Starting phenix.real_space_refine on Sun Jun 29 05:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bkb_16095/06_2025/8bkb_16095.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bkb_16095/06_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_16095/06_2025/8bkb_16095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bkb_16095/06_2025/8bkb_16095.map" model { file = "/net/cci-nas-00/data/ceres_data/8bkb_16095/06_2025/8bkb_16095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bkb_16095/06_2025/8bkb_16095.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 6 7.16 5 S 192 5.16 5 C 21216 2.51 5 N 5928 2.21 5 O 7797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 35139 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "Y" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1409 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "M" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "N" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "P" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "Q" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "S" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "T" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "V" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "W" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "Y" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Time building chain proxies: 22.18, per 1000 atoms: 0.63 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: 8.34 Conformation dependent library (CDL) restraints added in 4.1 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.299A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.291A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.291A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.298A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.300A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR Q 168 " --> pdb=" O GLY Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.291A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.292A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR S 168 " --> pdb=" O GLY S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR T 168 " --> pdb=" O GLY T 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR V 168 " --> pdb=" O GLY V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.302A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR W 168 " --> pdb=" O GLY W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.301A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR X 168 " --> pdb=" O GLY X 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 76 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 removed outlier: 4.290A pdb=" N GLU Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR Y 168 " --> pdb=" O GLY Y 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.68 Time building geometry restraints manager: 9.88 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: 0.07 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 74.160 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.220 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.13), residues: 4080 helix: 3.72 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 1.01 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 93 HIS 0.004 0.001 HIS T 118 PHE 0.014 0.003 PHE E 41 TYR 0.013 0.002 TYR D 137 ARG 0.006 0.001 ARG J 63 Details of bonding type rmsd hydrogen bonds : bond 0.09755 ( 2640) hydrogen bonds : angle 4.22586 ( 7920) covalent geometry : bond 0.00319 (34512) covalent geometry : angle 0.61238 (46416) *********************** 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 : 4.369 Fit side-chains REVERT: A 162 GLU cc_start: 0.6344 (mp0) cc_final: 0.5804 (mt-10) REVERT: B 162 GLU cc_start: 0.6291 (mp0) cc_final: 0.5752 (mt-10) REVERT: C 162 GLU cc_start: 0.6252 (mp0) cc_final: 0.5732 (mt-10) REVERT: D 162 GLU cc_start: 0.6330 (mp0) cc_final: 0.5778 (mt-10) REVERT: E 162 GLU cc_start: 0.6333 (mp0) cc_final: 0.5786 (mt-10) REVERT: F 162 GLU cc_start: 0.6279 (mp0) cc_final: 0.5733 (mt-10) REVERT: G 162 GLU cc_start: 0.6306 (mp0) cc_final: 0.5767 (mt-10) REVERT: H 162 GLU cc_start: 0.6283 (mp0) cc_final: 0.5737 (mt-10) REVERT: I 162 GLU cc_start: 0.6288 (mp0) cc_final: 0.5746 (mt-10) REVERT: J 162 GLU cc_start: 0.6262 (mp0) cc_final: 0.5736 (mt-10) REVERT: K 162 GLU cc_start: 0.6242 (mp0) cc_final: 0.5712 (mt-10) REVERT: L 162 GLU cc_start: 0.6303 (mp0) cc_final: 0.5766 (mt-10) REVERT: M 162 GLU cc_start: 0.6277 (mp0) cc_final: 0.5735 (mt-10) REVERT: N 162 GLU cc_start: 0.6346 (mp0) cc_final: 0.5799 (mt-10) REVERT: O 162 GLU cc_start: 0.6332 (mp0) cc_final: 0.5788 (mt-10) REVERT: P 162 GLU cc_start: 0.6278 (mp0) cc_final: 0.5741 (mt-10) REVERT: Q 162 GLU cc_start: 0.6292 (mp0) cc_final: 0.5754 (mt-10) REVERT: R 162 GLU cc_start: 0.6335 (mp0) cc_final: 0.5789 (mt-10) REVERT: S 162 GLU cc_start: 0.6305 (mp0) cc_final: 0.5773 (mt-10) REVERT: T 162 GLU cc_start: 0.6199 (mp0) cc_final: 0.5650 (mt-10) REVERT: V 162 GLU cc_start: 0.6265 (mp0) cc_final: 0.5723 (mt-10) REVERT: W 162 GLU cc_start: 0.6291 (mp0) cc_final: 0.5764 (mt-10) REVERT: X 162 GLU cc_start: 0.6284 (mp0) cc_final: 0.5757 (mt-10) REVERT: Y 162 GLU cc_start: 0.6325 (mp0) cc_final: 0.5780 (mt-10) outliers start: 51 outliers final: 25 residues processed: 983 average time/residue: 2.1466 time to fit residues: 2404.8963 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 : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain M residue 14 GLN Chi-restraints excluded: chain N residue 14 GLN Chi-restraints excluded: chain O residue 14 GLN Chi-restraints excluded: chain P residue 14 GLN Chi-restraints excluded: chain Q residue 14 GLN Chi-restraints excluded: chain R residue 14 GLN Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 14 GLN Chi-restraints excluded: chain T residue 14 GLN Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain Y residue 14 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.123643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.117442 restraints weight = 25995.758| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 0.36 r_work: 0.3073 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2703 rms_B_bonded: 4.32 restraints_weight: 0.1250 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 34512 Z= 0.234 Angle : 0.659 6.441 46416 Z= 0.360 Chirality : 0.040 0.121 4848 Planarity : 0.005 0.028 6096 Dihedral : 5.795 37.624 4585 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.51 % Allowed : 11.46 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.78 (0.13), residues: 4080 helix: 3.73 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.87 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP R 93 HIS 0.006 0.002 HIS P 118 PHE 0.017 0.004 PHE C 41 TYR 0.015 0.003 TYR D 137 ARG 0.006 0.001 ARG E 79 Details of bonding type rmsd hydrogen bonds : bond 0.06381 ( 2640) hydrogen bonds : angle 4.02964 ( 7920) covalent geometry : bond 0.00490 (34512) covalent geometry : angle 0.65859 (46416) *********************** 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 1068 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 940 time to evaluate : 4.557 Fit side-chains outliers start: 128 outliers final: 57 residues processed: 989 average time/residue: 2.1082 time to fit residues: 2395.2880 Evaluate side-chains 1013 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 956 time to evaluate : 4.309 ------------------------------------------------------------------------------- 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 86 LYS 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 86 LYS Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain S residue 86 LYS Chi-restraints excluded: chain S residue 165 MET Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET 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 86 LYS Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 86 LYS Chi-restraints excluded: chain Y residue 89 ASP 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 396 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 chunk 355 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 349 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN E 141 GLN F 83 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 GLN M 83 GLN M 141 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.119260 restraints weight = 24606.736| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 0.35 r_work: 0.3097 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.2726 rms_B_bonded: 4.23 restraints_weight: 0.1250 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.164 Angle : 0.558 6.028 46416 Z= 0.306 Chirality : 0.036 0.116 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.301 23.370 4513 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.93 % Allowed : 13.24 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.99 (0.13), residues: 4080 helix: 3.89 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.85 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP T 93 HIS 0.005 0.001 HIS L 128 PHE 0.015 0.003 PHE I 41 TYR 0.012 0.002 TYR T 137 ARG 0.004 0.001 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05655 ( 2640) hydrogen bonds : angle 3.83852 ( 7920) covalent geometry : bond 0.00342 (34512) covalent geometry : angle 0.55760 (46416) *********************** 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 1100 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 993 time to evaluate : 4.543 Fit side-chains outliers start: 107 outliers final: 60 residues processed: 1047 average time/residue: 1.9696 time to fit residues: 2379.2842 Evaluate side-chains 1053 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 993 time to evaluate : 4.295 ------------------------------------------------------------------------------- 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 86 LYS 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 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 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 139 SER 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 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 165 MET Chi-restraints excluded: chain S residue 86 LYS Chi-restraints excluded: chain S residue 139 SER 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 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 251 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 377 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN F 14 GLN ** F 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 GLN H 14 GLN H 83 GLN I 14 GLN I 83 GLN J 14 GLN J 83 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 14 GLN P 14 GLN P 83 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 GLN V 83 GLN W 14 GLN W 83 GLN X 14 GLN ** X 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.124558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.118251 restraints weight = 24483.214| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.35 r_work: 0.3092 rms_B_bonded: 0.72 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2720 rms_B_bonded: 4.24 restraints_weight: 0.1250 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34512 Z= 0.181 Angle : 0.579 6.155 46416 Z= 0.318 Chirality : 0.037 0.118 4848 Planarity : 0.004 0.027 6096 Dihedral : 4.312 19.363 4512 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.06 % Allowed : 11.95 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.86 (0.13), residues: 4080 helix: 3.80 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.82 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP C 93 HIS 0.005 0.002 HIS I 128 PHE 0.017 0.003 PHE C 41 TYR 0.013 0.002 TYR T 137 ARG 0.004 0.001 ARG E 79 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 2640) hydrogen bonds : angle 3.88895 ( 7920) covalent geometry : bond 0.00377 (34512) covalent geometry : angle 0.57918 (46416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 965 time to evaluate : 4.306 Fit side-chains REVERT: F 45 ASP cc_start: 0.8599 (p0) cc_final: 0.8343 (p0) REVERT: Y 45 ASP cc_start: 0.8603 (p0) cc_final: 0.8317 (p0) outliers start: 148 outliers final: 102 residues processed: 1041 average time/residue: 2.0038 time to fit residues: 2402.7770 Evaluate side-chains 1032 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 930 time to evaluate : 3.988 ------------------------------------------------------------------------------- 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 86 LYS 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 86 LYS 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 86 LYS 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 86 LYS 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 89 ASP 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 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 8 VAL 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 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 86 LYS 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 86 LYS 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 86 LYS 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 86 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 217 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 407 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 403 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN E 83 GLN F 14 GLN G 14 GLN G 83 GLN H 14 GLN H 83 GLN I 14 GLN I 83 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 P 83 GLN Q 14 GLN R 14 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 Y 14 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.123829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.117603 restraints weight = 25798.438| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.36 r_work: 0.3077 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2705 rms_B_bonded: 4.34 restraints_weight: 0.1250 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34512 Z= 0.228 Angle : 0.640 6.401 46416 Z= 0.353 Chirality : 0.040 0.122 4848 Planarity : 0.005 0.027 6096 Dihedral : 4.430 19.035 4512 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.23 % Allowed : 13.05 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.13), residues: 4080 helix: 3.55 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.70 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 93 HIS 0.006 0.002 HIS P 118 PHE 0.019 0.004 PHE F 41 TYR 0.015 0.003 TYR N 137 ARG 0.005 0.001 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.06253 ( 2640) hydrogen bonds : angle 4.00738 ( 7920) covalent geometry : bond 0.00480 (34512) covalent geometry : angle 0.64032 (46416) *********************** 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 1058 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 940 time to evaluate : 7.509 Fit side-chains outliers start: 118 outliers final: 62 residues processed: 991 average time/residue: 2.3853 time to fit residues: 2731.4961 Evaluate side-chains 1002 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 940 time to evaluate : 4.169 ------------------------------------------------------------------------------- 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 86 LYS 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 89 ASP 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 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 139 SER 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 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 86 LYS Chi-restraints excluded: chain S residue 139 SER 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 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 29 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 347 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 368 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 83 GLN B 14 GLN C 14 GLN D 14 GLN D 83 GLN E 14 GLN F 14 GLN G 14 GLN G 83 GLN H 14 GLN I 14 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 O 14 GLN O 83 GLN P 14 GLN Q 14 GLN Q 83 GLN R 14 GLN R 83 GLN S 14 GLN T 14 GLN T 83 GLN V 14 GLN W 14 GLN X 14 GLN X 83 GLN Y 14 GLN Y 83 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.125347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.119000 restraints weight = 24472.886| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 0.35 r_work: 0.3099 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2727 rms_B_bonded: 4.26 restraints_weight: 0.1250 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0749 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= 0.165 Angle : 0.560 6.082 46416 Z= 0.308 Chirality : 0.036 0.117 4848 Planarity : 0.004 0.028 6096 Dihedral : 4.318 19.606 4512 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.69 % Allowed : 13.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.90 (0.13), residues: 4080 helix: 3.83 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.83 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP C 93 HIS 0.005 0.001 HIS N 128 PHE 0.016 0.003 PHE T 41 TYR 0.012 0.002 TYR N 137 ARG 0.003 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 2640) hydrogen bonds : angle 3.84129 ( 7920) covalent geometry : bond 0.00345 (34512) covalent geometry : angle 0.55997 (46416) *********************** 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 1095 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 997 time to evaluate : 4.140 Fit side-chains outliers start: 98 outliers final: 78 residues processed: 1040 average time/residue: 2.5657 time to fit residues: 3086.3892 Evaluate side-chains 1031 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 953 time to evaluate : 6.578 ------------------------------------------------------------------------------- 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 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 139 SER Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 165 MET Chi-restraints excluded: chain G residue 14 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 165 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 165 MET Chi-restraints excluded: chain I residue 14 GLN Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 14 GLN Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 165 MET Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 165 MET Chi-restraints excluded: chain L residue 14 GLN Chi-restraints excluded: chain L residue 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 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 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 139 SER Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 14 GLN Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 14 GLN Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 165 MET Chi-restraints excluded: chain X residue 14 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 165 MET Chi-restraints excluded: chain Y residue 14 GLN Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 165 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 394 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 202 optimal weight: 0.0020 chunk 275 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- 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 B 83 GLN C 14 GLN D 14 GLN E 14 GLN E 83 GLN F 14 GLN F 83 GLN G 14 GLN H 14 GLN I 14 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 GLN K 14 GLN L 14 GLN M 14 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.119976 restraints weight = 26091.433| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 0.36 r_work: 0.3112 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work: 0.2735 rms_B_bonded: 4.35 restraints_weight: 0.1250 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.142 Angle : 0.531 5.893 46416 Z= 0.290 Chirality : 0.035 0.114 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.234 19.917 4512 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.60 % Allowed : 13.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.12 (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 TRP 0.014 0.003 TRP X 93 HIS 0.004 0.001 HIS K 128 PHE 0.014 0.003 PHE N 41 TYR 0.011 0.002 TYR N 137 ARG 0.002 0.001 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.05332 ( 2640) hydrogen bonds : angle 3.75220 ( 7920) covalent geometry : bond 0.00294 (34512) covalent geometry : angle 0.53127 (46416) *********************** 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 1101 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1006 time to evaluate : 4.462 Fit side-chains outliers start: 95 outliers final: 75 residues processed: 1029 average time/residue: 1.9277 time to fit residues: 2286.0465 Evaluate side-chains 1052 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 977 time to evaluate : 4.552 ------------------------------------------------------------------------------- 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 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 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 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 91 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 374 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN G 83 GLN H 14 GLN H 83 GLN I 14 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 GLN N 83 GLN O 14 GLN P 14 GLN P 83 GLN Q 14 GLN R 14 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 Y 14 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.124534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.118396 restraints weight = 25990.989| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 0.35 r_work: 0.3094 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2715 rms_B_bonded: 4.29 restraints_weight: 0.1250 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0847 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= 0.195 Angle : 0.609 6.174 46416 Z= 0.334 Chirality : 0.038 0.119 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.340 19.398 4512 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.33 % Allowed : 14.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.78 (0.13), residues: 4080 helix: 3.74 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.79 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP E 93 HIS 0.005 0.002 HIS E 128 PHE 0.018 0.003 PHE T 41 TYR 0.014 0.002 TYR V 137 ARG 0.004 0.001 ARG E 79 Details of bonding type rmsd hydrogen bonds : bond 0.05954 ( 2640) hydrogen bonds : angle 3.91850 ( 7920) covalent geometry : bond 0.00408 (34512) covalent geometry : angle 0.60894 (46416) *********************** 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 1039 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 954 time to evaluate : 4.428 Fit side-chains outliers start: 85 outliers final: 74 residues processed: 983 average time/residue: 2.1717 time to fit residues: 2464.8503 Evaluate side-chains 998 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 924 time to evaluate : 4.540 ------------------------------------------------------------------------------- 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 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 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 259 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 264 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 349 optimal weight: 8.9990 chunk 391 optimal weight: 9.9990 chunk 363 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 E 14 GLN E 83 GLN F 14 GLN F 83 GLN G 14 GLN H 14 GLN H 83 GLN I 14 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 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 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.126057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.119897 restraints weight = 26087.215| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 0.35 r_work: 0.3113 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work: 0.2736 rms_B_bonded: 4.34 restraints_weight: 0.1250 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0811 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= 0.147 Angle : 0.549 5.898 46416 Z= 0.300 Chirality : 0.036 0.114 4848 Planarity : 0.004 0.031 6096 Dihedral : 4.240 19.918 4512 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.36 % Allowed : 14.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.10 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP M 93 HIS 0.004 0.001 HIS L 128 PHE 0.015 0.003 PHE V 41 TYR 0.011 0.002 TYR C 137 ARG 0.003 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 2640) hydrogen bonds : angle 3.77638 ( 7920) covalent geometry : bond 0.00305 (34512) covalent geometry : angle 0.54857 (46416) *********************** 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 1081 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 995 time to evaluate : 4.497 Fit side-chains outliers start: 86 outliers final: 82 residues processed: 1011 average time/residue: 2.2572 time to fit residues: 2638.0981 Evaluate side-chains 1061 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 979 time to evaluate : 6.818 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 142 optimal weight: 10.0000 chunk 401 optimal weight: 1.9990 chunk 387 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 284 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN E 83 GLN F 14 GLN G 14 GLN G 83 GLN H 14 GLN H 83 GLN I 14 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 GLN N 83 GLN O 14 GLN P 14 GLN P 83 GLN Q 14 GLN R 14 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 Y 14 GLN Y 83 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.126831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.120668 restraints weight = 26078.441| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 0.35 r_work: 0.3124 rms_B_bonded: 0.74 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 1.43 restraints_weight: 0.2500 r_work: 0.2750 rms_B_bonded: 4.33 restraints_weight: 0.1250 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34512 Z= 0.132 Angle : 0.531 5.693 46416 Z= 0.288 Chirality : 0.035 0.113 4848 Planarity : 0.003 0.033 6096 Dihedral : 4.159 20.044 4512 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.33 % Allowed : 14.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.30 (0.13), residues: 4080 helix: 4.11 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.98 (0.24), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP Y 93 HIS 0.004 0.001 HIS F 128 PHE 0.013 0.002 PHE T 41 TYR 0.010 0.001 TYR N 137 ARG 0.003 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 2640) hydrogen bonds : angle 3.68924 ( 7920) covalent geometry : bond 0.00272 (34512) covalent geometry : angle 0.53060 (46416) ********************** 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 1074 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 989 time to evaluate : 4.434 Fit side-chains REVERT: S 116 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7895 (mt-10) REVERT: W 116 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7903 (mt-10) outliers start: 85 outliers final: 81 residues processed: 999 average time/residue: 2.0314 time to fit residues: 2373.8700 Evaluate side-chains 1065 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 984 time to evaluate : 4.553 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 389 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 306 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 323 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN B 83 GLN C 14 GLN C 83 GLN D 14 GLN E 14 GLN E 83 GLN F 14 GLN G 14 GLN G 83 GLN H 14 GLN H 83 GLN I 14 GLN I 83 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 P 83 GLN Q 14 GLN R 14 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 Y 14 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.124726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.118589 restraints weight = 25944.837| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 0.35 r_work: 0.3096 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2716 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0776 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= 0.192 Angle : 0.622 6.129 46416 Z= 0.341 Chirality : 0.038 0.119 4848 Planarity : 0.004 0.032 6096 Dihedral : 4.312 19.088 4512 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.11 % Allowed : 14.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.81 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP Y 93 HIS 0.005 0.002 HIS M 128 PHE 0.018 0.003 PHE V 41 TYR 0.013 0.002 TYR T 137 ARG 0.004 0.001 ARG S 79 Details of bonding type rmsd hydrogen bonds : bond 0.05910 ( 2640) hydrogen bonds : angle 3.90829 ( 7920) covalent geometry : bond 0.00402 (34512) covalent geometry : angle 0.62159 (46416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45697.42 seconds wall clock time: 797 minutes 28.86 seconds (47848.86 seconds total)