Starting phenix.real_space_refine on Tue Aug 26 06:02:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bkb_16095/08_2025/8bkb_16095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bkb_16095/08_2025/8bkb_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/cci-nas-00/data/ceres_data/8bkb_16095/08_2025/8bkb_16095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bkb_16095/08_2025/8bkb_16095.map" model { file = "/net/cci-nas-00/data/ceres_data/8bkb_16095/08_2025/8bkb_16095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bkb_16095/08_2025/8bkb_16095.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 120 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.84, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.69 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: 6.08 Time building geometry restraints manager: 3.42 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: 0.00 - 1.39: 44981 1.39 - 2.77: 1074 2.77 - 4.16: 251 4.16 - 5.54: 38 5.54 - 6.93: 72 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 3.040 nonbonded pdb=" OE1 GLU W 27 " pdb=" O HOH W 201 " model vdw 2.225 3.040 nonbonded pdb=" O ALA Q 163 " pdb=" O HOH Q 201 " model vdw 2.240 3.040 nonbonded pdb=" O ALA J 163 " pdb=" O HOH J 201 " model vdw 2.241 3.040 nonbonded pdb=" O ALA C 163 " pdb=" O HOH C 301 " model vdw 2.241 3.040 ... (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 Time spend for trying shortcut: 0.03 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.540 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- 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= 0.156 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG J 63 TYR 0.013 0.002 TYR D 137 PHE 0.014 0.003 PHE E 41 TRP 0.012 0.003 TRP A 93 HIS 0.004 0.001 HIS T 118 Details of bonding type rmsd covalent geometry : bond 0.00319 (34512) covalent geometry : angle 0.61238 (46416) hydrogen bonds : bond 0.09755 ( 2640) hydrogen bonds : angle 4.22586 ( 7920) *********************** 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 to be fit. rotamer outliers: 51 poor density : 983 time to evaluate : 1.500 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: 0.9234 time to fit residues: 1034.0021 Evaluate side-chains 1006 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 981 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 141 GLN W 141 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.118550 restraints weight = 24907.540| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.35 r_work: 0.3091 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2718 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0581 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= 0.180 Angle : 0.589 6.139 46416 Z= 0.321 Chirality : 0.037 0.118 4848 Planarity : 0.004 0.030 6096 Dihedral : 5.641 36.137 4585 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.32 % Allowed : 11.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.10 (0.13), residues: 4080 helix: 3.95 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.97 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 79 TYR 0.012 0.002 TYR D 137 PHE 0.016 0.003 PHE D 41 TRP 0.015 0.004 TRP W 93 HIS 0.005 0.002 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00372 (34512) covalent geometry : angle 0.58932 (46416) hydrogen bonds : bond 0.05921 ( 2640) hydrogen bonds : angle 3.89264 ( 7920) *********************** 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 1095 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 974 time to evaluate : 1.456 Fit side-chains outliers start: 121 outliers final: 47 residues processed: 1016 average time/residue: 0.8434 time to fit residues: 984.9338 Evaluate side-chains 995 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 948 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET 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 165 MET 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 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 86 LYS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET 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 86 LYS Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET 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 139 SER Chi-restraints excluded: chain X residue 165 MET 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 40 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 365 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 148 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 83 GLN B 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN D 83 GLN E 14 GLN E 83 GLN E 141 GLN F 14 GLN F 83 GLN G 14 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN H 14 GLN H 83 GLN I 14 GLN I 83 GLN J 14 GLN J 83 GLN K 14 GLN K 83 GLN L 14 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN M 14 GLN M 83 GLN M 141 GLN N 14 GLN N 83 GLN O 14 GLN O 83 GLN P 14 GLN P 83 GLN Q 14 GLN Q 83 GLN R 14 GLN R 83 GLN S 14 GLN S 83 GLN T 14 GLN T 83 GLN V 14 GLN V 83 GLN W 14 GLN W 83 GLN X 14 GLN X 83 GLN Y 14 GLN Y 83 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.117285 restraints weight = 25936.046| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 0.36 r_work: 0.3074 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2703 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 34512 Z= 0.240 Angle : 0.657 6.430 46416 Z= 0.361 Chirality : 0.040 0.123 4848 Planarity : 0.005 0.028 6096 Dihedral : 4.445 19.226 4512 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.76 % Allowed : 12.06 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.52 (0.13), residues: 4080 helix: 3.56 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 79 TYR 0.016 0.003 TYR J 137 PHE 0.018 0.004 PHE H 41 TRP 0.014 0.004 TRP W 93 HIS 0.006 0.002 HIS P 118 Details of bonding type rmsd covalent geometry : bond 0.00505 (34512) covalent geometry : angle 0.65735 (46416) hydrogen bonds : bond 0.06398 ( 2640) hydrogen bonds : angle 4.04799 ( 7920) *********************** 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 1071 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 934 time to evaluate : 1.090 Fit side-chains outliers start: 137 outliers final: 91 residues processed: 992 average time/residue: 0.8261 time to fit residues: 938.0555 Evaluate side-chains 1043 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 952 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 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 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 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 89 ASP 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 86 LYS 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 86 LYS 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 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 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 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 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain M residue 86 LYS 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 86 LYS 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 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 86 LYS 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 86 LYS 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 231 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 395 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.123569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.117362 restraints weight = 25741.784| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 0.36 r_work: 0.3075 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.2703 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 34512 Z= 0.244 Angle : 0.660 6.479 46416 Z= 0.364 Chirality : 0.040 0.124 4848 Planarity : 0.005 0.028 6096 Dihedral : 4.484 19.131 4512 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.82 % Allowed : 13.65 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.30 (0.12), residues: 4080 helix: 3.41 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.59 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 79 TYR 0.017 0.003 TYR D 137 PHE 0.019 0.004 PHE I 41 TRP 0.014 0.004 TRP O 93 HIS 0.007 0.002 HIS I 118 Details of bonding type rmsd covalent geometry : bond 0.00514 (34512) covalent geometry : angle 0.66030 (46416) hydrogen bonds : bond 0.06400 ( 2640) hydrogen bonds : angle 4.05224 ( 7920) *********************** 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 1064 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 961 time to evaluate : 1.413 Fit side-chains outliers start: 103 outliers final: 65 residues processed: 1014 average time/residue: 0.8571 time to fit residues: 998.4612 Evaluate side-chains 1006 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 941 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 165 MET 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 139 SER Chi-restraints excluded: chain D residue 165 MET 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 86 LYS Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET 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 86 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 86 LYS Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 86 LYS Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 165 MET Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 165 MET Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 165 MET 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 86 LYS Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 86 LYS Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 86 LYS Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET 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 139 SER Chi-restraints excluded: chain X residue 165 MET 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 368 optimal weight: 0.8980 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 274 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 83 GLN B 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN D 83 GLN E 14 GLN E 83 GLN F 14 GLN F 83 GLN G 14 GLN G 83 GLN H 14 GLN H 83 GLN I 14 GLN I 83 GLN J 14 GLN J 83 GLN K 14 GLN K 83 GLN L 14 GLN L 83 GLN M 14 GLN N 14 GLN N 83 GLN O 14 GLN O 83 GLN P 14 GLN P 83 GLN Q 14 GLN Q 83 GLN R 14 GLN R 83 GLN S 14 GLN S 83 GLN T 14 GLN V 14 GLN V 83 GLN W 14 GLN W 83 GLN X 14 GLN X 83 GLN Y 14 GLN Y 83 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.119596 restraints weight = 24612.679| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.35 r_work: 0.3108 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.2737 rms_B_bonded: 4.28 restraints_weight: 0.1250 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.003 0.042 34512 Z= 0.142 Angle : 0.525 5.857 46416 Z= 0.288 Chirality : 0.035 0.114 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.249 19.997 4512 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.82 % Allowed : 13.71 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.05 (0.13), residues: 4080 helix: 3.95 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.83 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 63 TYR 0.011 0.002 TYR A 137 PHE 0.014 0.003 PHE I 41 TRP 0.014 0.003 TRP C 93 HIS 0.004 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00293 (34512) covalent geometry : angle 0.52535 (46416) hydrogen bonds : bond 0.05314 ( 2640) hydrogen bonds : angle 3.75288 ( 7920) *********************** 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 1113 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1010 time to evaluate : 1.329 Fit side-chains outliers start: 103 outliers final: 72 residues processed: 1041 average time/residue: 0.8500 time to fit residues: 1018.2009 Evaluate side-chains 1050 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 978 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 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 349 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 354 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.126032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.119676 restraints weight = 24509.148| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 0.35 r_work: 0.3108 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.2737 rms_B_bonded: 4.29 restraints_weight: 0.1250 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0726 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= 0.146 Angle : 0.534 5.856 46416 Z= 0.292 Chirality : 0.035 0.114 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.221 19.870 4512 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.63 % Allowed : 13.90 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.12 (0.13), residues: 4080 helix: 3.99 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 79 TYR 0.011 0.002 TYR P 137 PHE 0.015 0.003 PHE N 41 TRP 0.014 0.003 TRP X 93 HIS 0.004 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00302 (34512) covalent geometry : angle 0.53372 (46416) hydrogen bonds : bond 0.05381 ( 2640) hydrogen bonds : angle 3.75174 ( 7920) *********************** 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 1096 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1000 time to evaluate : 1.251 Fit side-chains outliers start: 96 outliers final: 75 residues processed: 1024 average time/residue: 0.8088 time to fit residues: 954.2473 Evaluate side-chains 1070 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 995 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 8 VAL 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 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 8 VAL 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 8 VAL 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 183 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 320 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 256 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 303 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 318 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN E 83 GLN F 14 GLN G 14 GLN G 83 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN S 83 GLN S 141 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.125430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119267 restraints weight = 26083.460| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 0.35 r_work: 0.3102 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2722 rms_B_bonded: 4.33 restraints_weight: 0.1250 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.003 0.039 34512 Z= 0.165 Angle : 0.564 5.991 46416 Z= 0.309 Chirality : 0.036 0.116 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.269 19.701 4512 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.58 % Allowed : 13.95 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.96 (0.13), residues: 4080 helix: 3.87 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.84 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 79 TYR 0.012 0.002 TYR H 137 PHE 0.016 0.003 PHE I 41 TRP 0.014 0.003 TRP X 93 HIS 0.005 0.002 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00344 (34512) covalent geometry : angle 0.56380 (46416) hydrogen bonds : bond 0.05652 ( 2640) hydrogen bonds : angle 3.82091 ( 7920) *********************** 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 1089 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 995 time to evaluate : 1.537 Fit side-chains REVERT: V 116 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7886 (mt-10) outliers start: 94 outliers final: 85 residues processed: 1024 average time/residue: 0.8341 time to fit residues: 984.5198 Evaluate side-chains 1064 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 979 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 226 optimal weight: 9.9990 chunk 378 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 304 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 83 GLN B 14 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN F 14 GLN F 83 GLN G 14 GLN G 83 GLN H 14 GLN I 14 GLN I 83 GLN J 14 GLN J 83 GLN K 14 GLN K 83 GLN L 14 GLN L 83 GLN M 14 GLN M 83 GLN N 14 GLN N 83 GLN O 14 GLN ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN P 14 GLN P 83 GLN Q 14 GLN Q 83 GLN R 14 GLN ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 GLN S 14 GLN T 14 GLN T 83 GLN V 14 GLN V 83 GLN W 14 GLN W 83 GLN X 14 GLN X 83 GLN Y 14 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.126597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.120431 restraints weight = 26116.186| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 0.35 r_work: 0.3121 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2742 rms_B_bonded: 4.39 restraints_weight: 0.1250 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0743 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= 0.133 Angle : 0.519 5.731 46416 Z= 0.283 Chirality : 0.035 0.113 4848 Planarity : 0.003 0.032 6096 Dihedral : 4.158 20.083 4512 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.38 % Allowed : 13.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.28 (0.13), residues: 4080 helix: 4.11 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.94 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 63 TYR 0.010 0.001 TYR D 137 PHE 0.014 0.002 PHE T 41 TRP 0.014 0.003 TRP G 93 HIS 0.004 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00273 (34512) covalent geometry : angle 0.51901 (46416) hydrogen bonds : bond 0.05123 ( 2640) hydrogen bonds : angle 3.68177 ( 7920) *********************** 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 1078 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 991 time to evaluate : 1.302 Fit side-chains outliers start: 87 outliers final: 82 residues processed: 1001 average time/residue: 0.8342 time to fit residues: 959.2285 Evaluate side-chains 1044 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 962 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 53 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 336 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN M 83 GLN N 14 GLN N 83 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN T 83 GLN V 14 GLN W 14 GLN W 83 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.126615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.120464 restraints weight = 26059.698| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.35 r_work: 0.3120 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2745 rms_B_bonded: 4.30 restraints_weight: 0.1250 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0731 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= 0.134 Angle : 0.528 5.748 46416 Z= 0.288 Chirality : 0.035 0.113 4848 Planarity : 0.004 0.034 6096 Dihedral : 4.148 19.865 4512 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.41 % Allowed : 13.49 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.28 (0.13), residues: 4080 helix: 4.10 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.94 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 63 TYR 0.010 0.002 TYR I 137 PHE 0.014 0.002 PHE G 41 TRP 0.014 0.003 TRP S 93 HIS 0.004 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00276 (34512) covalent geometry : angle 0.52812 (46416) hydrogen bonds : bond 0.05123 ( 2640) hydrogen bonds : angle 3.68068 ( 7920) *********************** 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 1073 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 985 time to evaluate : 1.388 Fit side-chains REVERT: S 116 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7892 (mt-10) REVERT: V 116 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7897 (mt-10) outliers start: 88 outliers final: 88 residues processed: 1001 average time/residue: 0.8606 time to fit residues: 990.6613 Evaluate side-chains 1065 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 977 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 178 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 270 optimal weight: 0.0070 chunk 152 optimal weight: 4.9990 chunk 254 optimal weight: 20.0000 chunk 350 optimal weight: 1.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN N 83 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN ** W 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.125136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118989 restraints weight = 25938.413| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 0.35 r_work: 0.3105 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2727 rms_B_bonded: 4.30 restraints_weight: 0.1250 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0767 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= 0.172 Angle : 0.593 6.033 46416 Z= 0.325 Chirality : 0.037 0.117 4848 Planarity : 0.004 0.032 6096 Dihedral : 4.262 19.328 4512 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.55 % Allowed : 13.35 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.98 (0.13), residues: 4080 helix: 3.89 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.83 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 79 TYR 0.015 0.002 TYR V 12 PHE 0.017 0.003 PHE X 41 TRP 0.013 0.003 TRP S 93 HIS 0.005 0.002 HIS Y 128 Details of bonding type rmsd covalent geometry : bond 0.00359 (34512) covalent geometry : angle 0.59307 (46416) hydrogen bonds : bond 0.05698 ( 2640) hydrogen bonds : angle 3.84253 ( 7920) ********************** 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 1058 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 965 time to evaluate : 0.953 Fit side-chains REVERT: A 45 ASP cc_start: 0.8630 (p0) cc_final: 0.8357 (p0) REVERT: V 116 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7883 (mt-10) outliers start: 93 outliers final: 89 residues processed: 1005 average time/residue: 0.7894 time to fit residues: 914.9819 Evaluate side-chains 1046 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 957 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain Q residue 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 8 VAL 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 370 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN D 83 GLN E 14 GLN F 14 GLN F 83 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN ** J 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN L 14 GLN M 14 GLN M 83 GLN N 14 GLN N 83 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 14 GLN T 83 GLN V 14 GLN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 14 GLN W 83 GLN X 14 GLN Y 14 GLN Y 83 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.126589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.120418 restraints weight = 25991.821| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 0.35 r_work: 0.3123 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work: 0.2748 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0749 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= 0.137 Angle : 0.545 5.840 46416 Z= 0.297 Chirality : 0.035 0.124 4848 Planarity : 0.004 0.034 6096 Dihedral : 4.168 19.886 4512 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.74 % Allowed : 13.40 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.23 (0.13), residues: 4080 helix: 4.07 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.93 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 63 TYR 0.012 0.002 TYR O 12 PHE 0.014 0.002 PHE X 41 TRP 0.014 0.003 TRP X 93 HIS 0.004 0.001 HIS W 128 Details of bonding type rmsd covalent geometry : bond 0.00283 (34512) covalent geometry : angle 0.54525 (46416) hydrogen bonds : bond 0.05140 ( 2640) hydrogen bonds : angle 3.70090 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18316.85 seconds wall clock time: 311 minutes 9.33 seconds (18669.33 seconds total)