Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 22:45:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/08_2023/6vl6_21231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/08_2023/6vl6_21231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/08_2023/6vl6_21231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/08_2023/6vl6_21231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/08_2023/6vl6_21231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vl6_21231/08_2023/6vl6_21231.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 13788 2.51 5 N 3564 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 98": "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 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 98": "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 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "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 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 98": "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 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 98": "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 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 21504 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "C" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "D" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Q" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "G" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "R" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "H" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "T" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "J" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "U" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "K" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "L" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "W" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "M" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "X" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Time building chain proxies: 10.16, per 1000 atoms: 0.47 Number of scatterers: 21504 At special positions: 0 Unit cell: (162.15, 158.7, 156.4, 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 36 16.00 O 4116 8.00 N 3564 7.00 C 13788 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: 9.27 Conformation dependent library (CDL) restraints added in 3.0 seconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 36 through 50 Processing helix chain 'N' and resid 52 through 67 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'O' and resid 3 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 99 Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 56 through 71 Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 90 through 105 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 18 through 33 Processing helix chain 'P' and resid 36 through 50 Processing helix chain 'P' and resid 52 through 67 Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 40 through 55 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 90 through 105 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'Q' and resid 3 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 99 Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 40 through 55 Processing helix chain 'G' and resid 56 through 71 Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 90 through 105 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'R' and resid 3 through 16 Processing helix chain 'R' and resid 18 through 33 Processing helix chain 'R' and resid 36 through 50 Processing helix chain 'R' and resid 52 through 67 Processing helix chain 'R' and resid 70 through 84 Processing helix chain 'R' and resid 86 through 99 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 56 through 71 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 90 through 105 Processing helix chain 'H' and resid 108 through 122 Processing helix chain 'S' and resid 3 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 99 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 40 through 55 Processing helix chain 'I' and resid 56 through 71 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 90 through 105 Processing helix chain 'I' and resid 108 through 122 Processing helix chain 'T' and resid 3 through 16 Processing helix chain 'T' and resid 18 through 33 Processing helix chain 'T' and resid 36 through 50 Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 86 through 99 Processing helix chain 'J' and resid 5 through 20 Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 40 through 55 Processing helix chain 'J' and resid 56 through 71 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 90 through 105 Processing helix chain 'J' and resid 108 through 122 Processing helix chain 'U' and resid 3 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 99 Processing helix chain 'K' and resid 5 through 20 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 40 through 55 Processing helix chain 'K' and resid 56 through 71 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 90 through 105 Processing helix chain 'K' and resid 108 through 122 Processing helix chain 'V' and resid 3 through 16 Processing helix chain 'V' and resid 18 through 33 Processing helix chain 'V' and resid 36 through 50 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 70 through 84 Processing helix chain 'V' and resid 86 through 99 Processing helix chain 'L' and resid 5 through 20 Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 40 through 55 Processing helix chain 'L' and resid 56 through 71 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 90 through 105 Processing helix chain 'L' and resid 108 through 122 Processing helix chain 'W' and resid 3 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 99 Processing helix chain 'M' and resid 5 through 20 Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 40 through 55 Processing helix chain 'M' and resid 56 through 71 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 108 through 122 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 18 through 33 Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 70 through 84 Processing helix chain 'X' and resid 86 through 99 1764 hydrogen bonds defined for protein. 5292 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: 7.39 Time building geometry restraints manager: 9.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4212 1.32 - 1.44: 6379 1.44 - 1.56: 11225 1.56 - 1.68: 84 1.68 - 1.81: 72 Bond restraints: 21972 Sorted by residual: bond pdb=" NE1 TRP O 40 " pdb=" CE2 TRP O 40 " ideal model delta sigma weight residual 1.370 1.326 0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" NE1 TRP U 40 " pdb=" CE2 TRP U 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP Q 40 " pdb=" CE2 TRP Q 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP N 40 " pdb=" CE2 TRP N 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP B 40 " pdb=" CE2 TRP B 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.55e+01 ... (remaining 21967 not shown) Histogram of bond angle deviations from ideal: 100.69 - 107.32: 729 107.32 - 113.96: 10697 113.96 - 120.59: 11702 120.59 - 127.22: 6428 127.22 - 133.85: 168 Bond angle restraints: 29724 Sorted by residual: angle pdb=" C ASP S 33 " pdb=" N PRO S 34 " pdb=" CA PRO S 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.97e+01 angle pdb=" C ASP T 33 " pdb=" N PRO T 34 " pdb=" CA PRO T 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.96e+01 angle pdb=" C ASP N 33 " pdb=" N PRO N 34 " pdb=" CA PRO N 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP R 33 " pdb=" N PRO R 34 " pdb=" CA PRO R 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP W 33 " pdb=" N PRO W 34 " pdb=" CA PRO W 34 " ideal model delta sigma weight residual 119.82 127.98 -8.16 9.80e-01 1.04e+00 6.93e+01 ... (remaining 29719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12386 17.11 - 34.22: 539 34.22 - 51.33: 107 51.33 - 68.43: 48 68.43 - 85.54: 12 Dihedral angle restraints: 13092 sinusoidal: 5196 harmonic: 7896 Sorted by residual: dihedral pdb=" CB MET L 17 " pdb=" CG MET L 17 " pdb=" SD MET L 17 " pdb=" CE MET L 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.36 -39.36 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET F 17 " pdb=" CG MET F 17 " pdb=" SD MET F 17 " pdb=" CE MET F 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET J 17 " pdb=" CG MET J 17 " pdb=" SD MET J 17 " pdb=" CE MET J 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1719 0.065 - 0.130: 773 0.130 - 0.195: 398 0.195 - 0.260: 49 0.260 - 0.325: 25 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA ASN E 80 " pdb=" N ASN E 80 " pdb=" C ASN E 80 " pdb=" CB ASN E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ASN J 80 " pdb=" N ASN J 80 " pdb=" C ASN J 80 " pdb=" CB ASN J 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN K 80 " pdb=" N ASN K 80 " pdb=" C ASN K 80 " pdb=" CB ASN K 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2961 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 59 " -0.044 2.00e-02 2.50e+03 2.22e-02 9.84e+00 pdb=" CG TYR V 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR V 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR V 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR V 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR V 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR V 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 59 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 59 " 0.044 2.00e-02 2.50e+03 2.21e-02 9.75e+00 pdb=" CG TYR R 59 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR R 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 59 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR R 59 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR R 59 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 59 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR R 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 59 " -0.044 2.00e-02 2.50e+03 2.21e-02 9.73e+00 pdb=" CG TYR T 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR T 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR T 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR T 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR T 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR T 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 59 " -0.024 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 10121 2.92 - 3.42: 23687 3.42 - 3.91: 39439 3.91 - 4.41: 49797 4.41 - 4.90: 71062 Nonbonded interactions: 194106 Sorted by model distance: nonbonded pdb=" NZ LYS D 99 " pdb=" OD2 ASP O 88 " model vdw 2.431 2.520 nonbonded pdb=" NZ LYS C 99 " pdb=" OD2 ASP N 88 " model vdw 2.431 2.520 nonbonded pdb=" NZ LYS L 99 " pdb=" OD2 ASP W 88 " model vdw 2.431 2.520 nonbonded pdb=" NZ LYS A 99 " pdb=" OD2 ASP B 88 " model vdw 2.431 2.520 nonbonded pdb=" NZ LYS H 99 " pdb=" OD2 ASP S 88 " model vdw 2.431 2.520 ... (remaining 194101 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 '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' } ncs_group { reference = chain 'B' 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' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' 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' } pdb_interpretation.ncs_group { reference = chain 'B' 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' } Set refine NCS operators NCS operators will be refined. 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: 5.440 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: 0.020 Extract box with map and model: 20.020 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 56.940 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 0.086 21972 Z= 1.185 Angle : 1.456 8.182 29724 Z= 1.015 Chirality : 0.089 0.325 2964 Planarity : 0.008 0.041 3888 Dihedral : 11.376 85.543 8148 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.45 (0.14), residues: 2592 helix: 0.53 (0.09), residues: 2412 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.121 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2479 time to fit residues: 9.9143 Evaluate side-chains 11 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1498 Evaluate side-chains 31 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.3273 time to fit residues: 10.5032 Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 21972 Z= 0.237 Angle : 0.619 6.104 29724 Z= 0.333 Chirality : 0.043 0.180 2964 Planarity : 0.005 0.036 3888 Dihedral : 3.983 15.246 3072 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 1.44 (0.15), residues: 2592 helix: 1.15 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -1.20 (0.50), residues: 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0956 time to fit residues: 3.3785 Evaluate side-chains 21 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1346 Evaluate side-chains 25 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2252 time to fit residues: 5.9521 Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 155 optimal weight: 0.1980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 183 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21972 Z= 0.184 Angle : 0.735 15.072 29724 Z= 0.334 Chirality : 0.047 0.396 2964 Planarity : 0.004 0.026 3888 Dihedral : 4.228 14.518 3072 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.00 (0.15), residues: 2592 helix: 0.89 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -1.69 (0.48), residues: 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4502 Ramachandran restraints generated. 2251 Oldfield, 0 Emsley, 2251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.125 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1126 time to fit residues: 3.7573 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.124 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1633 Evaluate side-chains 24 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2530 time to fit residues: 6.3981 Evaluate side-chains 15 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 65 optimal weight: 0.0060 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 21972 Z= 0.293 Angle : 0.755 11.596 29724 Z= 0.365 Chirality : 0.045 0.235 2964 Planarity : 0.003 0.027 3888 Dihedral : 4.267 14.223 3072 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 0.80 (0.15), residues: 2592 helix: 0.78 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.02 (0.46), residues: 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.105 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0737 time to fit residues: 2.2170 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1402 Evaluate side-chains 22 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1967 time to fit residues: 4.6353 Evaluate side-chains 16 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.090 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 0.0170 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 0.0050 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 218 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 21972 Z= 0.293 Angle : 0.755 11.596 29724 Z= 0.365 Chirality : 0.044 0.235 2964 Planarity : 0.003 0.026 3888 Dihedral : 4.267 14.223 3072 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 28.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 0.80 (0.15), residues: 2592 helix: 0.78 (0.10), residues: 2436 sheet: None (None), residues: 0 loop : -2.02 (0.46), residues: 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.119 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0700 time to fit residues: 1.9183 Evaluate side-chains 12 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1590 Evaluate side-chains 21 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2126 time to fit residues: 4.7727 Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.0570 chunk 219 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 243 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 21972 Z= 0.216 Angle : 0.742 9.312 29724 Z= 0.365 Chirality : 0.041 0.134 2964 Planarity : 0.004 0.040 3888 Dihedral : 4.422 13.301 3072 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.34 (0.15), residues: 2592 helix: 0.50 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.54 (0.44), residues: 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4022 Ramachandran restraints generated. 2011 Oldfield, 0 Emsley, 2011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.121 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1164 time to fit residues: 3.1840 Evaluate side-chains 14 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1652 Evaluate side-chains 21 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2202 time to fit residues: 4.9474 Evaluate side-chains 14 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 138 optimal weight: 0.0470 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 0.0070 chunk 148 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 21972 Z= 0.216 Angle : 0.742 9.312 29724 Z= 0.365 Chirality : 0.041 0.134 2964 Planarity : 0.004 0.040 3888 Dihedral : 4.422 13.301 3072 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: 0.34 (0.15), residues: 2592 helix: 0.50 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.54 (0.44), residues: 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.104 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0687 time to fit residues: 1.8657 Evaluate side-chains 15 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1798 Evaluate side-chains 21 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2252 time to fit residues: 5.0231 Evaluate side-chains 15 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 0.0870 chunk 120 optimal weight: 4.9990 chunk 22 optimal weight: 0.0170 chunk 190 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 21972 Z= 0.212 Angle : 0.744 8.570 29724 Z= 0.370 Chirality : 0.045 0.155 2964 Planarity : 0.004 0.026 3888 Dihedral : 4.606 15.367 3072 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -0.14 (0.15), residues: 2592 helix: 0.22 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -3.14 (0.41), residues: 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3638 Ramachandran restraints generated. 1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.123 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1192 time to fit residues: 3.1363 Evaluate side-chains 16 residues out of total 94 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.125 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1607 Evaluate side-chains 22 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2603 time to fit residues: 6.0417 Evaluate side-chains 13 residues out of total 74 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7112 > 50: distance: 0 - 1: 28.030 distance: 1 - 2: 26.212 distance: 1 - 4: 43.314 distance: 2 - 3: 39.909 distance: 2 - 8: 52.452 distance: 3 - 34: 42.137 distance: 4 - 5: 58.466 distance: 5 - 6: 29.721 distance: 6 - 7: 29.863 distance: 8 - 9: 40.686 distance: 9 - 10: 16.637 distance: 9 - 12: 37.306 distance: 10 - 11: 48.533 distance: 10 - 20: 26.096 distance: 11 - 38: 27.869 distance: 12 - 13: 27.991 distance: 13 - 15: 56.352 distance: 15 - 17: 28.041 distance: 16 - 18: 45.844 distance: 17 - 18: 59.349 distance: 18 - 19: 29.331 distance: 20 - 21: 19.433 distance: 21 - 22: 56.906 distance: 21 - 24: 53.560 distance: 22 - 23: 10.416 distance: 22 - 29: 43.343 distance: 23 - 46: 45.253 distance: 24 - 25: 37.642 distance: 25 - 26: 47.727 distance: 26 - 27: 15.983 distance: 27 - 28: 8.999 distance: 29 - 30: 9.886 distance: 30 - 31: 33.527 distance: 31 - 32: 7.429 distance: 31 - 34: 7.847 distance: 32 - 51: 3.371 distance: 34 - 35: 40.308 distance: 35 - 36: 11.900 distance: 36 - 37: 26.218 distance: 36 - 38: 62.544 distance: 37 - 59: 41.715 distance: 39 - 40: 42.485 distance: 39 - 42: 56.548 distance: 40 - 41: 40.263 distance: 40 - 46: 47.661 distance: 41 - 71: 37.518 distance: 42 - 43: 41.152 distance: 43 - 44: 12.036 distance: 43 - 45: 43.118 distance: 46 - 47: 46.209 distance: 47 - 48: 43.825 distance: 47 - 50: 61.052 distance: 48 - 49: 39.626 distance: 48 - 51: 57.623 distance: 52 - 53: 47.614 distance: 52 - 55: 14.448 distance: 53 - 54: 21.303 distance: 53 - 59: 41.026 distance: 55 - 56: 39.588 distance: 56 - 57: 15.876 distance: 57 - 58: 51.462 distance: 59 - 60: 40.932 distance: 60 - 61: 41.335 distance: 60 - 63: 48.443 distance: 61 - 62: 53.823 distance: 63 - 64: 20.528 distance: 64 - 65: 44.201 distance: 64 - 66: 18.012 distance: 65 - 67: 40.947 distance: 66 - 68: 38.602 distance: 67 - 69: 38.675 distance: 72 - 73: 39.772 distance: 72 - 75: 55.208 distance: 73 - 74: 25.470 distance: 75 - 76: 52.945 distance: 76 - 77: 14.848 distance: 77 - 78: 21.804 distance: 78 - 79: 23.727 distance: 79 - 80: 32.401 distance: 79 - 81: 13.696