Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 14:11:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/05_2023/6vfh_21172.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/05_2023/6vfh_21172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/05_2023/6vfh_21172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/05_2023/6vfh_21172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/05_2023/6vfh_21172.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/05_2023/6vfh_21172.pdb" } resolution = 3.86 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 23556 2.51 5 N 6144 2.21 5 O 7164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 36984 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "C" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "E" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "I" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "K" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "M" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "O" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "Q" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "R" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "S" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "T" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "U" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "V" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "W" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "X" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Time building chain proxies: 17.47, per 1000 atoms: 0.47 Number of scatterers: 36984 At special positions: 0 Unit cell: (180.25, 179.22, 174.07, 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 120 16.00 O 7164 8.00 N 6144 7.00 C 23556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.97 Conformation dependent library (CDL) restraints added in 5.5 seconds 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 104 through 118 Processing helix chain 'B' and resid 2 through 29 Processing helix chain 'B' and resid 32 through 59 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 97 through 121 Processing helix chain 'B' and resid 125 through 152 Processing helix chain 'B' and resid 159 through 183 Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 250 through 277 Processing helix chain 'C' and resid 1 through 16 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 104 through 118 Processing helix chain 'D' and resid 2 through 29 Processing helix chain 'D' and resid 32 through 59 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 97 through 121 Processing helix chain 'D' and resid 125 through 152 Processing helix chain 'D' and resid 159 through 183 Processing helix chain 'D' and resid 187 through 214 Processing helix chain 'D' and resid 218 through 245 Processing helix chain 'D' and resid 250 through 277 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'F' and resid 2 through 29 Processing helix chain 'F' and resid 32 through 59 Processing helix chain 'F' and resid 63 through 89 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 97 through 121 Processing helix chain 'F' and resid 125 through 152 Processing helix chain 'F' and resid 159 through 183 Processing helix chain 'F' and resid 187 through 214 Processing helix chain 'F' and resid 218 through 245 Processing helix chain 'F' and resid 250 through 277 Processing helix chain 'G' and resid 1 through 16 Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 36 through 50 Processing helix chain 'G' and resid 52 through 67 Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 104 through 118 Processing helix chain 'H' and resid 2 through 29 Processing helix chain 'H' and resid 32 through 59 Processing helix chain 'H' and resid 63 through 89 Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 97 through 121 Processing helix chain 'H' and resid 125 through 152 Processing helix chain 'H' and resid 159 through 183 Processing helix chain 'H' and resid 187 through 214 Processing helix chain 'H' and resid 218 through 245 Processing helix chain 'H' and resid 250 through 277 Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 33 Processing helix chain 'I' and resid 36 through 50 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 86 through 101 Processing helix chain 'I' and resid 104 through 118 Processing helix chain 'J' and resid 2 through 29 Processing helix chain 'J' and resid 32 through 59 Processing helix chain 'J' and resid 63 through 89 Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 97 through 121 Processing helix chain 'J' and resid 125 through 152 Processing helix chain 'J' and resid 159 through 183 Processing helix chain 'J' and resid 187 through 214 Processing helix chain 'J' and resid 218 through 245 Processing helix chain 'J' and resid 250 through 277 Processing helix chain 'K' and resid 1 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 67 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 86 through 101 Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'L' and resid 2 through 29 Processing helix chain 'L' and resid 32 through 59 Processing helix chain 'L' and resid 63 through 89 Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 97 through 121 Processing helix chain 'L' and resid 125 through 152 Processing helix chain 'L' and resid 159 through 183 Processing helix chain 'L' and resid 187 through 214 Processing helix chain 'L' and resid 218 through 245 Processing helix chain 'L' and resid 250 through 277 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 36 through 50 Processing helix chain 'M' and resid 52 through 67 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 86 through 101 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'N' and resid 2 through 29 Processing helix chain 'N' and resid 32 through 59 Processing helix chain 'N' and resid 63 through 89 Processing helix chain 'N' and resid 91 through 95 Processing helix chain 'N' and resid 97 through 121 Processing helix chain 'N' and resid 125 through 152 Processing helix chain 'N' and resid 159 through 183 Processing helix chain 'N' and resid 187 through 214 Processing helix chain 'N' and resid 218 through 245 Processing helix chain 'N' and resid 250 through 277 Processing helix chain 'O' and resid 1 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 86 through 101 Processing helix chain 'O' and resid 104 through 118 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'P' and resid 32 through 59 Processing helix chain 'P' and resid 63 through 89 Processing helix chain 'P' and resid 91 through 95 Processing helix chain 'P' and resid 97 through 121 Processing helix chain 'P' and resid 125 through 152 Processing helix chain 'P' and resid 159 through 183 Processing helix chain 'P' and resid 187 through 214 Processing helix chain 'P' and resid 218 through 245 Processing helix chain 'P' and resid 250 through 277 Processing helix chain 'Q' and resid 1 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 86 through 101 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'R' and resid 2 through 29 Processing helix chain 'R' and resid 32 through 59 Processing helix chain 'R' and resid 63 through 89 Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 97 through 121 Processing helix chain 'R' and resid 125 through 152 Processing helix chain 'R' and resid 159 through 183 Processing helix chain 'R' and resid 187 through 214 Processing helix chain 'R' and resid 218 through 245 Processing helix chain 'R' and resid 250 through 277 Processing helix chain 'S' and resid 1 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 86 through 101 Processing helix chain 'S' and resid 104 through 118 Processing helix chain 'T' and resid 2 through 29 Processing helix chain 'T' and resid 32 through 59 Processing helix chain 'T' and resid 63 through 89 Processing helix chain 'T' and resid 91 through 95 Processing helix chain 'T' and resid 97 through 121 Processing helix chain 'T' and resid 125 through 152 Processing helix chain 'T' and resid 159 through 183 Processing helix chain 'T' and resid 187 through 214 Processing helix chain 'T' and resid 218 through 245 Processing helix chain 'T' and resid 250 through 277 Processing helix chain 'U' and resid 1 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 86 through 101 Processing helix chain 'U' and resid 104 through 118 Processing helix chain 'V' and resid 2 through 29 Processing helix chain 'V' and resid 32 through 59 Processing helix chain 'V' and resid 63 through 89 Processing helix chain 'V' and resid 91 through 95 Processing helix chain 'V' and resid 97 through 121 Processing helix chain 'V' and resid 125 through 152 Processing helix chain 'V' and resid 159 through 183 Processing helix chain 'V' and resid 187 through 214 Processing helix chain 'V' and resid 218 through 245 Processing helix chain 'V' and resid 250 through 277 Processing helix chain 'W' and resid 1 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 86 through 101 Processing helix chain 'W' and resid 104 through 118 Processing helix chain 'X' and resid 2 through 29 Processing helix chain 'X' and resid 32 through 59 Processing helix chain 'X' and resid 63 through 89 Processing helix chain 'X' and resid 91 through 95 Processing helix chain 'X' and resid 97 through 121 Processing helix chain 'X' and resid 125 through 152 Processing helix chain 'X' and resid 159 through 183 Processing helix chain 'X' and resid 187 through 214 Processing helix chain 'X' and resid 218 through 245 Processing helix chain 'X' and resid 250 through 277 3504 hydrogen bonds defined for protein. 10440 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: 13.73 Time building geometry restraints manager: 16.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8233 1.32 - 1.45: 10435 1.45 - 1.58: 18508 1.58 - 1.70: 12 1.70 - 1.83: 240 Bond restraints: 37428 Sorted by residual: bond pdb=" CB HIS T 92 " pdb=" CG HIS T 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB HIS P 92 " pdb=" CG HIS P 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS N 92 " pdb=" CG HIS N 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS B 92 " pdb=" CG HIS B 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS X 92 " pdb=" CG HIS X 92 " ideal model delta sigma weight residual 1.497 1.441 0.056 1.40e-02 5.10e+03 1.63e+01 ... (remaining 37423 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.72: 631 106.72 - 113.50: 20365 113.50 - 120.28: 17382 120.28 - 127.06: 12010 127.06 - 133.84: 180 Bond angle restraints: 50568 Sorted by residual: angle pdb=" C ASP M 67 " pdb=" N PRO M 68 " pdb=" CA PRO M 68 " ideal model delta sigma weight residual 119.82 127.54 -7.72 9.80e-01 1.04e+00 6.20e+01 angle pdb=" C ASP G 67 " pdb=" N PRO G 68 " pdb=" CA PRO G 68 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" C ASP C 67 " pdb=" N PRO C 68 " pdb=" CA PRO C 68 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" C ASP A 67 " pdb=" N PRO A 68 " pdb=" CA PRO A 68 " ideal model delta sigma weight residual 119.82 127.52 -7.70 9.80e-01 1.04e+00 6.17e+01 angle pdb=" C ASP I 67 " pdb=" N PRO I 68 " pdb=" CA PRO I 68 " ideal model delta sigma weight residual 119.82 127.51 -7.69 9.80e-01 1.04e+00 6.16e+01 ... (remaining 50563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.37: 21651 12.37 - 24.75: 1389 24.75 - 37.12: 84 37.12 - 49.50: 63 49.50 - 61.87: 81 Dihedral angle restraints: 23268 sinusoidal: 8952 harmonic: 14316 Sorted by residual: dihedral pdb=" C THR N 94 " pdb=" N THR N 94 " pdb=" CA THR N 94 " pdb=" CB THR N 94 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C THR L 94 " pdb=" N THR L 94 " pdb=" CA THR L 94 " pdb=" CB THR L 94 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C THR F 94 " pdb=" N THR F 94 " pdb=" CA THR F 94 " pdb=" CB THR F 94 " ideal model delta harmonic sigma weight residual -122.00 -130.89 8.89 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 23265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4035 0.076 - 0.152: 1518 0.152 - 0.228: 351 0.228 - 0.304: 24 0.304 - 0.380: 36 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CA ASP F 152 " pdb=" N ASP F 152 " pdb=" C ASP F 152 " pdb=" CB ASP F 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ASP V 152 " pdb=" N ASP V 152 " pdb=" C ASP V 152 " pdb=" CB ASP V 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA ASP X 152 " pdb=" N ASP X 152 " pdb=" C ASP X 152 " pdb=" CB ASP X 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5961 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 93 " -0.062 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR Q 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 93 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 93 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR Q 93 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 93 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 93 " -0.062 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR U 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR U 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR U 93 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR U 93 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR U 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR U 93 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR U 93 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 93 " -0.062 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR G 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR G 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR G 93 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR G 93 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR G 93 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 93 " -0.044 2.00e-02 2.50e+03 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 20522 2.98 - 3.46: 40952 3.46 - 3.94: 61187 3.94 - 4.42: 75458 4.42 - 4.90: 113052 Nonbonded interactions: 311171 Sorted by model distance: nonbonded pdb=" NZ LYS L 235 " pdb=" OE2 GLU V 7 " model vdw 2.497 2.520 nonbonded pdb=" NZ LYS F 235 " pdb=" OE2 GLU P 7 " model vdw 2.497 2.520 nonbonded pdb=" OE2 GLU H 7 " pdb=" NZ LYS V 235 " model vdw 2.497 2.520 nonbonded pdb=" NZ LYS B 235 " pdb=" OE2 GLU J 7 " model vdw 2.497 2.520 nonbonded pdb=" OE2 GLU D 7 " pdb=" NZ LYS X 235 " model vdw 2.497 2.520 ... (remaining 311166 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 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 9.850 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 89.020 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.019 0.083 37428 Z= 1.199 Angle : 1.388 8.973 50568 Z= 0.949 Chirality : 0.084 0.380 5964 Planarity : 0.008 0.032 6432 Dihedral : 9.310 61.873 13932 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 2.06 (0.10), residues: 4704 helix: 1.51 (0.06), residues: 4236 sheet: None (None), residues: 0 loop : 0.57 (0.26), residues: 468 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1526 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1526 average time/residue: 0.5871 time to fit residues: 1350.5794 Evaluate side-chains 710 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 710 time to evaluate : 4.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2097 ------------------------------------------------------------------------------- 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: 8.9990 chunk 191 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 184 optimal weight: 0.0050 chunk 357 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 414 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN B 216 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 216 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN F 184 ASN H 184 ASN H 216 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 GLN J 184 ASN J 216 HIS K 118 GLN L 184 ASN L 216 HIS ** M 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 184 ASN N 216 HIS O 84 GLN O 118 GLN P 184 ASN P 216 HIS ** Q 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN R 216 HIS ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 GLN T 184 ASN T 216 HIS ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 GLN V 184 ASN V 216 HIS ** W 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 118 GLN X 184 ASN X 216 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 37428 Z= 0.199 Angle : 0.545 9.090 50568 Z= 0.301 Chirality : 0.038 0.231 5964 Planarity : 0.004 0.031 6432 Dihedral : 3.412 15.973 5160 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 1.83 % 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: 4.49 (0.11), residues: 4704 helix: 3.16 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : 0.47 (0.27), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 989 time to evaluate : 4.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 30 residues processed: 1020 average time/residue: 0.4991 time to fit residues: 825.4637 Evaluate side-chains 709 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 679 time to evaluate : 4.231 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3344 time to fit residues: 24.8948 ------------------------------------------------------------------------------- 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: 6.9990 chunk 128 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 chunk 281 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 414 optimal weight: 0.9990 chunk 448 optimal weight: 0.9990 chunk 369 optimal weight: 0.9980 chunk 411 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 332 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN C 118 GLN D 60 ASN F 216 HIS I 61 GLN I 118 GLN J 122 ASN M 118 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 122 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 37428 Z= 0.185 Angle : 0.487 11.524 50568 Z= 0.269 Chirality : 0.036 0.175 5964 Planarity : 0.003 0.027 6432 Dihedral : 3.322 15.306 5160 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 1.38 % 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: 4.39 (0.11), residues: 4704 helix: 3.12 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : 0.17 (0.27), residues: 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 838 time to evaluate : 4.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 862 average time/residue: 0.4834 time to fit residues: 677.3084 Evaluate side-chains 691 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 666 time to evaluate : 3.911 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3265 time to fit residues: 21.2053 ------------------------------------------------------------------------------- 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: 1.9990 chunk 311 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 278 optimal weight: 0.6980 chunk 416 optimal weight: 0.8980 chunk 440 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 394 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 123 HIS H 60 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN M 118 GLN N 123 HIS P 60 ASN R 60 ASN ** V 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 122 ASN V 123 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 37428 Z= 0.174 Angle : 0.480 11.970 50568 Z= 0.258 Chirality : 0.036 0.195 5964 Planarity : 0.003 0.027 6432 Dihedral : 3.266 14.582 5160 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 1.52 % 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: 4.29 (0.11), residues: 4704 helix: 3.07 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : -0.12 (0.27), residues: 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 830 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 28 residues processed: 853 average time/residue: 0.4877 time to fit residues: 677.6124 Evaluate side-chains 706 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 678 time to evaluate : 4.259 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3319 time to fit residues: 23.3656 ------------------------------------------------------------------------------- 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: 0.8980 chunk 250 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 328 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 376 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 395 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 123 HIS F 184 ASN H 123 HIS H 246 ASN J 123 HIS L 123 HIS M 110 ASN N 60 ASN N 185 HIS P 123 HIS R 123 HIS R 246 ASN V 107 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 37428 Z= 0.168 Angle : 0.502 12.387 50568 Z= 0.267 Chirality : 0.037 0.242 5964 Planarity : 0.003 0.029 6432 Dihedral : 3.234 14.459 5160 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.41 % 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: 4.25 (0.11), residues: 4704 helix: 3.07 (0.07), residues: 4260 sheet: None (None), residues: 0 loop : -0.28 (0.26), residues: 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 803 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 23 residues processed: 831 average time/residue: 0.4981 time to fit residues: 676.3697 Evaluate side-chains 685 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 662 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3269 time to fit residues: 19.4492 ------------------------------------------------------------------------------- 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: 1.9990 chunk 396 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 258 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 441 optimal weight: 9.9990 chunk 366 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: