Starting phenix.real_space_refine on Sat Dec 16 12:25:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/12_2023/8bkb_16095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/12_2023/8bkb_16095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/12_2023/8bkb_16095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/12_2023/8bkb_16095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/12_2023/8bkb_16095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/12_2023/8bkb_16095.pdb" } resolution = 2.2 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= 0.007 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: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 7797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 140": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F ASP 45": "OD1" <-> "OD2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "G ASP 42": "OD1" <-> "OD2" Residue "G ASP 45": "OD1" <-> "OD2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "I ASP 42": "OD1" <-> "OD2" Residue "I ASP 45": "OD1" <-> "OD2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 140": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "L ASP 42": "OD1" <-> "OD2" Residue "L ASP 89": "OD1" <-> "OD2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L GLU 140": "OE1" <-> "OE2" Residue "L ASP 150": "OD1" <-> "OD2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M ASP 42": "OD1" <-> "OD2" Residue "M ASP 45": "OD1" <-> "OD2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ASP 150": "OD1" <-> "OD2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N ASP 45": "OD1" <-> "OD2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "N GLU 116": "OE1" <-> "OE2" Residue "N GLU 140": "OE1" <-> "OE2" Residue "O ASP 42": "OD1" <-> "OD2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O GLU 140": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P ASP 45": "OD1" <-> "OD2" Residue "P ASP 89": "OD1" <-> "OD2" Residue "P GLU 116": "OE1" <-> "OE2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q ASP 45": "OD1" <-> "OD2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q ASP 89": "OD1" <-> "OD2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q GLU 140": "OE1" <-> "OE2" Residue "Q GLU 162": "OE1" <-> "OE2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R ASP 89": "OD1" <-> "OD2" Residue "R GLU 116": "OE1" <-> "OE2" Residue "R ASP 150": "OD1" <-> "OD2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 140": "OE1" <-> "OE2" Residue "S ASP 150": "OD1" <-> "OD2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "T ASP 42": "OD1" <-> "OD2" Residue "T ASP 45": "OD1" <-> "OD2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T GLU 116": "OE1" <-> "OE2" Residue "T GLU 140": "OE1" <-> "OE2" Residue "V ASP 42": "OD1" <-> "OD2" Residue "V ASP 45": "OD1" <-> "OD2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V GLU 116": "OE1" <-> "OE2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W ASP 89": "OD1" <-> "OD2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W ASP 150": "OD1" <-> "OD2" Residue "W GLU 162": "OE1" <-> "OE2" Residue "X ASP 42": "OD1" <-> "OD2" Residue "X ASP 45": "OD1" <-> "OD2" Residue "X ASP 89": "OD1" <-> "OD2" Residue "X GLU 116": "OE1" <-> "OE2" Residue "X GLU 140": "OE1" <-> "OE2" Residue "X GLU 162": "OE1" <-> "OE2" Residue "Y ASP 89": "OD1" <-> "OD2" Residue "Y GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35139 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Y" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "N" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "P" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "Q" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "S" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "T" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "V" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "W" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "Y" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 18.71, per 1000 atoms: 0.53 Number of scatterers: 35139 At special positions: 0 Unit cell: (132.042, 132.042, 132.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 6 26.01 S 192 16.00 O 7797 8.00 N 5928 7.00 C 21216 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: 14.92 Conformation dependent library (CDL) restraints added in 6.1 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.299A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.291A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.291A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.298A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.291A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.292A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 76 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 removed outlier: 4.290A pdb=" N GLU Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR Y 168 " --> pdb=" O GLY Y 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 10.51 Time building geometry restraints manager: 15.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11495 1.34 - 1.46: 6649 1.46 - 1.58: 16056 1.58 - 1.70: 0 1.70 - 1.81: 312 Bond restraints: 34512 Sorted by residual: bond pdb=" CB GLN D 75 " pdb=" CG GLN D 75 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.39e-01 bond pdb=" CB GLN P 75 " pdb=" CG GLN P 75 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.97e-01 bond pdb=" CB GLN W 75 " pdb=" CG GLN W 75 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.86e-01 bond pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.67e-01 bond pdb=" CB CYS R 39 " pdb=" SG CYS R 39 " ideal model delta sigma weight residual 1.808 1.780 0.028 3.30e-02 9.18e+02 7.33e-01 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.39: 1008 107.39 - 114.01: 18771 114.01 - 120.64: 14925 120.64 - 127.27: 11352 127.27 - 133.90: 360 Bond angle restraints: 46416 Sorted by residual: angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP O 93 " pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C TRP A 93 " pdb=" N GLU A 94 " pdb=" CA GLU A 94 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C TRP D 93 " pdb=" N GLU D 94 " pdb=" CA GLU D 94 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 ... (remaining 46411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 18221 17.18 - 34.35: 1938 34.35 - 51.52: 497 51.52 - 68.70: 184 68.70 - 85.87: 160 Dihedral angle restraints: 21000 sinusoidal: 8760 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP R 93 " pdb=" C TRP R 93 " pdb=" N GLU R 94 " pdb=" CA GLU R 94 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TRP Y 93 " pdb=" C TRP Y 93 " pdb=" N GLU Y 94 " pdb=" CA GLU Y 94 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TRP G 93 " pdb=" C TRP G 93 " pdb=" N GLU G 94 " pdb=" CA GLU G 94 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2728 0.025 - 0.049: 1439 0.049 - 0.074: 362 0.074 - 0.099: 151 0.099 - 0.123: 168 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CG LEU O 72 " pdb=" CB LEU O 72 " pdb=" CD1 LEU O 72 " pdb=" CD2 LEU O 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CG LEU D 72 " pdb=" CB LEU D 72 " pdb=" CD1 LEU D 72 " pdb=" CD2 LEU D 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CG LEU N 72 " pdb=" CB LEU N 72 " pdb=" CD1 LEU N 72 " pdb=" CD2 LEU N 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 4845 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 94 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C GLU B 94 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU B 94 " 0.009 2.00e-02 2.50e+03 pdb=" N SER B 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 94 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLU T 94 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU T 94 " 0.009 2.00e-02 2.50e+03 pdb=" N SER T 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 94 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLU I 94 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU I 94 " 0.009 2.00e-02 2.50e+03 pdb=" N SER I 95 " 0.008 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5362 2.76 - 3.29: 35872 3.29 - 3.83: 68492 3.83 - 4.36: 80444 4.36 - 4.90: 129659 Nonbonded interactions: 319829 Sorted by model distance: nonbonded pdb=" OE1 GLU S 27 " pdb=" O HOH S 201 " model vdw 2.225 2.440 nonbonded pdb=" OE1 GLU W 27 " pdb=" O HOH W 201 " model vdw 2.225 2.440 nonbonded pdb=" O ALA Q 163 " pdb=" O HOH Q 201 " model vdw 2.240 2.440 nonbonded pdb=" O ALA J 163 " pdb=" O HOH J 201 " model vdw 2.241 2.440 nonbonded pdb=" O ALA C 163 " pdb=" O HOH C 301 " model vdw 2.241 2.440 ... (remaining 319824 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 'B' and resid 5 through 176) selection = (chain 'C' and resid 5 through 176) selection = (chain 'D' and resid 5 through 176) selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = (chain 'H' and resid 5 through 176) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = (chain 'N' and resid 5 through 176) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 5 through 176) selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.030 Extract box with map and model: 12.290 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 88.840 Find NCS groups from input model: 2.440 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: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.003 0.039 34512 Z= 0.204 Angle : 0.612 6.929 46416 Z= 0.335 Chirality : 0.038 0.123 4848 Planarity : 0.004 0.034 6096 Dihedral : 17.883 85.875 13080 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.40 % Allowed : 13.62 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.82 (0.13), residues: 4080 helix: 3.72 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.01 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 93 HIS 0.004 0.001 HIS T 118 PHE 0.014 0.003 PHE E 41 TYR 0.013 0.002 TYR D 137 ARG 0.006 0.001 ARG J 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 983 time to evaluate : 4.762 Fit side-chains outliers start: 51 outliers final: 25 residues processed: 983 average time/residue: 2.1274 time to fit residues: 2387.2035 Evaluate side-chains 1008 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 983 time to evaluate : 4.430 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 1.7053 time to fit residues: 55.9871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 GLN F 75 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 GLN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34512 Z= 0.283 Angle : 0.630 6.310 46416 Z= 0.344 Chirality : 0.039 0.119 4848 Planarity : 0.004 0.028 6096 Dihedral : 4.317 18.564 4512 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.02 % Allowed : 12.06 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.91 (0.13), residues: 4080 helix: 3.83 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.84 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 93 HIS 0.006 0.002 HIS H 118 PHE 0.017 0.004 PHE Q 41 TYR 0.015 0.003 TYR P 137 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 941 time to evaluate : 5.026 Fit side-chains outliers start: 110 outliers final: 52 residues processed: 978 average time/residue: 2.1139 time to fit residues: 2364.4295 Evaluate side-chains 1034 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 982 time to evaluate : 3.997 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 28 residues processed: 24 average time/residue: 1.2680 time to fit residues: 42.6629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 9.9990 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 83 GLN B 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN D 83 GLN E 14 GLN E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 14 GLN G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 14 GLN I 83 GLN J 14 GLN J 83 GLN K 14 GLN K 83 GLN L 14 GLN L 83 GLN M 14 GLN M 83 GLN N 14 GLN N 83 GLN O 14 GLN O 83 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN R 14 GLN R 83 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN T 14 GLN T 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 14 GLN W 83 GLN X 14 GLN X 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.183 Angle : 0.524 5.895 46416 Z= 0.286 Chirality : 0.035 0.114 4848 Planarity : 0.003 0.026 6096 Dihedral : 4.165 19.430 4512 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.77 % Allowed : 12.47 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.25 (0.13), residues: 4080 helix: 4.08 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.92 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 93 HIS 0.005 0.001 HIS D 128 PHE 0.013 0.003 PHE A 41 TYR 0.011 0.002 TYR N 137 ARG 0.003 0.001 ARG K 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1019 time to evaluate : 4.364 Fit side-chains outliers start: 101 outliers final: 80 residues processed: 1047 average time/residue: 2.0327 time to fit residues: 2444.0934 Evaluate side-chains 1087 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1007 time to evaluate : 4.248 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 28 residues processed: 52 average time/residue: 1.2733 time to fit residues: 86.4964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: