Starting phenix.real_space_refine on Sat Mar 23 00:29:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/03_2024/8bkb_16095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/03_2024/8bkb_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_16095/03_2024/8bkb_16095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/03_2024/8bkb_16095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/03_2024/8bkb_16095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bkb_16095/03_2024/8bkb_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-dev-5265/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: 18.32, 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: 14.87 Conformation dependent library (CDL) restraints added in 6.6 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: 2.59 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: 11.23 Time building geometry restraints manager: 15.90 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: 2.090 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: 12.690 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 90.980 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.330 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.160 ------------------------------------------------------------------------------- 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 : 4.176 Fit side-chains REVERT: A 162 GLU cc_start: 0.6344 (mp0) cc_final: 0.5804 (mt-10) REVERT: B 162 GLU cc_start: 0.6291 (mp0) cc_final: 0.5752 (mt-10) REVERT: C 162 GLU cc_start: 0.6252 (mp0) cc_final: 0.5732 (mt-10) REVERT: D 162 GLU cc_start: 0.6330 (mp0) cc_final: 0.5778 (mt-10) REVERT: E 162 GLU cc_start: 0.6333 (mp0) cc_final: 0.5786 (mt-10) REVERT: F 162 GLU cc_start: 0.6279 (mp0) cc_final: 0.5733 (mt-10) REVERT: G 162 GLU cc_start: 0.6306 (mp0) cc_final: 0.5767 (mt-10) REVERT: H 162 GLU cc_start: 0.6283 (mp0) cc_final: 0.5737 (mt-10) REVERT: I 162 GLU cc_start: 0.6288 (mp0) cc_final: 0.5746 (mt-10) REVERT: J 162 GLU cc_start: 0.6262 (mp0) cc_final: 0.5736 (mt-10) REVERT: K 162 GLU cc_start: 0.6242 (mp0) cc_final: 0.5712 (mt-10) REVERT: L 162 GLU cc_start: 0.6303 (mp0) cc_final: 0.5766 (mt-10) REVERT: M 162 GLU cc_start: 0.6277 (mp0) cc_final: 0.5735 (mt-10) REVERT: N 162 GLU cc_start: 0.6346 (mp0) cc_final: 0.5799 (mt-10) REVERT: O 162 GLU cc_start: 0.6332 (mp0) cc_final: 0.5788 (mt-10) REVERT: P 162 GLU cc_start: 0.6278 (mp0) cc_final: 0.5741 (mt-10) REVERT: Q 162 GLU cc_start: 0.6292 (mp0) cc_final: 0.5754 (mt-10) REVERT: R 162 GLU cc_start: 0.6335 (mp0) cc_final: 0.5789 (mt-10) REVERT: S 162 GLU cc_start: 0.6305 (mp0) cc_final: 0.5773 (mt-10) REVERT: T 162 GLU cc_start: 0.6199 (mp0) cc_final: 0.5650 (mt-10) REVERT: V 162 GLU cc_start: 0.6265 (mp0) cc_final: 0.5723 (mt-10) REVERT: W 162 GLU cc_start: 0.6291 (mp0) cc_final: 0.5764 (mt-10) REVERT: X 162 GLU cc_start: 0.6284 (mp0) cc_final: 0.5757 (mt-10) REVERT: Y 162 GLU cc_start: 0.6325 (mp0) cc_final: 0.5780 (mt-10) outliers start: 51 outliers final: 25 residues processed: 983 average time/residue: 2.0201 time to fit residues: 2264.5799 Evaluate side-chains 1006 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 981 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN 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: 10.0000 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: 0.8406 moved from start: 0.0577 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= 0.284 Angle : 0.635 6.314 46416 Z= 0.346 Chirality : 0.039 0.119 4848 Planarity : 0.005 0.028 6096 Dihedral : 6.215 46.968 4585 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 3.82 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP O 93 HIS 0.006 0.002 HIS K 118 PHE 0.017 0.004 PHE X 41 TYR 0.015 0.003 TYR P 137 ARG 0.005 0.001 ARG C 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 1057 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 947 time to evaluate : 4.272 Fit side-chains outliers start: 110 outliers final: 76 residues processed: 984 average time/residue: 2.1004 time to fit residues: 2345.6396 Evaluate side-chains 1023 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 947 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 86 LYS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 86 LYS Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 86 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain Y residue 165 MET 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: 6.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 371 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 368 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 83 GLN G 83 GLN 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 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0662 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= 0.261 Angle : 0.606 6.167 46416 Z= 0.333 Chirality : 0.038 0.118 4848 Planarity : 0.004 0.026 6096 Dihedral : 6.118 44.604 4585 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.02 % Allowed : 12.23 % 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: 4.77 (0.13), residues: 4080 helix: 3.74 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.75 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP B 93 HIS 0.005 0.002 HIS P 128 PHE 0.017 0.003 PHE I 41 TYR 0.014 0.002 TYR O 137 ARG 0.004 0.001 ARG P 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 1054 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 944 time to evaluate : 3.949 Fit side-chains outliers start: 110 outliers final: 105 residues processed: 982 average time/residue: 2.0671 time to fit residues: 2307.1011 Evaluate side-chains 1032 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 927 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 86 LYS Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 86 LYS Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 86 LYS Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 86 LYS Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 86 LYS Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 372 optimal weight: 8.9990 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 353 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 GLN C 83 GLN F 83 GLN H 83 GLN I 83 GLN N 83 GLN P 83 GLN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN W 83 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0599 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= 0.200 Angle : 0.538 5.963 46416 Z= 0.295 Chirality : 0.036 0.114 4848 Planarity : 0.004 0.026 6096 Dihedral : 5.853 40.859 4584 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.10 % Allowed : 12.75 % Favored : 84.16 % 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: 5.09 (0.13), residues: 4080 helix: 3.98 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.83 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP V 93 HIS 0.005 0.001 HIS M 128 PHE 0.015 0.003 PHE P 41 TYR 0.012 0.002 TYR T 137 ARG 0.003 0.001 ARG J 79 *********************** 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 1113 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1000 time to evaluate : 4.617 Fit side-chains outliers start: 113 outliers final: 74 residues processed: 1038 average time/residue: 1.9893 time to fit residues: 2358.9382 Evaluate side-chains 1054 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 980 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 0.0970 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.3784 ------------------------------------------------------------------------------- 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** A 83 GLN B 83 GLN C 83 GLN D 83 GLN ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN M 83 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 83 GLN P 83 GLN Q 83 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN V 83 GLN W 83 GLN ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0670 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= 0.234 Angle : 0.577 6.014 46416 Z= 0.317 Chirality : 0.037 0.118 4848 Planarity : 0.004 0.026 6096 Dihedral : 5.950 41.839 4584 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.66 % Allowed : 12.64 % Favored : 84.70 % 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: 4.89 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.82 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP K 93 HIS 0.005 0.002 HIS Y 128 PHE 0.016 0.003 PHE V 41 TYR 0.014 0.002 TYR B 137 ARG 0.004 0.001 ARG K 79 *********************** 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 1056 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 959 time to evaluate : 4.188 Fit side-chains outliers start: 97 outliers final: 74 residues processed: 985 average time/residue: 2.0244 time to fit residues: 2273.7459 Evaluate side-chains 1053 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 979 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET 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: 7.9990 chunk 77 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 83 GLN G 83 GLN 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 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34512 Z= 0.300 Angle : 0.641 6.379 46416 Z= 0.354 Chirality : 0.040 0.122 4848 Planarity : 0.005 0.032 6096 Dihedral : 6.141 43.965 4584 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.02 % Allowed : 12.50 % Favored : 84.48 % 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: 4.54 (0.13), residues: 4080 helix: 3.57 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.71 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP K 93 HIS 0.006 0.002 HIS H 128 PHE 0.019 0.004 PHE H 41 TYR 0.016 0.003 TYR N 137 ARG 0.005 0.001 ARG A 79 *********************** 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 1094 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 984 time to evaluate : 4.145 Fit side-chains outliers start: 110 outliers final: 74 residues processed: 1022 average time/residue: 1.9742 time to fit residues: 2304.4699 Evaluate side-chains 1007 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 933 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN G 83 GLN J 83 GLN K 83 GLN R 83 GLN S 83 GLN X 83 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0680 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= 0.223 Angle : 0.565 6.018 46416 Z= 0.311 Chirality : 0.036 0.118 4848 Planarity : 0.004 0.027 6096 Dihedral : 5.919 40.820 4584 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.17 % Allowed : 13.87 % Favored : 83.96 % 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: 4.93 (0.13), residues: 4080 helix: 3.86 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.81 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP D 93 HIS 0.005 0.002 HIS X 128 PHE 0.017 0.003 PHE H 41 TYR 0.013 0.002 TYR N 137 ARG 0.003 0.001 ARG Y 79 *********************** 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 1079 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1000 time to evaluate : 4.132 Fit side-chains outliers start: 79 outliers final: 73 residues processed: 1031 average time/residue: 1.9867 time to fit residues: 2345.4424 Evaluate side-chains 1061 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 988 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 250 optimal weight: 0.0970 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 overall best weight: 3.5584 ------------------------------------------------------------------------------- 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN I 83 GLN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 83 GLN P 83 GLN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN V 83 GLN W 83 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0664 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= 0.210 Angle : 0.555 5.953 46416 Z= 0.304 Chirality : 0.036 0.116 4848 Planarity : 0.004 0.029 6096 Dihedral : 5.859 40.156 4584 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.00 % Allowed : 13.68 % Favored : 84.32 % 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: 5.05 (0.13), residues: 4080 helix: 3.94 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.86 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP M 93 HIS 0.005 0.001 HIS X 128 PHE 0.015 0.003 PHE Y 41 TYR 0.013 0.002 TYR N 137 ARG 0.003 0.001 ARG J 79 *********************** 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 1080 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1007 time to evaluate : 3.965 Fit side-chains outliers start: 73 outliers final: 73 residues processed: 1019 average time/residue: 1.9500 time to fit residues: 2274.8512 Evaluate side-chains 1062 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 989 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET 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: 7.9990 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 7.9990 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 83 GLN C 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN N 83 GLN P 83 GLN R 83 GLN S 83 GLN V 83 GLN W 83 GLN X 83 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0700 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= 0.266 Angle : 0.622 6.157 46416 Z= 0.342 Chirality : 0.039 0.120 4848 Planarity : 0.004 0.028 6096 Dihedral : 6.016 41.637 4584 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.00 % Allowed : 14.04 % Favored : 83.96 % 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: 4.72 (0.13), residues: 4080 helix: 3.70 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.77 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP G 93 HIS 0.005 0.002 HIS Y 128 PHE 0.018 0.003 PHE P 41 TYR 0.016 0.003 TYR V 12 ARG 0.004 0.001 ARG H 79 *********************** 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 1014 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 941 time to evaluate : 3.616 Fit side-chains outliers start: 73 outliers final: 73 residues processed: 966 average time/residue: 1.9936 time to fit residues: 2199.9549 Evaluate side-chains 1003 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 930 time to evaluate : 3.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 9.9990 chunk 387 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.0680 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= 0.237 Angle : 0.596 5.973 46416 Z= 0.326 Chirality : 0.037 0.123 4848 Planarity : 0.004 0.031 6096 Dihedral : 5.967 41.148 4584 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.60 % Allowed : 13.43 % Favored : 83.96 % 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: 4.90 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP M 93 HIS 0.005 0.002 HIS T 128 PHE 0.017 0.003 PHE V 41 TYR 0.014 0.002 TYR K 12 ARG 0.003 0.001 ARG C 63 ********************** 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 1052 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 957 time to evaluate : 4.275 Fit side-chains outliers start: 95 outliers final: 73 residues processed: 981 average time/residue: 1.9809 time to fit residues: 2221.6378 Evaluate side-chains 1021 residues out of total 3648 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 948 time to evaluate : 4.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 165 MET Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 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: 8.9990 chunk 59 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN C 83 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.123828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.117780 restraints weight = 26135.077| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 0.35 r_work: 0.3083 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2702 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34512 Z= 0.321 Angle : 0.680 6.413 46416 Z= 0.374 Chirality : 0.041 0.124 4848 Planarity : 0.005 0.035 6096 Dihedral : 6.123 42.169 4584 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.00 % Allowed : 14.01 % Favored : 83.99 % 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: 4.47 (0.13), residues: 4080 helix: 3.51 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.72 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP I 93 HIS 0.006 0.002 HIS D 128 PHE 0.020 0.004 PHE Q 41 TYR 0.019 0.003 TYR L 12 ARG 0.005 0.001 ARG Y 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26968.90 seconds wall clock time: 470 minutes 18.12 seconds (28218.12 seconds total)