (cutoff:3.500A) removed outlier: 3.797A 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 204 through 208 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: 4.008A 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 105 Processing helix chain 'BM' and resid 111 through 116 Processing helix chain 'BM' and resid 118 through 135 removed outlier: 8.134A pdb=" N TYRBM 126 " --> pdb=" O HISBM 122 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLUBM 127 " --> pdb=" O GLNBM 123 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALABM 128 " --> pdb=" O GLYBM 124 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYRBM 133 " --> pdb=" O GLUBM 129 " (cutoff:3.500A) removed outlier: 3.552A 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 161 through 172 removed outlier: 4.348A pdb=" N PHEBM 165 " --> pdb=" O LYSBM 161 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SERBM 166 " --> pdb=" O THRBM 162 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHEBM 169 " --> pdb=" O PHEBM 165 " (cutoff:3.500A) removed outlier: 3.877A 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 250 through 263 removed outlier: 4.448A pdb=" N SERBM 254 " --> pdb=" O TYRBM 250 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALABM 255 " --> pdb=" O ASPBM 251 " (cutoff:3.500A) Processing helix chain 'BN' and resid 30 through 34 removed outlier: 3.825A pdb=" N GLUBN 34 " --> pdb=" O ASPBN 31 " (cutoff:3.500A) Processing helix chain 'BN' and resid 54 through 65 removed outlier: 3.512A 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: 7.352A pdb=" N LEUBL 238 " --> pdb=" O PROBL 287 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARGBL 240 " --> pdb=" O ILEBL 285 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILEBL 285 " --> pdb=" O ARGBL 240 " (cutoff:3.500A) removed outlier: 6.634A 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: 7.086A pdb=" N METBM 222 " --> pdb=" O LEUBM 272 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEUBM 272 " --> pdb=" O METBM 222 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARGBM 224 " --> pdb=" O ILEBM 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILEBM 270 " --> pdb=" O ARGBM 224 " (cutoff:3.500A) removed outlier: 6.757A 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: 7.832A pdb=" N VALBN 19 " --> pdb=" O PROBN 74 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VALBN 21 " --> pdb=" O ILEBN 72 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILEBN 72 " --> pdb=" O VALBN 21 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLUBN 23 " --> pdb=" O VALBN 70 " (cutoff:3.500A) 4063 hydrogen bonds defined for protein. 12036 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: 22.11 Time building geometry restraints manager: 14.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10171 1.32 - 1.45: 14228 1.45 - 1.57: 30338 1.57 - 1.70: 2 1.70 - 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 1.350 0.163 3.90e-02 6.57e+02 1.76e+01 bond pdb=" CA LYSBA 42 " pdb=" C LYSBA 42 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.27e-02 6.20e+03 1.27e+01 bond pdb=" CB THRBF 6 " pdb=" CG2 THRBF 6 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.18e+01 bond pdb=" CB VALBK 17 " pdb=" CG2 VALBK 17 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 9.92e+00 bond pdb=" CGA CYCAT 202 " pdb=" O2A CYCAT 202 " ideal model delta sigma weight residual 1.249 1.309 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 55025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 73644 3.67 - 7.35: 1074 7.35 - 11.02: 108 11.02 - 14.70: 23 14.70 - 18.37: 5 Bond angle restraints: 74854 Sorted by residual: angle pdb=" C ARGAU 147 " pdb=" CA ARGAU 147 " pdb=" CB ARGAU 147 " ideal model delta sigma weight residual 110.88 96.70 14.18 1.57e+00 4.06e-01 8.15e+01 angle pdb=" N ASPAJ 39 " pdb=" CA ASPAJ 39 " pdb=" CB ASPAJ 39 " ideal model delta sigma weight residual 110.12 120.27 -10.15 1.47e+00 4.63e-01 4.77e+01 angle pdb=" CA GLNAH 11 " pdb=" CB GLNAH 11 " pdb=" CG GLNAH 11 " ideal model delta sigma weight residual 114.10 101.61 12.49 2.00e+00 2.50e-01 3.90e+01 angle pdb=" CA ARGAR 150 " pdb=" CB ARGAR 150 " pdb=" CG ARGAR 150 " ideal model delta sigma weight residual 114.10 126.36 -12.26 2.00e+00 2.50e-01 3.76e+01 angle pdb=" CB METBN 59 " pdb=" CG METBN 59 " pdb=" SD METBN 59 " ideal model delta sigma weight residual 112.70 94.33 18.37 3.00e+00 1.11e-01 3.75e+01 ... (remaining 74849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 31035 18.12 - 36.24: 2192 36.24 - 54.36: 428 54.36 - 72.48: 250 72.48 - 90.59: 71 Dihedral angle restraints: 33976 sinusoidal: 14260 harmonic: 19716 Sorted by residual: dihedral pdb=" C ARGAU 147 " pdb=" N ARGAU 147 " pdb=" CA ARGAU 147 " pdb=" CB ARGAU 147 " ideal model delta harmonic sigma weight residual -122.60 -107.01 -15.59 0 2.50e+00 1.60e-01 3.89e+01 dihedral pdb=" C GLNAM 68 " pdb=" N GLNAM 68 " pdb=" CA GLNAM 68 " pdb=" CB GLNAM 68 " ideal model delta harmonic sigma weight residual -122.60 -135.86 13.26 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" N GLNAM 68 " pdb=" C GLNAM 68 " pdb=" CA GLNAM 68 " pdb=" CB GLNAM 68 " ideal model delta harmonic sigma weight residual 122.80 136.01 -13.21 0 2.50e+00 1.60e-01 2.79e+01 ... (remaining 33973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 8052 0.166 - 0.332: 113 0.332 - 0.499: 12 0.499 - 0.665: 2 0.665 - 0.831: 2 Chirality restraints: 8181 Sorted by residual: chirality pdb=" CG LEUAB 120 " pdb=" CB LEUAB 120 " pdb=" CD1 LEUAB 120 " pdb=" CD2 LEUAB 120 " both_signs ideal model delta sigma weight residual False -2.59 -1.76 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" CB THRBF 6 " pdb=" CA THRBF 6 " pdb=" OG1 THRBF 6 " pdb=" CG2 THRBF 6 " both_signs ideal model delta sigma weight residual False 2.55 1.83 0.72 2.00e-01 2.50e+01 1.31e+01 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 -2.03 -0.60 2.00e-01 2.50e+01 8.86e+00 ... (remaining 8178 not shown) Planarity restraints: 9805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYCAX 201 " -0.093 2.00e-02 2.50e+03 1.97e-01 8.72e+02 pdb=" OB CYCAX 201 " 0.196 2.00e-02 2.50e+03 pdb=" C1B CYCAX 201 " -0.037 2.00e-02 2.50e+03 pdb=" C2B CYCAX 201 " 0.128 2.00e-02 2.50e+03 pdb=" C3B CYCAX 201 " 0.153 2.00e-02 2.50e+03 pdb=" C4B CYCAX 201 " 0.032 2.00e-02 2.50e+03 pdb=" CAB CYCAX 201 " -0.412 2.00e-02 2.50e+03 pdb=" CHB CYCAX 201 " -0.195 2.00e-02 2.50e+03 pdb=" CMB CYCAX 201 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CYCAT 202 " -0.049 2.00e-02 2.50e+03 1.54e-01 5.35e+02 pdb=" C2A CYCAT 202 " 0.029 2.00e-02 2.50e+03 pdb=" C3A CYCAT 202 " -0.057 2.00e-02 2.50e+03 pdb=" C4A CYCAT 202 " 0.035 2.00e-02 2.50e+03 pdb=" CAA CYCAT 202 " 0.281 2.00e-02 2.50e+03 pdb=" CHA CYCAT 202 " -0.141 2.00e-02 2.50e+03 pdb=" CHB CYCAT 202 " 0.197 2.00e-02 2.50e+03 pdb=" CMA CYCAT 202 " -0.260 2.00e-02 2.50e+03 pdb=" NA CYCAT 202 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYCAB 201 " 0.021 2.00e-02 2.50e+03 1.50e-01 5.04e+02 pdb=" OB CYCAB 201 " -0.079 2.00e-02 2.50e+03 pdb=" C1B CYCAB 201 " 0.030 2.00e-02 2.50e+03 pdb=" C2B CYCAB 201 " -0.087 2.00e-02 2.50e+03 pdb=" C3B CYCAB 201 " -0.142 2.00e-02 2.50e+03 pdb=" C4B CYCAB 201 " -0.076 2.00e-02 2.50e+03 pdb=" CAB CYCAB 201 " 0.318 2.00e-02 2.50e+03 pdb=" CHB CYCAB 201 " 0.179 2.00e-02 2.50e+03 pdb=" CMB CYCAB 201 " -0.164 2.00e-02 2.50e+03 ... (remaining 9802 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 2373 2.66 - 3.22: 57633 3.22 - 3.78: 114463 3.78 - 4.34: 146831 4.34 - 4.90: 228586 Nonbonded interactions: 549886 Sorted by model distance: nonbonded pdb=" OE2 GLUBA 109 " pdb=" OG SERBK 39 " model vdw 2.102 3.040 nonbonded pdb=" OD2 ASPAI 108 " pdb=" O HOHAI 301 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASNBA 47 " pdb=" OG SERBA 50 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THRAI 104 " pdb=" O HOHAI 301 " model vdw 2.179 3.040 nonbonded pdb=" O HISBM 117 " pdb=" O HOHBM 301 " model vdw 2.181 3.040 ... (remaining 549881 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: 3.800 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: 0.080 Extract box with map and model: 1.750 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 105.640 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.800 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.008 0.163 55030 Z= 0.555 Angle : 1.117 18.370 74854 Z= 0.580 Chirality : 0.065 0.831 8181 Planarity : 0.012 0.197 9805 Dihedral : 14.646 90.594 21388 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.38 % Allowed : 1.95 % Favored : 97.67 % Cbeta Deviations : 0.16 % 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: 2.13 (0.10), residues: 6752 helix: 1.92 (0.07), residues: 5197 sheet: 0.95 (0.53), residues: 55 loop : -0.30 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRPAW 128 HIS 0.019 0.006 HISBL 117 PHE 0.035 0.004 PHEBE 122 TYR 0.053 0.004 TYRBN 75 ARG 0.026 0.002 ARGBJ 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 1274 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1254 time to evaluate : 4.690 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AD 84 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7792 (tmm160) REVERT: AL 134 MET cc_start: 0.7498 (mtm) cc_final: 0.7241 (mtm) REVERT: AP 117 TYR cc_start: 0.7297 (m-10) cc_final: 0.7032 (m-10) REVERT: AW 108 ASP cc_start: 0.6296 (m-30) cc_final: 0.6079 (m-30) REVERT: BD 115 GLU cc_start: 0.6271 (mp0) cc_final: 0.6020 (mp0) REVERT: BE 129 TYR cc_start: 0.7920 (m-80) cc_final: 0.7487 (m-80) REVERT: BM 247 LEU cc_start: 0.7945 (mt) cc_final: 0.7732 (mp) REVERT: BM 263 GLN cc_start: 0.6436 (mt0) cc_final: 0.5911 (mt0) outliers start: 20 outliers final: 6 residues processed: 1267 average time/residue: 1.3534 time to fit residues: 2197.8296 Evaluate side-chains 1131 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1125 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 42 LYS Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AY residue 49 GLN Chi-restraints excluded: chain BM residue 8 GLN Chi-restraints excluded: chain BM residue 80 GLU Chi-restraints excluded: chain BM residue 186 SER 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: 0.5980 chunk 283 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 344 optimal weight: 0.9980 chunk 272 optimal weight: 0.6980 chunk 528 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 393 optimal weight: 0.9990 chunk 612 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN AA 49 GLN AA 78 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 132 GLN AI 15 GLN AI 78 GLN AM 25 GLN AM 39 GLN AO 47 ASN AO 49 GLN AO 61 ASN AP 146 ASN AR 35 ASN AT 47 ASN AT 63 GLN AU 25 GLN AU 78 GLN AW 15 GLN AW 68 GLN AX 47 ASN AX 132 GLN AY 25 GLN AY 139 ASN BA 61 ASN BA 78 GLN BA 151 ASN BC 15 GLN BD 65 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 54 ASN BG 15 GLN BG 47 ASN BJ 132 GLN BK 13 GLN BK 72 ASN BK 143 ASN BK 163 ASN ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 195 GLN BL 267 GLN BM 52 GLN BM 159 ASN BM 170 GLN BM 220 ASN BM 252 ASN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 55030 Z= 0.235 Angle : 0.616 10.734 74854 Z= 0.301 Chirality : 0.039 0.278 8181 Planarity : 0.004 0.053 9805 Dihedral : 10.041 80.084 10015 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.16 % Favored : 98.83 % Rotamer: Outliers : 1.16 % Allowed : 8.86 % Favored : 89.98 % 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: 2.26 (0.07), residues: 5198 sheet: 0.98 (0.51), residues: 55 loop : -0.25 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAC 128 HIS 0.006 0.002 HISAQ 140 PHE 0.013 0.002 PHEBK 103 TYR 0.023 0.001 TYRBK 134 ARG 0.008 0.001 ARGBB 15 *********************** 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 1189 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1128 time to evaluate : 4.707 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AD 84 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7787 (tmm160) REVERT: AF 79 MET cc_start: 0.8346 (tpp) cc_final: 0.7932 (tpp) REVERT: AG 1 MET cc_start: 0.7163 (tpt) cc_final: 0.5977 (tpt) REVERT: AL 134 MET cc_start: 0.7717 (mtm) cc_final: 0.7290 (mtm) REVERT: AP 7 ARG cc_start: 0.7677 (tpp-160) cc_final: 0.7454 (tpp-160) REVERT: BD 115 GLU cc_start: 0.6531 (mp0) cc_final: 0.6261 (mp0) REVERT: BK 26 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6120 (mm-30) REVERT: BM 84 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6049 (mm-40) REVERT: BM 247 LEU cc_start: 0.7917 (mt) cc_final: 0.7708 (mp) outliers start: 61 outliers final: 24 residues processed: 1152 average time/residue: 1.4051 time to fit residues: 2057.5959 Evaluate side-chains 1121 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1096 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AG residue 152 SER Chi-restraints excluded: chain AJ residue 40 SER Chi-restraints excluded: chain AM residue 116 ASP Chi-restraints excluded: chain AN residue 40 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AN residue 166 ARG Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 139 LEU Chi-restraints excluded: chain AR residue 53 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AX residue 39 ASP Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain BA residue 1 MET Chi-restraints excluded: chain BA residue 50 SER Chi-restraints excluded: chain BB residue 126 SER Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 141 ILE Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BI residue 109 GLU Chi-restraints excluded: chain BM residue 84 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 340 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 509 optimal weight: 4.9990 chunk 416 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 613 optimal weight: 2.9990 chunk 662 optimal weight: 0.8980 chunk 546 optimal weight: 0.9980 chunk 608 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 491 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 15 GLN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 47 ASN AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 15 GLN AL 63 GLN AM 25 GLN AS 72 ASN AT 63 GLN AU 25 GLN AW 15 GLN AX 35 ASN AY 139 ASN BA 61 ASN BC 15 GLN BD 35 ASN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BF 54 ASN BG 15 GLN BI 139 ASN BK 74 GLN BL 181 GLN BL 267 GLN BM 52 GLN BM 92 GLN BM 159 ASN BM 170 GLN BM 197 ASN BM 220 ASN BM 258 GLN ** BM 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55030 Z= 0.218 Angle : 0.570 10.502 74854 Z= 0.278 Chirality : 0.038 0.206 8181 Planarity : 0.004 0.046 9805 Dihedral : 9.855 85.817 10001 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.02 % Favored : 98.95 % Rotamer: Outliers : 1.40 % Allowed : 11.12 % Favored : 87.48 % 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: 2.77 (0.10), residues: 6752 helix: 2.41 (0.07), residues: 5199 sheet: 0.93 (0.55), residues: 53 loop : -0.20 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPBM 146 HIS 0.006 0.002 HISBC 140 PHE 0.012 0.001 PHEBK 103 TYR 0.019 0.001 TYRBN 75 ARG 0.007 0.000 ARGBL 9 *********************** 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 1183 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1109 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 46 ASP cc_start: 0.7272 (m-30) cc_final: 0.7016 (m-30) REVERT: AF 79 MET cc_start: 0.8322 (tpp) cc_final: 0.7970 (tpp) REVERT: AL 134 MET cc_start: 0.7692 (mtm) cc_final: 0.7239 (mtm) REVERT: AM 156 TYR cc_start: 0.7360 (t80) cc_final: 0.7044 (t80) REVERT: AO 30 ARG cc_start: 0.7901 (tpt90) cc_final: 0.7585 (tpt170) REVERT: AP 7 ARG cc_start: 0.7706 (tpp-160) cc_final: 0.7465 (tpp-160) REVERT: AS 17 ARG cc_start: 0.7434 (mtp85) cc_final: 0.7067 (mtp-110) REVERT: BD 115 GLU cc_start: 0.6511 (mp0) cc_final: 0.6212 (mp0) REVERT: BD 136 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5658 (mp0) REVERT: BK 26 GLU cc_start: 0.6348 (mm-30) cc_final: 0.6144 (mm-30) REVERT: BM 80 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5718 (tm-30) REVERT: BM 247 LEU cc_start: 0.7942 (mt) cc_final: 0.7733 (mp) outliers start: 74 outliers final: 33 residues processed: 1128 average time/residue: 1.4314 time to fit residues: 2048.1118 Evaluate side-chains 1125 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1090 time to evaluate : 4.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AE residue 96 THR Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AN residue 40 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AR residue 3 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 1 MET Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain BA residue 50 SER Chi-restraints excluded: chain BD residue 136 GLU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BH residue 141 ILE Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 53 GLU Chi-restraints excluded: chain BL residue 177 SER Chi-restraints excluded: chain BL residue 237 LYS Chi-restraints excluded: chain BM residue 80 GLU Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 272 LEU Chi-restraints excluded: chain BN residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 605 optimal weight: 1.9990 chunk 461 optimal weight: 0.5980 chunk 318 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 292 optimal weight: 0.8980 chunk 411 optimal weight: 3.9990 chunk 615 optimal weight: 0.0870 chunk 651 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 chunk 583 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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** AD 68 GLN AD 111 ASN AF 54 ASN ** AF 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 15 GLN AL 63 GLN AN 132 GLN AP 42 ASN AR 35 ASN AT 63 GLN AU 25 GLN AW 15 GLN AY 139 ASN BA 61 ASN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BG 15 GLN BK 13 GLN BK 74 GLN BK 163 ASN ** BL 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN ** BM 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 159 ASN BM 170 GLN BM 220 ASN BM 258 GLN BM 263 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55030 Z= 0.182 Angle : 0.542 10.268 74854 Z= 0.265 Chirality : 0.037 0.226 8181 Planarity : 0.004 0.051 9805 Dihedral : 9.820 88.382 10001 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 1.59 % Allowed : 11.99 % Favored : 86.42 % 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: 2.92 (0.10), residues: 6752 helix: 2.52 (0.07), residues: 5205 sheet: 0.82 (0.55), residues: 53 loop : -0.17 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.005 0.002 HISAI 140 PHE 0.013 0.001 PHEAD 98 TYR 0.022 0.001 TYRBI 153 ARG 0.008 0.000 ARGBD 77 *********************** 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 1198 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1114 time to evaluate : 4.657 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 46 ASP cc_start: 0.7232 (m-30) cc_final: 0.6991 (m-30) REVERT: AD 37 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7799 (ttm110) REVERT: AF 79 MET cc_start: 0.8258 (tpp) cc_final: 0.7925 (tpp) REVERT: AL 134 MET cc_start: 0.7662 (mtm) cc_final: 0.7180 (mtm) REVERT: AM 156 TYR cc_start: 0.7341 (t80) cc_final: 0.7033 (t80) REVERT: AS 17 ARG cc_start: 0.7428 (mtp85) cc_final: 0.7002 (mtp-110) REVERT: BD 115 GLU cc_start: 0.6528 (mp0) cc_final: 0.6226 (mp0) REVERT: BM 247 LEU cc_start: 0.7931 (mt) cc_final: 0.7721 (mp) outliers start: 84 outliers final: 40 residues processed: 1140 average time/residue: 1.4312 time to fit residues: 2069.9396 Evaluate side-chains 1120 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1080 time to evaluate : 4.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 28 SER Chi-restraints excluded: chain AD residue 66 LEU Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AG residue 152 SER Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AL residue 103 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 3 ASP Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AW residue 39 GLN Chi-restraints excluded: chain AX residue 39 ASP Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AY residue 21 SER Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain BA residue 50 SER Chi-restraints excluded: chain BB residue 101 ASP Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BD residue 171 VAL Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 53 GLU Chi-restraints excluded: chain BL residue 177 SER Chi-restraints excluded: chain BL residue 237 LYS Chi-restraints excluded: chain BM residue 30 GLU Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 249 SER Chi-restraints excluded: chain BM residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 542 optimal weight: 4.9990 chunk 369 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 485 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 555 optimal weight: 0.7980 chunk 450 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 584 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** AF 11 GLN AF 72 ASN AI 15 GLN AI 139 ASN AL 63 GLN AM 25 GLN AO 15 GLN AT 63 GLN AW 15 GLN AX 65 GLN AY 139 ASN BA 61 ASN BB 11 GLN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BK 74 GLN BK 163 ASN BL 92 GLN ** BL 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 111 GLN ** BM 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 159 ASN BM 220 ASN BM 258 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 55030 Z= 0.259 Angle : 0.565 10.414 74854 Z= 0.275 Chirality : 0.039 0.291 8181 Planarity : 0.004 0.046 9805 Dihedral : 9.721 89.210 10001 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.87 % Rotamer: Outliers : 1.89 % Allowed : 12.14 % Favored : 85.97 % 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: 2.94 (0.10), residues: 6752 helix: 2.53 (0.07), residues: 5204 sheet: 0.82 (0.56), residues: 53 loop : -0.15 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPBM 146 HIS 0.007 0.003 HISAS 140 PHE 0.017 0.001 PHEAD 98 TYR 0.022 0.001 TYRBN 75 ARG 0.010 0.001 ARGAF 15 *********************** 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 1208 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1108 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 46 ASP cc_start: 0.7263 (m-30) cc_final: 0.7036 (m-30) REVERT: AD 37 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7801 (ttm110) REVERT: AE 1 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6545 (mtm) REVERT: AF 79 MET cc_start: 0.8296 (tpp) cc_final: 0.7981 (tpp) REVERT: AG 108 ASP cc_start: 0.6779 (m-30) cc_final: 0.6527 (m-30) REVERT: AK 137 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7730 (ttpt) REVERT: AL 134 MET cc_start: 0.7722 (mtm) cc_final: 0.7153 (mtm) REVERT: AM 25 GLN cc_start: 0.7129 (mt0) cc_final: 0.6922 (mt0) REVERT: AM 156 TYR cc_start: 0.7376 (t80) cc_final: 0.6988 (t80) REVERT: BD 115 GLU cc_start: 0.6548 (mp0) cc_final: 0.6247 (mp0) REVERT: BD 136 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5684 (mp0) REVERT: BJ 117 TYR cc_start: 0.7892 (m-10) cc_final: 0.7690 (m-10) REVERT: BK 69 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6737 (mt0) REVERT: BM 247 LEU cc_start: 0.7994 (mt) cc_final: 0.7789 (mp) outliers start: 100 outliers final: 51 residues processed: 1146 average time/residue: 1.4245 time to fit residues: 2069.1816 Evaluate side-chains 1134 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1079 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 87 GLU Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 28 SER Chi-restraints excluded: chain AD residue 66 LEU Chi-restraints excluded: chain AE residue 1 MET Chi-restraints excluded: chain AE residue 96 THR Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AG residue 152 SER Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AK residue 137 LYS Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AO residue 3 THR Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 3 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AW residue 39 GLN Chi-restraints excluded: chain AX residue 39 ASP Chi-restraints excluded: chain AX residue 49 SER Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AY residue 21 SER Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain BA residue 39 GLN Chi-restraints excluded: chain BC residue 111 LEU Chi-restraints excluded: chain BD residue 136 GLU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BD residue 171 VAL Chi-restraints excluded: chain BE residue 19 LEU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BI residue 123 ASP Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 69 GLN Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 53 GLU Chi-restraints excluded: chain BL residue 177 SER Chi-restraints excluded: chain BL residue 237 LYS Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 249 SER Chi-restraints excluded: chain BM residue 272 LEU Chi-restraints excluded: chain BN residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 219 optimal weight: 0.7980 chunk 586 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 652 optimal weight: 0.9990 chunk 541 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 47 ASN AF 72 ASN AI 15 GLN AI 139 ASN AK 68 GLN AL 63 GLN AO 15 GLN AO 119 ASN AR 35 ASN AT 63 GLN AU 25 GLN BA 61 ASN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BG 15 GLN BG 139 ASN BK 74 GLN BK 185 HIS BL 92 GLN ** BL 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 52 GLN BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN BM 220 ASN BM 258 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 55030 Z= 0.268 Angle : 0.570 10.434 74854 Z= 0.277 Chirality : 0.039 0.301 8181 Planarity : 0.004 0.047 9805 Dihedral : 9.711 89.039 10001 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.92 % Favored : 98.99 % Rotamer: Outliers : 1.97 % Allowed : 12.44 % Favored : 85.59 % 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: 2.50 (0.07), residues: 5225 sheet: 0.70 (0.56), residues: 54 loop : -0.19 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBM 146 HIS 0.006 0.003 HISAS 140 PHE 0.016 0.002 PHEBF 98 TYR 0.023 0.001 TYRBN 75 ARG 0.011 0.001 ARGBG 120 *********************** 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 1198 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1094 time to evaluate : 4.711 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AA 46 ASP cc_start: 0.7242 (m-30) cc_final: 0.7029 (m-30) REVERT: AD 37 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7801 (ttm110) REVERT: AE 1 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6566 (mtm) REVERT: AL 134 MET cc_start: 0.7694 (mtm) cc_final: 0.7181 (mtm) REVERT: AM 156 TYR cc_start: 0.7395 (t80) cc_final: 0.7083 (t80) REVERT: AS 17 ARG cc_start: 0.7433 (mtp85) cc_final: 0.6942 (mtp-110) REVERT: BD 86 MET cc_start: 0.7575 (mtp) cc_final: 0.7363 (mtt) REVERT: BD 115 GLU cc_start: 0.6554 (mp0) cc_final: 0.6246 (mp0) REVERT: BD 136 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: BK 69 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6739 (mt0) outliers start: 104 outliers final: 54 residues processed: 1129 average time/residue: 1.4305 time to fit residues: 2041.8101 Evaluate side-chains 1135 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1078 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 GLU Chi-restraints excluded: chain AB residue 94 THR Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AC residue 123 ASP Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 28 SER Chi-restraints excluded: chain AD residue 66 LEU Chi-restraints excluded: chain AE residue 1 MET Chi-restraints excluded: chain AE residue 96 THR Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AG residue 152 SER Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AM residue 111 LEU Chi-restraints excluded: chain AN residue 40 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AP residue 99 THR Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 3 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AX residue 39 ASP Chi-restraints excluded: chain AX residue 49 SER Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AY residue 21 SER Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain AZ residue 150 ARG Chi-restraints excluded: chain BA residue 39 GLN Chi-restraints excluded: chain BC residue 111 LEU Chi-restraints excluded: chain BD residue 136 GLU Chi-restraints excluded: chain BD residue 171 VAL Chi-restraints excluded: chain BE residue 19 LEU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 69 GLN Chi-restraints excluded: chain BK residue 187 ARG Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 53 GLU Chi-restraints excluded: chain BL residue 237 LYS Chi-restraints excluded: chain BM residue 80 GLU Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 249 SER Chi-restraints excluded: chain BM residue 272 LEU Chi-restraints excluded: chain BN residue 19 VAL Chi-restraints excluded: chain BN residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 628 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 371 optimal weight: 0.9980 chunk 476 optimal weight: 0.9980 chunk 368 optimal weight: 0.8980 chunk 548 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 chunk 649 optimal weight: 0.9990 chunk 406 optimal weight: 0.8980 chunk 396 optimal weight: 3.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** AF 72 ASN AH 11 GLN AI 15 GLN AL 63 GLN AM 25 GLN AO 15 GLN AR 35 ASN AT 63 GLN AX 65 GLN BA 61 ASN BC 15 GLN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BG 15 GLN BG 139 ASN BH 146 ASN BI 73 ASN BK 74 GLN BL 92 GLN BL 176 ASN BL 181 GLN BL 195 GLN BM 42 GLN BM 52 GLN BM 111 GLN ** BM 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 159 ASN BM 170 GLN BM 220 ASN BM 258 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 55030 Z= 0.226 Angle : 0.555 10.363 74854 Z= 0.271 Chirality : 0.038 0.203 8181 Planarity : 0.004 0.049 9805 Dihedral : 9.712 89.428 10001 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 0.99 % Favored : 98.95 % Rotamer: Outliers : 1.82 % Allowed : 13.16 % Favored : 85.02 % 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: 3.00 (0.10), residues: 6752 helix: 2.58 (0.07), residues: 5204 sheet: 0.73 (0.57), residues: 54 loop : -0.15 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBM 146 HIS 0.006 0.002 HISAI 140 PHE 0.015 0.001 PHEAD 98 TYR 0.021 0.001 TYRBN 75 ARG 0.012 0.000 ARGAF 77 *********************** 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 1190 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1094 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AD 37 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7797 (ttm110) REVERT: AE 1 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6546 (mtm) REVERT: AM 156 TYR cc_start: 0.7381 (t80) cc_final: 0.7063 (t80) REVERT: AR 1 MET cc_start: 0.7369 (ptt) cc_final: 0.7059 (ptm) REVERT: AS 17 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6983 (mtp-110) REVERT: BD 86 MET cc_start: 0.7534 (mtp) cc_final: 0.7326 (mtt) REVERT: BD 115 GLU cc_start: 0.6546 (mp0) cc_final: 0.6244 (mp0) REVERT: BK 69 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6690 (mt0) REVERT: BL 83 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7398 (mttp) outliers start: 96 outliers final: 57 residues processed: 1123 average time/residue: 1.4499 time to fit residues: 2058.8215 Evaluate side-chains 1155 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1095 time to evaluate : 4.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 39 GLN Chi-restraints excluded: chain AB residue 17 GLU Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AC residue 123 ASP Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 28 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 1 MET Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AP residue 99 THR Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 3 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AW residue 39 GLN Chi-restraints excluded: chain AX residue 39 ASP Chi-restraints excluded: chain AX residue 49 SER Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain AZ residue 150 ARG Chi-restraints excluded: chain BA residue 39 GLN Chi-restraints excluded: chain BC residue 50 SER Chi-restraints excluded: chain BC residue 111 LEU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BD residue 171 VAL Chi-restraints excluded: chain BE residue 19 LEU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 15 GLN Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BI residue 123 ASP Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 69 GLN Chi-restraints excluded: chain BK residue 187 ARG Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 53 GLU Chi-restraints excluded: chain BL residue 62 LEU Chi-restraints excluded: chain BL residue 83 LYS Chi-restraints excluded: chain BL residue 237 LYS Chi-restraints excluded: chain BM residue 80 GLU Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 249 SER Chi-restraints excluded: chain BM residue 272 LEU Chi-restraints excluded: chain BN residue 19 VAL Chi-restraints excluded: chain BN residue 39 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 401 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 chunk 387 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 413 optimal weight: 0.9980 chunk 442 optimal weight: 0.7980 chunk 321 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 510 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 72 ASN AH 11 GLN AI 139 ASN AK 139 ASN AL 63 GLN AM 25 GLN AO 15 GLN AT 35 ASN AT 63 GLN BA 61 ASN BB 146 ASN BC 15 GLN BD 35 ASN ** BD 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 139 ASN BG 139 ASN BI 73 ASN BK 74 GLN BL 92 GLN ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 42 GLN BM 52 GLN BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN BM 220 ASN BM 258 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 55030 Z= 0.215 Angle : 0.553 10.316 74854 Z= 0.271 Chirality : 0.037 0.206 8181 Planarity : 0.004 0.049 9805 Dihedral : 9.701 89.593 10001 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.01 % Favored : 98.92 % Rotamer: Outliers : 1.70 % Allowed : 13.58 % Favored : 84.72 % 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: 3.02 (0.10), residues: 6752 helix: 2.60 (0.07), residues: 5202 sheet: 0.72 (0.57), residues: 54 loop : -0.16 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBM 146 HIS 0.006 0.002 HISAI 140 PHE 0.015 0.001 PHEAD 98 TYR 0.025 0.001 TYRAD 92 ARG 0.012 0.000 ARGAF 15 *********************** 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 1209 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1119 time to evaluate : 4.678 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AD 37 ARG cc_start: 0.8029 (ttm-80) cc_final: 0.7785 (ttm110) REVERT: AE 1 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6573 (mtm) REVERT: AF 79 MET cc_start: 0.8229 (tpp) cc_final: 0.7938 (tpp) REVERT: AM 156 TYR cc_start: 0.7392 (t80) cc_final: 0.7072 (t80) REVERT: AR 1 MET cc_start: 0.7381 (ptt) cc_final: 0.7070 (ptm) REVERT: AS 17 ARG cc_start: 0.7378 (mtp85) cc_final: 0.6924 (mtp-110) REVERT: BD 86 MET cc_start: 0.7530 (mtp) cc_final: 0.7327 (mtt) REVERT: BD 115 GLU cc_start: 0.6546 (mp0) cc_final: 0.6249 (mp0) REVERT: BK 69 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6677 (mt0) outliers start: 90 outliers final: 55 residues processed: 1147 average time/residue: 1.3891 time to fit residues: 2023.9622 Evaluate side-chains 1157 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1100 time to evaluate : 4.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 17 GLU Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AC residue 123 ASP Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 28 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 1 MET Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AG residue 152 SER Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AK residue 137 LYS Chi-restraints excluded: chain AK residue 139 ASN Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AL residue 103 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AP residue 99 THR Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 3 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AW residue 39 GLN Chi-restraints excluded: chain AY residue 21 SER Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain AZ residue 150 ARG Chi-restraints excluded: chain BA residue 39 GLN Chi-restraints excluded: chain BC residue 111 LEU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BD residue 171 VAL Chi-restraints excluded: chain BE residue 19 LEU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 116 ASP Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 69 GLN Chi-restraints excluded: chain BK residue 129 VAL Chi-restraints excluded: chain BK residue 187 ARG Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 53 GLU Chi-restraints excluded: chain BL residue 62 LEU Chi-restraints excluded: chain BL residue 237 LYS Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 249 SER Chi-restraints excluded: chain BM residue 272 LEU Chi-restraints excluded: chain BN residue 39 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 590 optimal weight: 0.7980 chunk 622 optimal weight: 0.9990 chunk 567 optimal weight: 0.1980 chunk 605 optimal weight: 0.8980 chunk 364 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 475 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 547 optimal weight: 0.5980 chunk 572 optimal weight: 3.9990 chunk 603 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** AF 72 ASN AH 11 GLN AI 139 ASN AL 63 GLN AO 15 GLN AT 35 ASN AT 63 GLN BA 61 ASN BB 146 ASN BC 15 GLN BD 35 ASN BD 72 ASN BE 139 ASN BG 15 GLN BG 139 ASN BI 73 ASN BK 74 GLN BL 92 GLN BL 181 GLN BL 195 GLN BM 42 GLN BM 52 GLN BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN BM 220 ASN BM 258 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 55030 Z= 0.187 Angle : 0.546 10.243 74854 Z= 0.269 Chirality : 0.037 0.213 8181 Planarity : 0.004 0.050 9805 Dihedral : 9.708 89.865 10001 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.92 % Favored : 98.99 % Rotamer: Outliers : 1.42 % Allowed : 14.22 % Favored : 84.36 % 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: 3.07 (0.10), residues: 6752 helix: 2.63 (0.07), residues: 5202 sheet: 0.75 (0.57), residues: 54 loop : -0.16 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPBK 60 HIS 0.005 0.002 HISAM 140 PHE 0.014 0.001 PHEAD 98 TYR 0.023 0.001 TYRAD 92 ARG 0.012 0.000 ARGAF 15 *********************** 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 1189 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1114 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AD 1 MET cc_start: 0.7578 (ttm) cc_final: 0.7228 (ttm) REVERT: AD 37 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7775 (ttm110) REVERT: AE 1 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6586 (mtm) REVERT: AF 79 MET cc_start: 0.8221 (tpp) cc_final: 0.7935 (tpp) REVERT: AM 156 TYR cc_start: 0.7379 (t80) cc_final: 0.7033 (t80) REVERT: AS 17 ARG cc_start: 0.7310 (mtp85) cc_final: 0.6850 (mtp-110) REVERT: BD 86 MET cc_start: 0.7483 (mtp) cc_final: 0.7273 (mtp) REVERT: BD 115 GLU cc_start: 0.6544 (mp0) cc_final: 0.6242 (mp0) REVERT: BK 69 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6691 (mt0) outliers start: 75 outliers final: 47 residues processed: 1139 average time/residue: 1.3888 time to fit residues: 2013.0700 Evaluate side-chains 1150 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1101 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 39 GLN Chi-restraints excluded: chain AB residue 17 GLU Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 28 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 1 MET Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AP residue 99 THR Chi-restraints excluded: chain AQ residue 1 MET Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AW residue 39 GLN Chi-restraints excluded: chain AY residue 21 SER Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain AZ residue 150 ARG Chi-restraints excluded: chain BA residue 39 GLN Chi-restraints excluded: chain BC residue 50 SER Chi-restraints excluded: chain BC residue 111 LEU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 19 LEU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 69 GLN Chi-restraints excluded: chain BK residue 129 VAL Chi-restraints excluded: chain BK residue 187 ARG Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BL residue 62 LEU Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 249 SER Chi-restraints excluded: chain BM residue 272 LEU Chi-restraints excluded: chain BN residue 39 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 397 optimal weight: 1.9990 chunk 640 optimal weight: 0.3980 chunk 390 optimal weight: 0.8980 chunk 303 optimal weight: 0.7980 chunk 445 optimal weight: 0.9980 chunk 671 optimal weight: 2.9990 chunk 618 optimal weight: 2.9990 chunk 534 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 413 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 ASN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 72 ASN AH 11 GLN AI 139 ASN AK 139 ASN AL 63 GLN AO 15 GLN AR 35 ASN AT 35 ASN AT 63 GLN AX 35 ASN AX 65 GLN BA 61 ASN BB 146 ASN BE 139 ASN BG 15 GLN BI 73 ASN BK 74 GLN BK 163 ASN BL 92 GLN ** BL 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 42 GLN BM 52 GLN BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN BM 220 ASN BM 263 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55030 Z= 0.176 Angle : 0.540 10.174 74854 Z= 0.266 Chirality : 0.037 0.224 8181 Planarity : 0.004 0.047 9805 Dihedral : 9.680 89.904 10001 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.99 % Favored : 98.93 % Rotamer: Outliers : 1.29 % Allowed : 14.62 % Favored : 84.09 % 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: 3.09 (0.10), residues: 6752 helix: 2.66 (0.07), residues: 5202 sheet: 0.83 (0.57), residues: 53 loop : -0.17 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPBK 60 HIS 0.005 0.002 HISAU 140 PHE 0.015 0.001 PHEAD 98 TYR 0.024 0.001 TYRAD 92 ARG 0.011 0.000 ARGAF 15 ********************** 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 1187 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1119 time to evaluate : 5.064 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNAX 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLNBN 4 " (corrupted residue). Skipping it. REVERT: AD 1 MET cc_start: 0.7560 (ttm) cc_final: 0.7222 (ttm) REVERT: AD 37 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7775 (ttm110) REVERT: AE 1 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6596 (mtm) REVERT: AF 79 MET cc_start: 0.8220 (tpp) cc_final: 0.7933 (tpp) REVERT: AM 156 TYR cc_start: 0.7381 (t80) cc_final: 0.7068 (t80) REVERT: AS 1 MET cc_start: 0.6521 (mtp) cc_final: 0.6139 (mtp) REVERT: AS 17 ARG cc_start: 0.7318 (mtp85) cc_final: 0.6862 (mtp-110) REVERT: BD 115 GLU cc_start: 0.6546 (mp0) cc_final: 0.6244 (mp0) REVERT: BK 69 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6688 (mt0) outliers start: 68 outliers final: 47 residues processed: 1141 average time/residue: 1.3885 time to fit residues: 2016.3747 Evaluate side-chains 1148 residues out of total 5280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1099 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 39 GLN Chi-restraints excluded: chain AB residue 17 GLU Chi-restraints excluded: chain AC residue 111 LEU Chi-restraints excluded: chain AD residue 10 SER Chi-restraints excluded: chain AD residue 39 ASP Chi-restraints excluded: chain AE residue 1 MET Chi-restraints excluded: chain AE residue 127 SER Chi-restraints excluded: chain AF residue 127 VAL Chi-restraints excluded: chain AG residue 152 SER Chi-restraints excluded: chain AI residue 1 MET Chi-restraints excluded: chain AK residue 139 ASN Chi-restraints excluded: chain AL residue 49 SER Chi-restraints excluded: chain AL residue 103 SER Chi-restraints excluded: chain AN residue 76 SER Chi-restraints excluded: chain AN residue 103 SER Chi-restraints excluded: chain AP residue 22 SER Chi-restraints excluded: chain AP residue 39 ASP Chi-restraints excluded: chain AP residue 99 THR Chi-restraints excluded: chain AQ residue 1 MET Chi-restraints excluded: chain AQ residue 116 ASP Chi-restraints excluded: chain AR residue 20 SER Chi-restraints excluded: chain AR residue 150 ARG Chi-restraints excluded: chain AS residue 116 ASP Chi-restraints excluded: chain AT residue 103 SER Chi-restraints excluded: chain AU residue 109 GLU Chi-restraints excluded: chain AW residue 39 GLN Chi-restraints excluded: chain AX residue 65 GLN Chi-restraints excluded: chain AY residue 21 SER Chi-restraints excluded: chain AY residue 116 ASP Chi-restraints excluded: chain AZ residue 28 SER Chi-restraints excluded: chain AZ residue 150 ARG Chi-restraints excluded: chain BA residue 39 GLN Chi-restraints excluded: chain BC residue 50 SER Chi-restraints excluded: chain BC residue 111 LEU Chi-restraints excluded: chain BD residue 141 ILE Chi-restraints excluded: chain BE residue 19 LEU Chi-restraints excluded: chain BE residue 50 SER Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BH residue 39 ASP Chi-restraints excluded: chain BI residue 39 GLN Chi-restraints excluded: chain BI residue 51 LEU Chi-restraints excluded: chain BK residue 17 VAL Chi-restraints excluded: chain BK residue 69 GLN Chi-restraints excluded: chain BK residue 129 VAL Chi-restraints excluded: chain BK residue 187 ARG Chi-restraints excluded: chain BK residue 194 ILE Chi-restraints excluded: chain BL residue 5 THR Chi-restraints excluded: chain BM residue 93 ASN Chi-restraints excluded: chain BM residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 674 random chunks: chunk 424 optimal weight: 1.9990 chunk 569 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 493 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 535 optimal weight: 0.0000 chunk 224 optimal weight: 3.9990 chunk 549 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 35 ASN ** AA 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 72 ASN AF 146 ASN AH 11 GLN AK 139 ASN AL 63 GLN AN 65 GLN AO 15 GLN AT 35 ASN AT 63 GLN BA 61 ASN BD 35 ASN BE 139 ASN BG 139 ASN BI 73 ASN BK 74 GLN BK 163 ASN ** BK 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 92 GLN ** BL 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BL 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 195 GLN BM 42 GLN BM 52 GLN BM 111 GLN BM 157 GLN BM 159 ASN BM 170 GLN BM 220 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.125829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119923 restraints weight = 70269.925| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.03 r_work: 0.3717 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.265 55030 Z= 0.266 Angle : 0.652 59.089 74854 Z= 0.350 Chirality : 0.039 0.717 8181 Planarity : 0.004 0.213 9805 Dihedral : 9.679 89.837 10001 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.99 % Favored : 98.93 % Rotamer: Outliers : 1.19 % Allowed : 15.08 % Favored : 83.73 % Cbeta Deviations : 0.03 % 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: 3.07 (0.10), residues: 6752 helix: 2.64 (0.07), residues: 5202 sheet: 0.82 (0.58), residues: 53 loop : -0.19 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPBK 60 HIS 0.005 0.002 HISAU 140 PHE 0.014 0.001 PHEAD 98 TYR 0.021 0.001 TYRAD 92 ARG 0.009 0.000 ARGAF 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27610.92 seconds wall clock time: 469 minutes 58.08 seconds (28198.08 seconds total)