Starting phenix.real_space_refine on Tue Aug 26 05:53:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk9_16093/08_2025/8bk9_16093.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk9_16093/08_2025/8bk9_16093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bk9_16093/08_2025/8bk9_16093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk9_16093/08_2025/8bk9_16093.map" model { file = "/net/cci-nas-00/data/ceres_data/8bk9_16093/08_2025/8bk9_16093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk9_16093/08_2025/8bk9_16093.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 7636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34978 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} 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: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "M" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "N" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "O" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "Q" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "T" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "V" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "W" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "Y" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Time building chain proxies: 6.83, per 1000 atoms: 0.20 Number of scatterers: 34978 At special positions: 0 Unit cell: (132.997, 132.997, 132.997, 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 7636 8.00 N 5928 7.00 C 21216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 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 158 Processing helix chain 'A' and resid 163 through 174 removed outlier: 4.358A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.115A 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 158 Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.372A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.144A 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 158 Processing helix chain 'C' and resid 163 through 174 removed outlier: 4.410A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.191A 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 158 Processing helix chain 'D' and resid 163 through 174 removed outlier: 4.424A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.191A 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 158 Processing helix chain 'E' and resid 163 through 174 removed outlier: 4.356A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.102A 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 158 Processing helix chain 'F' and resid 163 through 174 removed outlier: 4.424A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 4.180A 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 158 Processing helix chain 'G' and resid 163 through 174 removed outlier: 4.360A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.113A 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 158 Processing helix chain 'H' and resid 163 through 174 removed outlier: 4.420A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.186A 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 158 Processing helix chain 'I' and resid 163 through 174 removed outlier: 4.422A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.187A 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 158 Processing helix chain 'J' and resid 163 through 174 removed outlier: 4.409A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.190A 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 158 Processing helix chain 'K' and resid 163 through 174 removed outlier: 4.411A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.191A 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 158 Processing helix chain 'L' and resid 163 through 174 removed outlier: 4.350A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 4.122A 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 158 Processing helix chain 'M' and resid 163 through 174 removed outlier: 4.422A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.187A 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 158 Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.365A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 4.126A 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 158 Processing helix chain 'O' and resid 163 through 174 removed outlier: 4.356A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.111A 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 158 Processing helix chain 'P' and resid 163 through 174 removed outlier: 4.423A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 4.187A 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 158 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 4.359A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.116A 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 158 Processing helix chain 'R' and resid 163 through 174 removed outlier: 4.421A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 4.185A 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 158 Processing helix chain 'S' and resid 163 through 174 removed outlier: 4.352A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.130A 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 158 Processing helix chain 'T' and resid 163 through 174 removed outlier: 4.369A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 4.140A 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 158 Processing helix chain 'V' and resid 163 through 174 removed outlier: 4.423A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 4.188A 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 158 Processing helix chain 'W' and resid 163 through 174 removed outlier: 4.360A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.115A 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 158 Processing helix chain 'X' and resid 163 through 174 removed outlier: 4.350A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 4.121A 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 158 Processing helix chain 'Y' and resid 163 through 174 removed outlier: 4.423A pdb=" N GLU Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR Y 168 " --> pdb=" O GLY Y 164 " (cutoff:3.500A) 2616 hydrogen bonds defined for protein. 7848 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: 5.68 Time building geometry restraints manager: 2.74 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: 11480 1.34 - 1.46: 4680 1.46 - 1.57: 18040 1.57 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34512 Sorted by residual: bond pdb=" CB GLU G 62 " pdb=" CG GLU G 62 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.42e+00 bond pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CG GLU E 62 " pdb=" CD GLU E 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CB GLN W 75 " pdb=" CG GLN W 75 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.45e-01 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 45594 1.67 - 3.34: 597 3.34 - 5.01: 147 5.01 - 6.68: 54 6.68 - 8.36: 24 Bond angle restraints: 46416 Sorted by residual: angle pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " pdb=" CD GLU E 62 " ideal model delta sigma weight residual 112.60 118.87 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CB GLU B 62 " pdb=" CG GLU B 62 " pdb=" CD GLU B 62 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.70e+00 3.46e-01 1.35e+01 angle pdb=" CB GLU G 62 " pdb=" CG GLU G 62 " pdb=" CD GLU G 62 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.70e+00 3.46e-01 1.33e+01 angle pdb=" C TRP X 93 " pdb=" N GLU X 94 " pdb=" CA GLU X 94 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.76e+00 angle pdb=" C TRP P 93 " pdb=" N GLU P 94 " pdb=" CA GLU P 94 " ideal model delta sigma weight residual 121.54 127.17 -5.63 1.91e+00 2.74e-01 8.70e+00 ... (remaining 46411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 18487 17.78 - 35.56: 1724 35.56 - 53.34: 525 53.34 - 71.13: 216 71.13 - 88.91: 48 Dihedral angle restraints: 21000 sinusoidal: 8760 harmonic: 12240 Sorted by residual: 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 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TRP P 93 " pdb=" C TRP P 93 " pdb=" N GLU P 94 " pdb=" CA GLU P 94 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA TRP T 93 " pdb=" C TRP T 93 " pdb=" N GLU T 94 " pdb=" CA GLU T 94 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2861 0.024 - 0.048: 1184 0.048 - 0.073: 518 0.073 - 0.097: 112 0.097 - 0.121: 173 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO G 127 " pdb=" N PRO G 127 " pdb=" C PRO G 127 " pdb=" CB PRO G 127 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO M 127 " pdb=" N PRO M 127 " pdb=" C PRO M 127 " pdb=" CB PRO M 127 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 4845 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 94 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C GLU N 94 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU N 94 " 0.010 2.00e-02 2.50e+03 pdb=" N SER N 95 " 0.009 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 1.49e-02 2.23e+00 pdb=" C GLU T 94 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU T 94 " 0.010 2.00e-02 2.50e+03 pdb=" N SER T 95 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU M 94 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C GLU M 94 " -0.026 2.00e-02 2.50e+03 pdb=" O GLU M 94 " 0.010 2.00e-02 2.50e+03 pdb=" N SER M 95 " 0.009 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5123 2.76 - 3.29: 35326 3.29 - 3.83: 67743 3.83 - 4.36: 78067 4.36 - 4.90: 131985 Nonbonded interactions: 318244 Sorted by model distance: nonbonded pdb=" O ALA R 163 " pdb=" O HOH R 201 " model vdw 2.222 3.040 nonbonded pdb=" O ALA I 163 " pdb=" O HOH I 201 " model vdw 2.222 3.040 nonbonded pdb=" O ALA D 163 " pdb=" O HOH D 301 " model vdw 2.222 3.040 nonbonded pdb=" O ALA C 163 " pdb=" O HOH C 301 " model vdw 2.222 3.040 nonbonded pdb=" O ALA J 163 " pdb=" O HOH J 201 " model vdw 2.222 3.040 ... (remaining 318239 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 176) 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' 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' selection = (chain 'V' and resid 5 through 176) 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: 0.010 Normalize map: mean=0, sd=1: 3.440 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.100 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 0.047 34512 Z= 0.155 Angle : 0.606 8.356 46416 Z= 0.322 Chirality : 0.037 0.121 4848 Planarity : 0.004 0.025 6096 Dihedral : 17.004 88.907 13080 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.49 % Allowed : 8.88 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.72 (0.13), residues: 4080 helix: 3.61 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 90 TYR 0.015 0.002 TYR V 137 PHE 0.017 0.003 PHE D 41 TRP 0.009 0.002 TRP E 93 HIS 0.004 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00326 (34512) covalent geometry : angle 0.60609 (46416) hydrogen bonds : bond 0.08042 ( 2616) hydrogen bonds : angle 3.75047 ( 7848) *********************** 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 764 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 746 time to evaluate : 1.389 Fit side-chains outliers start: 18 outliers final: 0 residues processed: 758 average time/residue: 0.9549 time to fit residues: 812.1513 Evaluate side-chains 725 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 60 HIS B 83 GLN C 60 HIS C 83 GLN D 83 GLN E 60 HIS E 83 GLN F 83 GLN G 60 HIS G 83 GLN H 83 GLN I 60 HIS I 83 GLN J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.131246 restraints weight = 29396.114| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 0.50 r_work: 0.3355 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.3012 rms_B_bonded: 4.67 restraints_weight: 0.1250 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34512 Z= 0.099 Angle : 0.450 5.743 46416 Z= 0.243 Chirality : 0.033 0.113 4848 Planarity : 0.003 0.021 6096 Dihedral : 3.753 19.992 4512 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.16 % Allowed : 9.24 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.56 (0.13), residues: 4080 helix: 4.26 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 79 TYR 0.012 0.001 TYR V 137 PHE 0.011 0.002 PHE B 41 TRP 0.008 0.002 TRP E 93 HIS 0.002 0.001 HIS V 118 Details of bonding type rmsd covalent geometry : bond 0.00204 (34512) covalent geometry : angle 0.45039 (46416) hydrogen bonds : bond 0.04030 ( 2616) hydrogen bonds : angle 3.16773 ( 7848) *********************** 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 737 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 731 time to evaluate : 1.125 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 731 average time/residue: 0.9119 time to fit residues: 753.9287 Evaluate side-chains 709 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 709 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 342 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 313 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 370 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 60 HIS B 83 GLN C 60 HIS C 83 GLN D 60 HIS D 83 GLN E 60 HIS E 83 GLN F 60 HIS F 83 GLN G 60 HIS G 83 GLN H 60 HIS H 83 GLN I 60 HIS I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126521 restraints weight = 28943.818| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 0.51 r_work: 0.3290 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.2939 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 34512 Z= 0.157 Angle : 0.550 5.982 46416 Z= 0.299 Chirality : 0.036 0.118 4848 Planarity : 0.004 0.026 6096 Dihedral : 3.925 19.766 4512 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.15 % Allowed : 8.83 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.35 (0.13), residues: 4080 helix: 4.10 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.08 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 63 TYR 0.014 0.002 TYR V 137 PHE 0.018 0.003 PHE K 41 TRP 0.009 0.002 TRP E 93 HIS 0.004 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00341 (34512) covalent geometry : angle 0.55001 (46416) hydrogen bonds : bond 0.05461 ( 2616) hydrogen bonds : angle 3.44597 ( 7848) *********************** 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 817 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 775 time to evaluate : 1.148 Fit side-chains REVERT: C 62 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: I 62 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: K 62 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: L 62 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: O 62 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: Q 62 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8362 (mp0) outliers start: 42 outliers final: 0 residues processed: 787 average time/residue: 0.9469 time to fit residues: 836.8813 Evaluate side-chains 733 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 727 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain O residue 62 GLU Chi-restraints excluded: chain Q residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 241 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 404 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 272 optimal weight: 0.0170 chunk 64 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128756 restraints weight = 28807.217| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.50 r_work: 0.3321 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2975 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34512 Z= 0.119 Angle : 0.491 5.573 46416 Z= 0.266 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.018 6096 Dihedral : 3.814 20.004 4512 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.36 % Allowed : 9.21 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.57 (0.13), residues: 4080 helix: 4.26 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.16 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 63 TYR 0.011 0.001 TYR W 137 PHE 0.014 0.002 PHE Y 41 TRP 0.009 0.002 TRP C 93 HIS 0.003 0.001 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00253 (34512) covalent geometry : angle 0.49060 (46416) hydrogen bonds : bond 0.04631 ( 2616) hydrogen bonds : angle 3.28229 ( 7848) *********************** 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 750 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 737 time to evaluate : 1.108 Fit side-chains REVERT: A 62 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8430 (mp0) REVERT: C 62 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: D 62 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: F 62 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: H 62 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: I 62 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: J 62 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: L 62 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: M 62 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: Q 62 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8374 (mp0) outliers start: 13 outliers final: 0 residues processed: 737 average time/residue: 0.9621 time to fit residues: 794.8156 Evaluate side-chains 712 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 702 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain Q residue 62 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 397 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 369 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 60 HIS B 83 GLN C 83 GLN D 83 GLN E 60 HIS E 83 GLN F 83 GLN G 60 HIS G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125846 restraints weight = 28967.524| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 0.50 r_work: 0.3284 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.2932 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34512 Z= 0.183 Angle : 0.591 6.168 46416 Z= 0.321 Chirality : 0.037 0.122 4848 Planarity : 0.004 0.029 6096 Dihedral : 3.978 19.476 4512 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.07 % Allowed : 9.13 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.09 (0.13), residues: 4080 helix: 3.89 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.10 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.016 0.002 TYR W 137 PHE 0.021 0.003 PHE N 41 TRP 0.009 0.002 TRP Q 93 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00405 (34512) covalent geometry : angle 0.59065 (46416) hydrogen bonds : bond 0.05769 ( 2616) hydrogen bonds : angle 3.53913 ( 7848) *********************** 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 759 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 720 time to evaluate : 0.910 Fit side-chains outliers start: 39 outliers final: 0 residues processed: 720 average time/residue: 0.9855 time to fit residues: 794.7155 Evaluate side-chains 692 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 39 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 367 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 60 HIS C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 60 HIS I 83 GLN J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.125779 restraints weight = 28817.987| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 0.51 r_work: 0.3278 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.2927 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34512 Z= 0.177 Angle : 0.595 6.298 46416 Z= 0.323 Chirality : 0.037 0.122 4848 Planarity : 0.004 0.029 6096 Dihedral : 3.992 19.628 4512 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.16 % Allowed : 9.38 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.97 (0.13), residues: 4080 helix: 3.81 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.06 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.016 0.002 TYR T 137 PHE 0.022 0.003 PHE H 41 TRP 0.009 0.002 TRP J 93 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00390 (34512) covalent geometry : angle 0.59451 (46416) hydrogen bonds : bond 0.05687 ( 2616) hydrogen bonds : angle 3.52702 ( 7848) *********************** 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 726 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 720 time to evaluate : 1.018 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 720 average time/residue: 0.9387 time to fit residues: 758.2150 Evaluate side-chains 724 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 175 optimal weight: 9.9990 chunk 341 optimal weight: 0.2980 chunk 391 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 60 HIS C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 60 HIS I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.133193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126699 restraints weight = 29025.266| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 0.50 r_work: 0.3293 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2942 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34512 Z= 0.150 Angle : 0.558 6.042 46416 Z= 0.303 Chirality : 0.036 0.118 4848 Planarity : 0.003 0.022 6096 Dihedral : 3.946 20.009 4512 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.14 % Allowed : 10.58 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.19 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.11 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 63 TYR 0.015 0.002 TYR T 137 PHE 0.018 0.003 PHE D 41 TRP 0.010 0.002 TRP M 93 HIS 0.004 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00327 (34512) covalent geometry : angle 0.55783 (46416) hydrogen bonds : bond 0.05334 ( 2616) hydrogen bonds : angle 3.45004 ( 7848) *********************** 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 716 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 711 time to evaluate : 1.421 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 711 average time/residue: 1.0014 time to fit residues: 797.4418 Evaluate side-chains 694 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 381 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 321 optimal weight: 1.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 60 HIS C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 60 HIS I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 60 HIS L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125941 restraints weight = 29057.519| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 0.50 r_work: 0.3284 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 1.54 restraints_weight: 0.2500 r_work: 0.2933 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34512 Z= 0.167 Angle : 0.589 6.232 46416 Z= 0.319 Chirality : 0.037 0.120 4848 Planarity : 0.004 0.025 6096 Dihedral : 3.988 19.968 4512 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.19 % Allowed : 10.39 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.99 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 1.08 (0.25), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 63 TYR 0.015 0.002 TYR T 137 PHE 0.020 0.003 PHE K 41 TRP 0.009 0.002 TRP J 93 HIS 0.004 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00367 (34512) covalent geometry : angle 0.58875 (46416) hydrogen bonds : bond 0.05601 ( 2616) hydrogen bonds : angle 3.50671 ( 7848) *********************** 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 706 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 699 time to evaluate : 1.418 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 699 average time/residue: 0.9208 time to fit residues: 722.5440 Evaluate side-chains 675 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 177 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN B 83 GLN C 83 GLN D 60 HIS D 83 GLN E 83 GLN F 60 HIS F 83 GLN G 83 GLN H 60 HIS H 83 GLN I 83 GLN J 60 HIS J 83 GLN K 83 GLN L 83 GLN M 60 HIS M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124716 restraints weight = 28882.414| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 0.50 r_work: 0.3267 rms_B_bonded: 0.81 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.2916 rms_B_bonded: 4.60 restraints_weight: 0.1250 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34512 Z= 0.239 Angle : 0.687 6.716 46416 Z= 0.372 Chirality : 0.040 0.131 4848 Planarity : 0.005 0.030 6096 Dihedral : 4.093 19.253 4512 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.63 % Allowed : 9.92 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.45 (0.13), residues: 4080 helix: 3.44 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.90 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 63 TYR 0.018 0.003 TYR G 137 PHE 0.024 0.004 PHE N 41 TRP 0.008 0.002 TRP L 93 HIS 0.005 0.002 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00528 (34512) covalent geometry : angle 0.68745 (46416) hydrogen bonds : bond 0.06349 ( 2616) hydrogen bonds : angle 3.66748 ( 7848) *********************** 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 737 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 714 time to evaluate : 1.109 Fit side-chains outliers start: 23 outliers final: 0 residues processed: 714 average time/residue: 1.0108 time to fit residues: 809.3985 Evaluate side-chains 686 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 686 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 320 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 397 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.132046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125525 restraints weight = 29031.572| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.50 r_work: 0.3275 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2924 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34512 Z= 0.197 Angle : 0.632 6.360 46416 Z= 0.342 Chirality : 0.038 0.127 4848 Planarity : 0.004 0.026 6096 Dihedral : 4.069 20.052 4512 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.16 % Allowed : 10.77 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.58 (0.13), residues: 4080 helix: 3.54 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.91 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 63 TYR 0.018 0.002 TYR L 137 PHE 0.024 0.003 PHE G 41 TRP 0.009 0.002 TRP F 93 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00434 (34512) covalent geometry : angle 0.63231 (46416) hydrogen bonds : bond 0.05900 ( 2616) hydrogen bonds : angle 3.59191 ( 7848) ********************** 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 703 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 697 time to evaluate : 1.332 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 697 average time/residue: 1.0223 time to fit residues: 799.1570 Evaluate side-chains 676 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 676 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 272 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN B 83 GLN C 83 GLN D 83 GLN E 83 GLN F 83 GLN G 83 GLN H 83 GLN I 83 GLN J 83 GLN K 83 GLN L 83 GLN M 83 GLN N 83 GLN O 83 GLN P 83 GLN Q 83 GLN R 83 GLN S 83 GLN T 83 GLN V 83 GLN W 83 GLN X 83 GLN Y 83 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125109 restraints weight = 28926.448| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.50 r_work: 0.3273 rms_B_bonded: 0.82 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 1.53 restraints_weight: 0.2500 r_work: 0.2922 rms_B_bonded: 4.60 restraints_weight: 0.1250 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34512 Z= 0.213 Angle : 0.667 6.416 46416 Z= 0.360 Chirality : 0.039 0.127 4848 Planarity : 0.004 0.028 6096 Dihedral : 4.087 19.843 4512 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.25 % Allowed : 11.16 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.42 (0.13), residues: 4080 helix: 3.42 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.87 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.019 0.002 TYR R 137 PHE 0.023 0.004 PHE B 41 TRP 0.009 0.002 TRP B 93 HIS 0.005 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00471 (34512) covalent geometry : angle 0.66749 (46416) hydrogen bonds : bond 0.06089 ( 2616) hydrogen bonds : angle 3.62618 ( 7848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17031.33 seconds wall clock time: 289 minutes 23.98 seconds (17363.98 seconds total)