Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 17:28:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/10_2023/8bkb_16095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/10_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_16095/10_2023/8bkb_16095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/10_2023/8bkb_16095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/10_2023/8bkb_16095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/10_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-1.21rc1-5097/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: 18.42, per 1000 atoms: 0.52 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: 15.40 Conformation dependent library (CDL) restraints added in 5.2 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: 3.01 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: 11.12 Time building geometry restraints manager: 16.29 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.860 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 92.350 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.290 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.950 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.339 Fit side-chains outliers start: 51 outliers final: 25 residues processed: 983 average time/residue: 2.0787 time to fit residues: 2331.9789 Evaluate side-chains 1008 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 983 time to evaluate : 4.664 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 1.7526 time to fit residues: 57.0447 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.910 Fit side-chains outliers start: 110 outliers final: 52 residues processed: 978 average time/residue: 2.1545 time to fit residues: 2398.5050 Evaluate side-chains 1034 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 982 time to evaluate : 4.635 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 28 residues processed: 24 average time/residue: 1.4894 time to fit residues: 48.7794 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.343 Fit side-chains outliers start: 101 outliers final: 80 residues processed: 1047 average time/residue: 2.0216 time to fit residues: 2423.4160 Evaluate side-chains 1087 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1007 time to evaluate : 4.337 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 28 residues processed: 52 average time/residue: 1.2973 time to fit residues: 87.9594 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 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 83 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN T 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN X 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0702 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= 0.249 Angle : 0.589 6.068 46416 Z= 0.324 Chirality : 0.038 0.119 4848 Planarity : 0.004 0.025 6096 Dihedral : 4.275 19.108 4512 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.93 % Allowed : 12.09 % 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: 4.87 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 888 *********************** REFINEMENT MACRO_CYCLE 4 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 1070 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 963 time to evaluate : 4.563 Fit side-chains outliers start: 107 outliers final: 80 residues processed: 1005 average time/residue: 2.1467 time to fit residues: 2459.6193 Evaluate side-chains 1041 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 961 time to evaluate : 4.809 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 39 residues processed: 41 average time/residue: 1.6059 time to fit residues: 84.0729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 353 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN J 83 GLN L 83 GLN M 83 GLN N 83 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 83 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN T 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0753 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= 0.248 Angle : 0.591 6.103 46416 Z= 0.325 Chirality : 0.038 0.118 4848 Planarity : 0.004 0.025 6096 Dihedral : 4.284 19.151 4512 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.26 % Allowed : 12.61 % Favored : 84.13 % 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: 3.78 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 888 *********************** REFINEMENT MACRO_CYCLE 5 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 1097 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 978 time to evaluate : 4.397 Fit side-chains outliers start: 119 outliers final: 78 residues processed: 1032 average time/residue: 2.0526 time to fit residues: 2424.5390 Evaluate side-chains 1039 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 961 time to evaluate : 3.974 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 54 residues processed: 24 average time/residue: 1.3731 time to fit residues: 45.5867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 14 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 14 GLN I 83 GLN J 14 GLN K 14 GLN K 83 GLN L 14 GLN M 14 GLN N 14 GLN N 83 GLN O 14 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 14 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** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0779 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= 0.255 Angle : 0.601 6.152 46416 Z= 0.331 Chirality : 0.038 0.118 4848 Planarity : 0.004 0.026 6096 Dihedral : 4.303 19.137 4512 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.36 % Allowed : 13.54 % Favored : 84.10 % 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: 4.73 (0.13), residues: 4080 helix: 3.72 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.73 (0.24), residues: 888 *********************** REFINEMENT MACRO_CYCLE 6 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 1057 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 971 time to evaluate : 4.568 Fit side-chains outliers start: 86 outliers final: 79 residues processed: 1013 average time/residue: 2.1088 time to fit residues: 2439.9781 Evaluate side-chains 1017 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 938 time to evaluate : 4.362 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 40 residues processed: 39 average time/residue: 1.5308 time to fit residues: 76.7444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 14 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN J 83 GLN L 83 GLN M 83 GLN N 83 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 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34512 Z= 0.229 Angle : 0.573 6.050 46416 Z= 0.315 Chirality : 0.037 0.117 4848 Planarity : 0.004 0.028 6096 Dihedral : 4.259 19.335 4512 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.91 % Allowed : 12.99 % Favored : 84.10 % 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: 4.92 (0.13), residues: 4080 helix: 3.85 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.81 (0.24), residues: 888 *********************** REFINEMENT MACRO_CYCLE 7 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 1085 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 979 time to evaluate : 4.846 Fit side-chains outliers start: 106 outliers final: 65 residues processed: 1022 average time/residue: 2.1311 time to fit residues: 2485.0118 Evaluate side-chains 1015 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 950 time to evaluate : 4.410 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 39 residues processed: 26 average time/residue: 1.4439 time to fit residues: 50.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 chunk 267 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN G 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 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 83 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 GLN T 83 GLN ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN X 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34512 Z= 0.202 Angle : 0.551 5.971 46416 Z= 0.302 Chirality : 0.036 0.115 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.203 19.513 4512 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.73 % Allowed : 14.20 % Favored : 84.07 % 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: 5.13 (0.13), residues: 4080 helix: 4.01 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 888 *********************** REFINEMENT MACRO_CYCLE 8 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: 63 poor density : 988 time to evaluate : 4.667 Fit side-chains outliers start: 63 outliers final: 62 residues processed: 1027 average time/residue: 2.0720 time to fit residues: 2435.2154 Evaluate side-chains 1016 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 954 time to evaluate : 4.311 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 39 residues processed: 23 average time/residue: 1.3861 time to fit residues: 44.0784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 346 optimal weight: 9.9990 chunk 365 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 83 GLN C 83 GLN ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN J 83 GLN K 83 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN N 83 GLN ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN X 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0793 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= 0.224 Angle : 0.585 5.964 46416 Z= 0.321 Chirality : 0.037 0.116 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.238 19.373 4512 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.95 % Allowed : 14.01 % Favored : 84.05 % 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: 4.99 (0.13), residues: 4080 helix: 3.90 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 888 *********************** REFINEMENT MACRO_CYCLE 9 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 1015 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 944 time to evaluate : 4.363 Fit side-chains outliers start: 71 outliers final: 47 residues processed: 983 average time/residue: 2.1911 time to fit residues: 2458.6083 Evaluate side-chains 992 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 945 time to evaluate : 4.546 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 39 residues processed: 8 average time/residue: 1.4823 time to fit residues: 20.0671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 10.0000 chunk 387 optimal weight: 8.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 10.0000 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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 K 14 GLN L 14 GLN M 14 GLN M 83 GLN N 14 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 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** 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34512 Z= 0.252 Angle : 0.615 6.068 46416 Z= 0.338 Chirality : 0.038 0.119 4848 Planarity : 0.004 0.027 6096 Dihedral : 4.284 19.186 4512 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.17 % Allowed : 13.79 % Favored : 84.05 % 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: 4.85 (0.13), residues: 4080 helix: 3.79 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.80 (0.24), residues: 888 ********************** REFINEMENT MACRO_CYCLE 10 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 1031 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 952 time to evaluate : 4.399 Fit side-chains outliers start: 79 outliers final: 54 residues processed: 991 average time/residue: 2.1067 time to fit residues: 2380.4268 Evaluate side-chains 1001 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 947 time to evaluate : 4.428 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 39 residues processed: 15 average time/residue: 1.7967 time to fit residues: 37.1909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 332 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** H 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN J 83 GLN K 83 GLN L 83 GLN N 83 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN ** Q 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** Y 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.123809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117815 restraints weight = 26090.913| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 0.35 r_work: 0.3086 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2715 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34512 Z= 0.268 Angle : 0.633 6.133 46416 Z= 0.347 Chirality : 0.039 0.131 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.308 19.174 4512 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.78 % Allowed : 14.09 % Favored : 84.13 % 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: 4.78 (0.13), residues: 4080 helix: 3.74 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.79 (0.24), residues: 888 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28456.07 seconds wall clock time: 498 minutes 22.96 seconds (29902.96 seconds total)