Starting phenix.real_space_refine (version: dev) on Mon Feb 20 21:21:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oae_12775/02_2023/7oae_12775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oae_12775/02_2023/7oae_12775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oae_12775/02_2023/7oae_12775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oae_12775/02_2023/7oae_12775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oae_12775/02_2023/7oae_12775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oae_12775/02_2023/7oae_12775.pdb" } resolution = 2.0 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= 0.000 sd= 0.002 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 Process input model Symmetric amino acids flipped Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12768 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "G" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "M" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "U" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "O" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "P" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "R" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "V" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "X" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Y" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Z" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "0" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "1" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "2" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "3" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "4" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "5" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "8" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "9" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "a" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "b" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "c" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "d" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "e" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "f" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 7.40, per 1000 atoms: 0.58 Number of scatterers: 12768 At special positions: 0 Unit cell: (121.569, 126.531, 105.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 294 16.00 O 2268 8.00 N 2226 7.00 C 7980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=126, symmetry=0 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 39 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 37 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 37 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 39 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 15 " - pdb=" SG CYS I 37 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 39 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 37 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 37 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 39 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 15 " - pdb=" SG CYS M 37 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 39 " distance=2.03 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 15 " - pdb=" SG CYS N 37 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 39 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 15 " - pdb=" SG CYS T 37 " distance=2.03 Simple disulfide: pdb=" SG CYS T 19 " - pdb=" SG CYS T 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 15 " - pdb=" SG CYS U 37 " distance=2.03 Simple disulfide: pdb=" SG CYS U 19 " - pdb=" SG CYS U 39 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 39 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 37 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 39 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 15 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 39 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 39 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 15 " - pdb=" SG CYS S 37 " distance=2.03 Simple disulfide: pdb=" SG CYS S 19 " - pdb=" SG CYS S 39 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 15 " - pdb=" SG CYS V 37 " distance=2.03 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 39 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 15 " - pdb=" SG CYS W 37 " distance=2.03 Simple disulfide: pdb=" SG CYS W 19 " - pdb=" SG CYS W 39 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 15 " - pdb=" SG CYS X 37 " distance=2.03 Simple disulfide: pdb=" SG CYS X 19 " - pdb=" SG CYS X 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 15 " - pdb=" SG CYS Y 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 4 " - pdb=" SG CYS Z 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 15 " - pdb=" SG CYS Z 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 19 " - pdb=" SG CYS Z 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 4 " - pdb=" SG CYS 0 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 15 " - pdb=" SG CYS 0 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 19 " - pdb=" SG CYS 0 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 4 " - pdb=" SG CYS 1 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 15 " - pdb=" SG CYS 1 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 19 " - pdb=" SG CYS 1 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 4 " - pdb=" SG CYS 2 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 15 " - pdb=" SG CYS 2 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 19 " - pdb=" SG CYS 2 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 4 " - pdb=" SG CYS 3 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 15 " - pdb=" SG CYS 3 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 19 " - pdb=" SG CYS 3 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 4 " - pdb=" SG CYS 4 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 15 " - pdb=" SG CYS 4 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 19 " - pdb=" SG CYS 4 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 4 " - pdb=" SG CYS 5 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 15 " - pdb=" SG CYS 5 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 19 " - pdb=" SG CYS 5 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 4 " - pdb=" SG CYS 6 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 15 " - pdb=" SG CYS 6 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 19 " - pdb=" SG CYS 6 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 4 " - pdb=" SG CYS 7 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 15 " - pdb=" SG CYS 7 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 19 " - pdb=" SG CYS 7 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 4 " - pdb=" SG CYS 8 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 15 " - pdb=" SG CYS 8 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 19 " - pdb=" SG CYS 8 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 4 " - pdb=" SG CYS 9 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 19 " - pdb=" SG CYS 9 39 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 30 " distance=2.03 Simple disulfide: pdb=" SG CYS a 15 " - pdb=" SG CYS a 37 " distance=2.03 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 39 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 30 " distance=2.03 Simple disulfide: pdb=" SG CYS b 15 " - pdb=" SG CYS b 37 " distance=2.03 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS b 39 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 30 " distance=2.03 Simple disulfide: pdb=" SG CYS c 15 " - pdb=" SG CYS c 37 " distance=2.03 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS c 39 " distance=2.03 Simple disulfide: pdb=" SG CYS d 4 " - pdb=" SG CYS d 30 " distance=2.03 Simple disulfide: pdb=" SG CYS d 15 " - pdb=" SG CYS d 37 " distance=2.03 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 39 " distance=2.03 Simple disulfide: pdb=" SG CYS e 4 " - pdb=" SG CYS e 30 " distance=2.03 Simple disulfide: pdb=" SG CYS e 15 " - pdb=" SG CYS e 37 " distance=2.03 Simple disulfide: pdb=" SG CYS e 19 " - pdb=" SG CYS e 39 " distance=2.03 Simple disulfide: pdb=" SG CYS f 4 " - pdb=" SG CYS f 30 " distance=2.03 Simple disulfide: pdb=" SG CYS f 15 " - pdb=" SG CYS f 37 " distance=2.03 Simple disulfide: pdb=" SG CYS f 19 " - pdb=" SG CYS f 39 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 1.8 seconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 42 sheets defined 47.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.649A pdb=" N ILE B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 31 through 35 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.649A pdb=" N ILE I 22 " --> pdb=" O HIS I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 13 through 21 Processing helix chain 'M' and resid 31 through 35 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 13 through 21 Processing helix chain 'N' and resid 31 through 35 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 13 through 21 Processing helix chain 'T' and resid 31 through 35 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE U 22 " --> pdb=" O HIS U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 13 through 21 Processing helix chain 'O' and resid 31 through 35 Processing helix chain 'P' and resid 5 through 9 Processing helix chain 'P' and resid 13 through 21 Processing helix chain 'P' and resid 31 through 35 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 21 Processing helix chain 'Q' and resid 31 through 35 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 31 through 35 Processing helix chain 'S' and resid 5 through 9 Processing helix chain 'S' and resid 13 through 21 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE V 22 " --> pdb=" O HIS V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 35 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 13 through 21 Processing helix chain 'W' and resid 31 through 35 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 31 through 35 Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 13 through 21 Processing helix chain 'Y' and resid 31 through 35 Processing helix chain 'Z' and resid 5 through 9 Processing helix chain 'Z' and resid 13 through 21 Processing helix chain 'Z' and resid 31 through 35 Processing helix chain '0' and resid 5 through 9 Processing helix chain '0' and resid 13 through 21 Processing helix chain '0' and resid 31 through 35 Processing helix chain '1' and resid 5 through 9 Processing helix chain '1' and resid 13 through 21 Processing helix chain '1' and resid 31 through 35 Processing helix chain '2' and resid 5 through 9 Processing helix chain '2' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE 2 22 " --> pdb=" O HIS 2 18 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 35 Processing helix chain '3' and resid 5 through 9 Processing helix chain '3' and resid 13 through 21 Processing helix chain '3' and resid 31 through 35 Processing helix chain '4' and resid 5 through 9 Processing helix chain '4' and resid 13 through 21 Processing helix chain '4' and resid 31 through 35 Processing helix chain '5' and resid 5 through 9 Processing helix chain '5' and resid 13 through 21 Processing helix chain '5' and resid 31 through 35 Processing helix chain '6' and resid 5 through 9 Processing helix chain '6' and resid 13 through 21 Processing helix chain '6' and resid 31 through 35 Processing helix chain '7' and resid 5 through 9 Processing helix chain '7' and resid 13 through 21 Processing helix chain '7' and resid 31 through 35 Processing helix chain '8' and resid 5 through 9 Processing helix chain '8' and resid 13 through 21 Processing helix chain '8' and resid 31 through 35 Processing helix chain '9' and resid 5 through 9 Processing helix chain '9' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE 9 22 " --> pdb=" O HIS 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 31 through 35 Processing helix chain 'a' and resid 5 through 9 Processing helix chain 'a' and resid 13 through 21 Processing helix chain 'a' and resid 31 through 35 Processing helix chain 'b' and resid 5 through 9 Processing helix chain 'b' and resid 13 through 21 Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'c' and resid 5 through 9 Processing helix chain 'c' and resid 13 through 21 Processing helix chain 'c' and resid 31 through 35 Processing helix chain 'd' and resid 5 through 9 Processing helix chain 'd' and resid 13 through 21 Processing helix chain 'd' and resid 31 through 35 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 13 through 21 Processing helix chain 'e' and resid 31 through 35 Processing helix chain 'f' and resid 5 through 9 Processing helix chain 'f' and resid 13 through 21 Processing helix chain 'f' and resid 31 through 35 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AA6, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'I' and resid 28 through 30 Processing sheet with id=AA9, first strand: chain 'J' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain 'L' and resid 28 through 30 Processing sheet with id=AB3, first strand: chain 'M' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain 'N' and resid 28 through 30 Processing sheet with id=AB5, first strand: chain 'T' and resid 28 through 30 Processing sheet with id=AB6, first strand: chain 'U' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'O' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'P' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'Q' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'S' and resid 28 through 30 Processing sheet with id=AC4, first strand: chain 'V' and resid 28 through 30 Processing sheet with id=AC5, first strand: chain 'W' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'X' and resid 28 through 30 Processing sheet with id=AC7, first strand: chain 'Y' and resid 28 through 30 Processing sheet with id=AC8, first strand: chain 'Z' and resid 28 through 30 Processing sheet with id=AC9, first strand: chain '0' and resid 28 through 30 Processing sheet with id=AD1, first strand: chain '1' and resid 28 through 30 Processing sheet with id=AD2, first strand: chain '2' and resid 28 through 30 Processing sheet with id=AD3, first strand: chain '3' and resid 28 through 30 Processing sheet with id=AD4, first strand: chain '4' and resid 28 through 30 Processing sheet with id=AD5, first strand: chain '5' and resid 28 through 30 Processing sheet with id=AD6, first strand: chain '6' and resid 28 through 30 Processing sheet with id=AD7, first strand: chain '7' and resid 28 through 30 Processing sheet with id=AD8, first strand: chain '8' and resid 28 through 30 Processing sheet with id=AD9, first strand: chain '9' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'a' and resid 28 through 30 Processing sheet with id=AE2, first strand: chain 'b' and resid 28 through 30 Processing sheet with id=AE3, first strand: chain 'c' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'd' and resid 28 through 30 Processing sheet with id=AE5, first strand: chain 'e' and resid 28 through 30 Processing sheet with id=AE6, first strand: chain 'f' and resid 28 through 30 420 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3948 1.34 - 1.46: 3478 1.46 - 1.58: 5384 1.58 - 1.69: 0 1.69 - 1.81: 336 Bond restraints: 13146 Sorted by residual: bond pdb=" CB TRP 2 8 " pdb=" CG TRP 2 8 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.31e+00 bond pdb=" CB TRP I 8 " pdb=" CG TRP I 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.31e+00 bond pdb=" CB TRP V 8 " pdb=" CG TRP V 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.29e+00 bond pdb=" CB TRP U 8 " pdb=" CG TRP U 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.27e+00 bond pdb=" CB TRP B 8 " pdb=" CG TRP B 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.25e+00 ... (remaining 13141 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.55: 294 106.55 - 113.42: 6178 113.42 - 120.29: 5074 120.29 - 127.16: 5674 127.16 - 134.03: 210 Bond angle restraints: 17430 Sorted by residual: angle pdb=" C MET a 13 " pdb=" CA MET a 13 " pdb=" CB MET a 13 " ideal model delta sigma weight residual 111.23 108.64 2.59 1.63e+00 3.76e-01 2.53e+00 angle pdb=" C MET W 13 " pdb=" CA MET W 13 " pdb=" CB MET W 13 " ideal model delta sigma weight residual 111.23 108.65 2.58 1.63e+00 3.76e-01 2.51e+00 angle pdb=" C MET 3 13 " pdb=" CA MET 3 13 " pdb=" CB MET 3 13 " ideal model delta sigma weight residual 111.23 108.65 2.58 1.63e+00 3.76e-01 2.51e+00 angle pdb=" C MET J 13 " pdb=" CA MET J 13 " pdb=" CB MET J 13 " ideal model delta sigma weight residual 111.23 108.66 2.57 1.63e+00 3.76e-01 2.49e+00 angle pdb=" C MET A 13 " pdb=" CA MET A 13 " pdb=" CB MET A 13 " ideal model delta sigma weight residual 111.23 108.66 2.57 1.63e+00 3.76e-01 2.49e+00 ... (remaining 17425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.57: 6834 11.57 - 23.13: 714 23.13 - 34.70: 156 34.70 - 46.27: 42 46.27 - 57.83: 24 Dihedral angle restraints: 7770 sinusoidal: 3318 harmonic: 4452 Sorted by residual: dihedral pdb=" SG CYS I 19 " pdb=" CB CYS I 39 " pdb=" SG CYS I 39 " pdb=" CA CYS I 39 " ideal model delta sinusoidal sigma weight residual 79.00 40.53 38.47 1 2.00e+01 2.50e-03 5.21e+00 dihedral pdb=" SG CYS 2 19 " pdb=" CB CYS 2 39 " pdb=" SG CYS 2 39 " pdb=" CA CYS 2 39 " ideal model delta sinusoidal sigma weight residual 79.00 40.54 38.46 1 2.00e+01 2.50e-03 5.21e+00 dihedral pdb=" SG CYS 9 19 " pdb=" CB CYS 9 39 " pdb=" SG CYS 9 39 " pdb=" CA CYS 9 39 " ideal model delta sinusoidal sigma weight residual 79.00 40.54 38.46 1 2.00e+01 2.50e-03 5.21e+00 ... (remaining 7767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 681 0.024 - 0.048: 289 0.048 - 0.073: 236 0.073 - 0.097: 100 0.097 - 0.121: 122 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA PRO N 7 " pdb=" N PRO N 7 " pdb=" C PRO N 7 " pdb=" CB PRO N 7 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO R 7 " pdb=" N PRO R 7 " pdb=" C PRO R 7 " pdb=" CB PRO R 7 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO T 7 " pdb=" N PRO T 7 " pdb=" C PRO T 7 " pdb=" CB PRO T 7 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 1425 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY 9 6 " 0.016 5.00e-02 4.00e+02 2.37e-02 9.01e-01 pdb=" N PRO 9 7 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO 9 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 9 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 2 6 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.93e-01 pdb=" N PRO 2 7 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO 2 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 2 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 6 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.91e-01 pdb=" N PRO I 7 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO I 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 7 " 0.013 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5512 2.93 - 3.42: 11385 3.42 - 3.92: 23277 3.92 - 4.41: 25147 4.41 - 4.90: 42143 Nonbonded interactions: 107464 Sorted by model distance: nonbonded pdb=" NZ LYS E 14 " pdb=" OD2 ASP G 11 " model vdw 2.440 2.520 nonbonded pdb=" N ASP U 12 " pdb=" OD1 ASP U 12 " model vdw 2.445 2.520 nonbonded pdb=" N ASP 2 12 " pdb=" OD1 ASP 2 12 " model vdw 2.445 2.520 nonbonded pdb=" N ASP V 12 " pdb=" OD1 ASP V 12 " model vdw 2.446 2.520 nonbonded pdb=" N ASP B 12 " pdb=" OD1 ASP B 12 " model vdw 2.446 2.520 ... (remaining 107459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 4 Type Number sf(0) Gaussians S 294 5.16 5 C 7980 2.51 5 N 2226 2.21 5 O 2268 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: 0.010 Normalize map: mean=0, sd=1: 1.700 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: 0.010 Extract box with map and model: 6.540 Check model and map are aligned: 0.210 Process input model: 34.560 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.041 13146 Z= 0.493 Angle : 0.526 3.501 17430 Z= 0.314 Chirality : 0.049 0.121 1428 Planarity : 0.003 0.024 2268 Dihedral : 9.441 57.834 4704 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.21), residues: 1596 helix: 1.78 (0.28), residues: 378 sheet: -0.91 (0.31), residues: 378 loop : 0.02 (0.19), residues: 840 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 385 average time/residue: 1.6568 time to fit residues: 678.3476 Evaluate side-chains 309 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1522 time to fit residues: 2.2643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 6.9990 chunk 127 optimal weight: 0.0980 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 0.0470 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 HIS F 16 HIS ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 HIS S 17 ASN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 HIS 4 16 HIS 5 16 HIS 6 17 ASN 7 17 ASN a 17 ASN c 16 HIS d 17 ASN ** e 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 13146 Z= 0.109 Angle : 0.413 6.178 17430 Z= 0.220 Chirality : 0.041 0.121 1428 Planarity : 0.003 0.026 2268 Dihedral : 2.808 11.361 1806 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.22), residues: 1596 helix: 1.21 (0.28), residues: 420 sheet: -0.64 (0.31), residues: 378 loop : 0.28 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 325 time to evaluate : 1.622 Fit side-chains outliers start: 23 outliers final: 4 residues processed: 330 average time/residue: 1.7805 time to fit residues: 622.5054 Evaluate side-chains 316 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 312 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.8882 time to fit residues: 3.9377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 17 ASN L 16 HIS L 17 ASN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 13146 Z= 0.409 Angle : 0.505 4.764 17430 Z= 0.278 Chirality : 0.048 0.119 1428 Planarity : 0.004 0.032 2268 Dihedral : 3.619 19.991 1806 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.21), residues: 1596 helix: 1.04 (0.27), residues: 420 sheet: -0.62 (0.30), residues: 378 loop : 0.10 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 310 time to evaluate : 1.565 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 9 residues processed: 313 average time/residue: 1.7690 time to fit residues: 586.7728 Evaluate side-chains 310 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 301 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 1.1971 time to fit residues: 9.7181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 13146 Z= 0.221 Angle : 0.445 6.354 17430 Z= 0.241 Chirality : 0.043 0.120 1428 Planarity : 0.004 0.032 2268 Dihedral : 3.232 15.719 1806 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.21), residues: 1596 helix: 1.04 (0.27), residues: 420 sheet: -0.50 (0.30), residues: 378 loop : 0.16 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 312 time to evaluate : 1.632 Fit side-chains outliers start: 22 outliers final: 5 residues processed: 315 average time/residue: 1.7718 time to fit residues: 591.3928 Evaluate side-chains 313 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 308 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 0.8352 time to fit residues: 3.7339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 HIS X 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 16 HIS 0 16 HIS ** 5 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 16 HIS 6 17 ASN ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 HIS d 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 13146 Z= 0.399 Angle : 0.512 7.316 17430 Z= 0.278 Chirality : 0.048 0.116 1428 Planarity : 0.004 0.033 2268 Dihedral : 3.677 19.190 1806 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.21), residues: 1596 helix: 1.80 (0.27), residues: 378 sheet: -0.59 (0.30), residues: 378 loop : 0.19 (0.19), residues: 840 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 310 time to evaluate : 1.525 Fit side-chains outliers start: 31 outliers final: 8 residues processed: 314 average time/residue: 1.7843 time to fit residues: 593.3805 Evaluate side-chains 316 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 308 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 4 average time/residue: 1.2913 time to fit residues: 7.4869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 0.0770 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 16 HIS ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13146 Z= 0.153 Angle : 0.459 8.084 17430 Z= 0.241 Chirality : 0.042 0.120 1428 Planarity : 0.004 0.030 2268 Dihedral : 3.071 13.870 1806 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.21), residues: 1596 helix: 1.02 (0.27), residues: 420 sheet: -0.43 (0.30), residues: 378 loop : 0.20 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 321 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 325 average time/residue: 1.7570 time to fit residues: 605.8659 Evaluate side-chains 311 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1591 time to fit residues: 2.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.0970 chunk 74 optimal weight: 6.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 16 HIS X 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 17 ASN 5 16 HIS 6 16 HIS ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 HIS ** c 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 16 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13146 Z= 0.165 Angle : 0.458 6.359 17430 Z= 0.240 Chirality : 0.043 0.125 1428 Planarity : 0.004 0.030 2268 Dihedral : 2.930 14.863 1806 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.21), residues: 1596 helix: 1.05 (0.27), residues: 420 sheet: -0.40 (0.30), residues: 378 loop : 0.27 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 317 time to evaluate : 1.584 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 321 average time/residue: 1.7682 time to fit residues: 602.0357 Evaluate side-chains 315 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.0404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 0.0770 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 16 HIS ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13146 Z= 0.187 Angle : 0.491 7.603 17430 Z= 0.255 Chirality : 0.043 0.120 1428 Planarity : 0.004 0.030 2268 Dihedral : 2.940 12.852 1806 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.21), residues: 1596 helix: 0.99 (0.27), residues: 420 sheet: -0.39 (0.30), residues: 378 loop : 0.29 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 311 time to evaluate : 1.438 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 314 average time/residue: 1.7982 time to fit residues: 598.1730 Evaluate side-chains 316 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 310 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 3 average time/residue: 0.1515 time to fit residues: 2.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 150 optimal weight: 0.0670 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 HIS ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 13146 Z= 0.170 Angle : 0.485 8.280 17430 Z= 0.249 Chirality : 0.043 0.120 1428 Planarity : 0.004 0.029 2268 Dihedral : 2.828 13.152 1806 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.21), residues: 1596 helix: 1.05 (0.27), residues: 420 sheet: -0.37 (0.30), residues: 378 loop : 0.32 (0.20), residues: 798 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 309 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 312 average time/residue: 1.8181 time to fit residues: 602.3311 Evaluate side-chains 315 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 4 average time/residue: 0.8647 time to fit residues: 5.8325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 0.0980 chunk 141 optimal weight: 0.9980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 HIS ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13146 Z= 0.218 Angle : 0.523 10.509 17430 Z= 0.267 Chirality : 0.044 0.124 1428 Planarity : 0.004 0.029 2268 Dihedral : 2.951 12.857 1806 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.21), residues: 1596 helix: 1.04 (0.27), residues: 420 sheet: -0.40 (0.30), residues: 378 loop : 0.29 (0.20), residues: 798 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 310 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 314 average time/residue: 1.8014 time to fit residues: 599.2942 Evaluate side-chains 312 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 308 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.4274 time to fit residues: 3.3916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 55 optimal weight: 0.0270 chunk 137 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 HIS ** c 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.104118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.062593 restraints weight = 19219.130| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.22 r_work: 0.2658 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9271 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 13146 Z= 0.119 Angle : 0.467 9.368 17430 Z= 0.237 Chirality : 0.041 0.125 1428 Planarity : 0.003 0.028 2268 Dihedral : 2.613 14.305 1806 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.22), residues: 1596 helix: 1.08 (0.27), residues: 420 sheet: -0.29 (0.30), residues: 378 loop : 0.44 (0.21), residues: 798 =============================================================================== Job complete usr+sys time: 8771.50 seconds wall clock time: 154 minutes 11.09 seconds (9251.09 seconds total)