Starting phenix.real_space_refine (version: dev) on Wed Dec 21 05:48:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/12_2022/6zka_11242_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.010 sd= 0.057 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "v TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 40800 Number of models: 1 Model: "" Number of chains: 74 Chain: "A" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "H" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'3PE': 1, 'DCQ': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 276 Unusual residues: {'3PE': 3, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 188 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "m" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "K" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "L" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Classifications: {'water': 156} Link IDs: {None: 155} Chain: "M" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "N" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "X" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "k" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "m" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "p" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "r" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "s" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "t" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "w" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "x" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "z" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "4" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 23.37, per 1000 atoms: 0.57 Number of scatterers: 40800 At special positions: 0 Unit cell: (155.5, 144.5, 239, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 279 16.00 P 34 15.00 O 8224 8.00 N 6282 7.00 C 25981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.22 Conformation dependent library (CDL) restraints added in 6.4 seconds 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 4 sheets defined 62.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.771A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 30 Proline residue: H 12 - end of helix removed outlier: 3.550A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.784A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.698A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.534A pdb=" N ILE J 5 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 46 Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.064A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.871A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.588A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.356A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 24 removed outlier: 3.729A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.912A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.569A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.884A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.597A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.016A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.986A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.335A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.539A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.378A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.626A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.606A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.720A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.656A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 4.588A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.541A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.098A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.729A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.596A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 removed outlier: 3.638A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.318A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 171 removed outlier: 3.885A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.507A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.914A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.941A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.451A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 248 removed outlier: 4.249A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 5.183A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR M 259 " --> pdb=" O PHE M 256 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 4.323A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER M 273 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.913A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.881A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.697A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.009A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix removed outlier: 3.530A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.044A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.609A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.957A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.626A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.630A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.572A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.669A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.246A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.610A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 20 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.870A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 74 removed outlier: 4.208A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU Y 57 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU Y 58 " --> pdb=" O CYS Y 55 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA Y 66 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU Y 67 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU Y 68 " --> pdb=" O CYS Y 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG Y 71 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN Y 72 " --> pdb=" O PHE Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.541A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 3.830A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.351A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 131 through 141 removed outlier: 4.509A pdb=" N GLU k 136 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG k 140 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.367A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 4.175A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 272 through 274 No H-bonds generated for 'chain 'k' and resid 272 through 274' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 3.953A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.608A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 38 removed outlier: 4.183A pdb=" N ARG n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 45 through 52 removed outlier: 4.659A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.805A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 removed outlier: 3.571A pdb=" N TYR p 22 " --> pdb=" O PRO p 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 19 through 22' Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.814A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.515A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 91 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 124 Processing helix chain 'q' and resid 129 through 137 Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 68 through 72 Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 73 Processing helix chain 't' and resid 92 through 96 removed outlier: 4.291A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 140 removed outlier: 3.833A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 45 through 48 No H-bonds generated for 'chain 'u' and resid 45 through 48' Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.003A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 34 removed outlier: 3.648A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU y 15 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.295A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU y 32 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 30 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.981A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing sheet with id= A, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= B, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= C, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.680A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.451A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 1946 hydrogen bonds defined for protein. 5385 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: 13.34 Time building geometry restraints manager: 20.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6477 1.32 - 1.45: 10773 1.45 - 1.58: 22697 1.58 - 1.70: 67 1.70 - 1.83: 505 Bond restraints: 40519 Sorted by residual: bond pdb=" C GLY A 110 " pdb=" N LEU A 111 " ideal model delta sigma weight residual 1.329 1.203 0.126 1.33e-02 5.65e+03 8.94e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.00e-02 1.00e+04 4.25e+01 bond pdb=" OB3 CDL L 704 " pdb=" PB2 CDL L 704 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" OB3 CDL o 502 " pdb=" PB2 CDL o 502 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.00e-02 1.00e+04 3.67e+01 ... (remaining 40514 not shown) Histogram of bond angle deviations from ideal: 94.14 - 102.53: 263 102.53 - 110.93: 13742 110.93 - 119.32: 20485 119.32 - 127.72: 19645 127.72 - 136.11: 546 Bond angle restraints: 54681 Sorted by residual: angle pdb=" CA3 CDL L 704 " pdb=" OA5 CDL L 704 " pdb=" PA1 CDL L 704 " ideal model delta sigma weight residual 121.27 129.38 -8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" CA3 CDL Y 201 " pdb=" OA5 CDL Y 201 " pdb=" PA1 CDL Y 201 " ideal model delta sigma weight residual 121.27 127.77 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA3 CDL M 503 " pdb=" OA5 CDL M 503 " pdb=" PA1 CDL M 503 " ideal model delta sigma weight residual 121.27 127.59 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA3 CDL V 203 " pdb=" OA5 CDL V 203 " pdb=" PA1 CDL V 203 " ideal model delta sigma weight residual 121.27 126.33 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N HIS L 230 " pdb=" CA HIS L 230 " pdb=" C HIS L 230 " ideal model delta sigma weight residual 109.81 120.71 -10.90 2.21e+00 2.05e-01 2.43e+01 ... (remaining 54676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 23651 30.55 - 61.10: 638 61.10 - 91.66: 26 91.66 - 122.21: 2 122.21 - 152.76: 3 Dihedral angle restraints: 24320 sinusoidal: 10559 harmonic: 13761 Sorted by residual: dihedral pdb=" C5' AMP k 501 " pdb=" O5' AMP k 501 " pdb=" P AMP k 501 " pdb=" O3P AMP k 501 " ideal model delta sinusoidal sigma weight residual 300.00 147.24 152.76 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C2' AMP k 501 " pdb=" C1' AMP k 501 " pdb=" N9 AMP k 501 " pdb=" C4 AMP k 501 " ideal model delta sinusoidal sigma weight residual 91.55 -52.23 143.78 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" CA ARG l 104 " pdb=" C ARG l 104 " pdb=" N PRO l 105 " pdb=" CA PRO l 105 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 24317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 5909 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.175: 0 4.175 - 5.219: 5 Chirality restraints: 5914 Sorted by residual: chirality pdb=" CB4 CDL V 204 " pdb=" CB3 CDL V 204 " pdb=" CB6 CDL V 204 " pdb=" OB6 CDL V 204 " both_signs ideal model delta sigma weight residual False -2.57 2.64 -5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" CB4 CDL Y 201 " pdb=" CB3 CDL Y 201 " pdb=" CB6 CDL Y 201 " pdb=" OB6 CDL Y 201 " both_signs ideal model delta sigma weight residual False -2.57 2.57 -5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" CB4 CDL L 704 " pdb=" CB3 CDL L 704 " pdb=" CB6 CDL L 704 " pdb=" OB6 CDL L 704 " both_signs ideal model delta sigma weight residual False -2.57 2.56 -5.14 2.00e-01 2.50e+01 6.60e+02 ... (remaining 5911 not shown) Planarity restraints: 6668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " 0.005 2.00e-02 2.50e+03 8.72e-02 2.28e+02 pdb=" C1M DCQ H 501 " 0.153 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.044 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.057 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " -0.045 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " -0.068 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " 0.207 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " 0.025 2.00e-02 2.50e+03 3.38e-02 2.00e+01 pdb=" CG PHE K 53 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.035 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP A 106 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.018 2.00e-02 2.50e+03 ... (remaining 6665 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3178 2.73 - 3.27: 40703 3.27 - 3.82: 77345 3.82 - 4.36: 96677 4.36 - 4.90: 154686 Nonbonded interactions: 372589 Sorted by model distance: nonbonded pdb=" OE1 GLU K 70 " pdb=" O HOH K 201 " model vdw 2.189 2.440 nonbonded pdb=" OD1 ASP l 4 " pdb=" O HOH l 201 " model vdw 2.262 2.440 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.262 2.440 nonbonded pdb=" O PRO 4 6 " pdb=" O HOH 4 501 " model vdw 2.268 2.440 nonbonded pdb=" O ASN v 87 " pdb=" O HOH v 201 " model vdw 2.272 2.440 ... (remaining 372584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 279 5.16 5 C 25981 2.51 5 N 6282 2.21 5 O 8224 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.240 Check model and map are aligned: 0.590 Convert atoms to be neutral: 0.380 Process input model: 106.930 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 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 : 0.009 0.139 40519 Z= 0.552 Angle : 1.025 15.043 54681 Z= 0.530 Chirality : 0.159 5.219 5914 Planarity : 0.008 0.087 6668 Dihedral : 12.790 152.760 15411 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -2.18 (0.10), residues: 4621 helix: -1.35 (0.08), residues: 2996 sheet: -1.02 (1.05), residues: 20 loop : -1.31 (0.14), residues: 1605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1001 time to evaluate : 5.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1003 average time/residue: 1.7313 time to fit residues: 2074.6059 Evaluate side-chains 744 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 5.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 5.9990 chunk 345 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 414 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 83 ASN A 85 ASN H 47 GLN H 138 GLN H 317 GLN K 7 ASN K 52 HIS K 83 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 ASN M 20 ASN M 81 GLN N 222 ASN N 235 ASN V 88 ASN X 33 ASN Z 106 GLN Z 120 HIS Z 123 ASN ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN k 180 GLN k 200 GLN k 239 GLN l 6 GLN l 69 GLN n 32 GLN o 12 GLN o 61 GLN p 32 GLN q 23 ASN s 43 GLN u 16 GLN u 24 GLN v 137 ASN w 86 GLN x 36 ASN y 30 ASN z 58 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 40519 Z= 0.226 Angle : 0.593 11.729 54681 Z= 0.295 Chirality : 0.042 0.244 5914 Planarity : 0.005 0.055 6668 Dihedral : 12.812 141.876 6107 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -0.02 (0.12), residues: 4621 helix: 0.44 (0.09), residues: 2998 sheet: -0.10 (1.09), residues: 20 loop : -0.70 (0.15), residues: 1603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 778 time to evaluate : 4.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 20 residues processed: 823 average time/residue: 1.6738 time to fit residues: 1659.5471 Evaluate side-chains 761 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 741 time to evaluate : 5.652 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 11 residues processed: 9 average time/residue: 1.1880 time to fit residues: 20.7253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 344 optimal weight: 6.9990 chunk 281 optimal weight: 40.0000 chunk 114 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 448 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 chunk 411 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 332 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN H 194 ASN K 7 ASN K 25 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 199 GLN L 270 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN M 175 ASN N 36 ASN N 134 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN Z 133 GLN k 89 ASN k 180 GLN l 6 GLN l 96 HIS n 32 GLN p 32 GLN q 53 ASN q 89 ASN t 17 GLN u 16 GLN u 24 GLN v 56 GLN w 86 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 40519 Z= 0.248 Angle : 0.587 11.843 54681 Z= 0.292 Chirality : 0.042 0.205 5914 Planarity : 0.005 0.051 6668 Dihedral : 12.305 142.434 6107 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.89 (0.12), residues: 4621 helix: 1.10 (0.09), residues: 3007 sheet: 0.84 (1.14), residues: 20 loop : -0.24 (0.16), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 753 time to evaluate : 4.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 39 residues processed: 806 average time/residue: 1.7184 time to fit residues: 1668.8876 Evaluate side-chains 770 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 731 time to evaluate : 5.262 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 18 residues processed: 21 average time/residue: 0.6130 time to fit residues: 26.9317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 278 optimal weight: 7.9990 chunk 416 optimal weight: 0.6980 chunk 440 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN H 47 GLN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN N 91 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 129 GLN Z 130 GLN Z 143 HIS k 89 ASN k 141 GLN k 180 GLN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 69 GLN m 70 GLN n 32 GLN p 32 GLN t 168 HIS u 24 GLN v 56 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 40519 Z= 0.389 Angle : 0.658 12.372 54681 Z= 0.326 Chirality : 0.046 0.233 5914 Planarity : 0.005 0.055 6668 Dihedral : 12.533 146.128 6107 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.04 (0.12), residues: 4621 helix: 1.18 (0.09), residues: 3001 sheet: 1.34 (1.19), residues: 20 loop : -0.11 (0.16), residues: 1600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 720 time to evaluate : 5.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 52 residues processed: 786 average time/residue: 1.7484 time to fit residues: 1662.7227 Evaluate side-chains 768 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 716 time to evaluate : 4.698 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 32 residues processed: 20 average time/residue: 0.9676 time to fit residues: 32.5207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 395 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 171 GLN H 194 ASN K 7 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN N 63 GLN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN k 180 GLN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 69 GLN n 32 GLN p 32 GLN u 24 GLN v 56 GLN w 86 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 40519 Z= 0.288 Angle : 0.597 11.779 54681 Z= 0.297 Chirality : 0.043 0.204 5914 Planarity : 0.004 0.050 6668 Dihedral : 12.270 145.345 6107 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.26 (0.12), residues: 4621 helix: 1.34 (0.09), residues: 3013 sheet: 1.60 (1.19), residues: 20 loop : -0.03 (0.16), residues: 1588 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 739 time to evaluate : 5.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 54 residues processed: 802 average time/residue: 1.7237 time to fit residues: 1660.5064 Evaluate side-chains 764 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 710 time to evaluate : 3.836 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 32 residues processed: 22 average time/residue: 1.1050 time to fit residues: 38.3172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 0.9990 chunk 396 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 258 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 441 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN H 47 GLN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 447 ASN M 20 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 ASN n 32 GLN p 32 GLN t 123 GLN u 24 GLN u 58 GLN v 56 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 40519 Z= 0.225 Angle : 0.564 11.108 54681 Z= 0.280 Chirality : 0.041 0.199 5914 Planarity : 0.004 0.048 6668 Dihedral : 11.984 144.412 6107 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.44 (0.13), residues: 4621 helix: 1.48 (0.09), residues: 3021 sheet: 1.68 (1.19), residues: 20 loop : 0.06 (0.16), residues: 1580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 728 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 46 residues processed: 783 average time/residue: 1.7503 time to fit residues: 1655.4516 Evaluate side-chains 754 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 708 time to evaluate : 5.149 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 35 residues processed: 11 average time/residue: 1.0819 time to fit residues: 22.5110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 251 optimal weight: 0.1980 chunk 322 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 439 optimal weight: 5.9990 chunk 275 optimal weight: 30.0000 chunk 267 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 171 GLN H 194 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN M 192 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 GLN p 32 GLN t 123 GLN u 24 GLN v 56 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 40519 Z= 0.320 Angle : 0.618 11.870 54681 Z= 0.306 Chirality : 0.044 0.251 5914 Planarity : 0.005 0.049 6668 Dihedral : 12.109 146.892 6107 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.43 (0.12), residues: 4621 helix: 1.44 (0.09), residues: 3009 sheet: 1.66 (1.21), residues: 20 loop : 0.12 (0.16), residues: 1592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 717 time to evaluate : 4.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 52 residues processed: 776 average time/residue: 1.7342 time to fit residues: 1624.0148 Evaluate side-chains 766 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 714 time to evaluate : 5.054 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 38 residues processed: 14 average time/residue: 1.0574 time to fit residues: 26.2400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 262 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 85 ASN H 47 GLN H 171 GLN K 7 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 509 HIS M 20 ASN M 192 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN k 180 GLN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS n 32 GLN p 32 GLN t 123 GLN u 24 GLN u 58 GLN v 56 GLN z 58 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 40519 Z= 0.154 Angle : 0.532 9.947 54681 Z= 0.264 Chirality : 0.039 0.194 5914 Planarity : 0.004 0.054 6668 Dihedral : 11.512 142.977 6107 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.68 (0.13), residues: 4621 helix: 1.67 (0.10), residues: 3007 sheet: 1.91 (1.22), residues: 20 loop : 0.14 (0.16), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 755 time to evaluate : 5.012 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 36 residues processed: 802 average time/residue: 1.7917 time to fit residues: 1754.2042 Evaluate side-chains 731 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 695 time to evaluate : 4.555 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 2 average time/residue: 0.4808 time to fit residues: 7.7412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 9.9990 chunk 421 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 321 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 370 optimal weight: 20.0000 chunk 387 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN M 192 ASN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS n 32 GLN p 32 GLN t 123 GLN u 24 GLN v 56 GLN v 87 ASN w 27 GLN z 58 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 40519 Z= 0.272 Angle : 0.591 11.429 54681 Z= 0.292 Chirality : 0.042 0.218 5914 Planarity : 0.004 0.068 6668 Dihedral : 11.623 145.487 6107 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.65 (0.13), residues: 4621 helix: 1.61 (0.09), residues: 3015 sheet: 2.04 (1.21), residues: 20 loop : 0.23 (0.16), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 702 time to evaluate : 4.751 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 38 residues processed: 746 average time/residue: 1.7292 time to fit residues: 1552.5168 Evaluate side-chains 734 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 696 time to evaluate : 5.080 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 1.4073 time to fit residues: 11.7869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 433 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 301 optimal weight: 8.9990 chunk 454 optimal weight: 8.9990 chunk 418 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN H 47 GLN H 171 GLN K 7 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS n 32 GLN t 123 GLN u 24 GLN u 58 GLN v 56 GLN v 104 HIS w 27 GLN z 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 40519 Z= 0.251 Angle : 0.589 11.478 54681 Z= 0.291 Chirality : 0.042 0.204 5914 Planarity : 0.004 0.062 6668 Dihedral : 11.626 146.511 6107 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.65 (0.13), residues: 4621 helix: 1.60 (0.09), residues: 3005 sheet: 2.15 (1.22), residues: 20 loop : 0.24 (0.16), residues: 1596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 703 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 40 residues processed: 742 average time/residue: 1.7417 time to fit residues: 1559.8686 Evaluate side-chains 739 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 699 time to evaluate : 4.997 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 36 residues processed: 4 average time/residue: 0.7826 time to fit residues: 11.4511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 333 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 362 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 372 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 85 ASN H 47 GLN H 171 GLN H 194 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN l 26 HIS n 32 GLN p 32 GLN t 123 GLN u 24 GLN v 56 GLN w 27 GLN z 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.088969 restraints weight = 50907.885| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.29 r_work: 0.2874 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 40519 Z= 0.197 Angle : 0.562 11.085 54681 Z= 0.277 Chirality : 0.040 0.190 5914 Planarity : 0.004 0.072 6668 Dihedral : 11.412 145.633 6107 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.73 (0.13), residues: 4621 helix: 1.67 (0.09), residues: 3011 sheet: 2.25 (1.23), residues: 20 loop : 0.25 (0.16), residues: 1590 =============================================================================== Job complete usr+sys time: 25016.55 seconds wall clock time: 439 minutes 10.14 seconds (26350.14 seconds total)