Starting phenix.real_space_refine on Fri Mar 6 22:46:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bka_16094/03_2026/8bka_16094.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bka_16094/03_2026/8bka_16094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bka_16094/03_2026/8bka_16094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bka_16094/03_2026/8bka_16094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bka_16094/03_2026/8bka_16094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bka_16094/03_2026/8bka_16094.map" } resolution = 2.7 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= 0.004 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 8751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36093 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: "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: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "E" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "F" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "J" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "K" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Classifications: {'water': 98} Link IDs: {None: 97} Chain: "M" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "P" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "Q" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "R" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "S" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "T" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "V" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "W" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "X" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "Y" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Time building chain proxies: 9.32, per 1000 atoms: 0.26 Number of scatterers: 36093 At special positions: 0 Unit cell: (134.25, 134.25, 134.25, 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 8751 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 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: 0.81 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: 4.118A pdb=" N GLU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.827A 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: 4.115A pdb=" N GLU B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.821A 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: 4.142A pdb=" N GLU C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.852A 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: 4.121A pdb=" N GLU D 167 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 3.822A 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: 4.111A pdb=" N GLU E 167 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 3.819A 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: 4.113A pdb=" N GLU F 167 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.827A 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: 4.134A pdb=" N GLU G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 3.835A 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: 4.118A pdb=" N GLU H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 3.819A 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: 4.136A pdb=" N GLU I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 3.850A 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: 4.132A pdb=" N GLU J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 3.842A 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: 4.151A pdb=" N GLU K 167 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 3.850A 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: 4.139A pdb=" N GLU L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) removed outlier: 3.845A 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: 4.131A pdb=" N GLU M 167 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.836A 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: 4.116A pdb=" N GLU N 167 " --> pdb=" O ALA N 163 " (cutoff:3.500A) removed outlier: 3.826A 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: 4.149A pdb=" N GLU O 167 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 3.845A 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: 4.152A pdb=" N GLU P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.826A 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: 4.119A pdb=" N GLU Q 167 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 3.828A 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: 4.137A pdb=" N GLU R 167 " --> pdb=" O ALA R 163 " (cutoff:3.500A) removed outlier: 3.839A 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: 4.114A pdb=" N GLU S 167 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 3.821A 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: 4.136A pdb=" N GLU T 167 " --> pdb=" O ALA T 163 " (cutoff:3.500A) removed outlier: 3.834A 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: 4.109A pdb=" N GLU V 167 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 3.827A 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: 4.141A pdb=" N GLU W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 3.850A 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: 4.134A pdb=" N GLU X 167 " --> pdb=" O ALA X 163 " (cutoff:3.500A) removed outlier: 3.835A 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: 4.116A pdb=" N GLU Y 167 " --> pdb=" O ALA Y 163 " (cutoff:3.500A) removed outlier: 3.821A 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: 7.53 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11475 1.34 - 1.46: 4663 1.46 - 1.57: 18062 1.57 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34512 Sorted by residual: bond pdb=" C TYR W 136 " pdb=" N TYR W 137 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.71e-01 bond pdb=" C TYR H 136 " pdb=" N TYR H 137 " ideal model delta sigma weight residual 1.332 1.319 0.014 1.40e-02 5.10e+03 9.30e-01 bond pdb=" C TYR S 136 " pdb=" N TYR S 137 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 9.16e-01 bond pdb=" C TYR B 136 " pdb=" N TYR B 137 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 8.95e-01 bond pdb=" C TYR D 136 " pdb=" N TYR D 137 " ideal model delta sigma weight residual 1.332 1.319 0.013 1.40e-02 5.10e+03 8.87e-01 ... (remaining 34507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 45202 1.42 - 2.84: 955 2.84 - 4.26: 131 4.26 - 5.68: 103 5.68 - 7.09: 25 Bond angle restraints: 46416 Sorted by residual: angle pdb=" C TYR I 136 " pdb=" N TYR I 137 " pdb=" CA TYR I 137 " ideal model delta sigma weight residual 122.08 117.05 5.03 1.53e+00 4.27e-01 1.08e+01 angle pdb=" C TYR G 136 " pdb=" N TYR G 137 " pdb=" CA TYR G 137 " ideal model delta sigma weight residual 122.08 117.13 4.95 1.53e+00 4.27e-01 1.05e+01 angle pdb=" C TYR M 136 " pdb=" N TYR M 137 " pdb=" CA TYR M 137 " ideal model delta sigma weight residual 122.08 117.23 4.85 1.53e+00 4.27e-01 1.01e+01 angle pdb=" C TRP H 93 " pdb=" N GLU H 94 " pdb=" CA GLU H 94 " ideal model delta sigma weight residual 121.54 127.02 -5.48 1.91e+00 2.74e-01 8.22e+00 angle pdb=" C TRP O 93 " pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.01e+00 ... (remaining 46411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 18064 17.81 - 35.62: 1998 35.62 - 53.42: 537 53.42 - 71.23: 287 71.23 - 89.04: 114 Dihedral angle restraints: 21000 sinusoidal: 8760 harmonic: 12240 Sorted by residual: dihedral pdb=" CA ASP V 92 " pdb=" CB ASP V 92 " pdb=" CG ASP V 92 " pdb=" OD1 ASP V 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.85 59.85 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP T 92 " pdb=" CB ASP T 92 " pdb=" CG ASP T 92 " pdb=" OD1 ASP T 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.81 59.81 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP R 92 " pdb=" CB ASP R 92 " pdb=" CG ASP R 92 " pdb=" OD1 ASP R 92 " ideal model delta sinusoidal sigma weight residual -30.00 -89.79 59.79 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2975 0.027 - 0.055: 1289 0.055 - 0.082: 340 0.082 - 0.110: 172 0.110 - 0.137: 72 Chirality restraints: 4848 Sorted by residual: chirality pdb=" CG LEU M 72 " pdb=" CB LEU M 72 " pdb=" CD1 LEU M 72 " pdb=" CD2 LEU M 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CG LEU S 72 " pdb=" CB LEU S 72 " pdb=" CD1 LEU S 72 " pdb=" CD2 LEU S 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CG LEU Y 72 " pdb=" CB LEU Y 72 " pdb=" CD1 LEU Y 72 " pdb=" CD2 LEU Y 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 4845 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Y 87 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO Y 88 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO Y 88 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO Y 88 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 83 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" CD GLN F 83 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN F 83 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN F 83 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO F 88 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.019 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1588 2.73 - 3.27: 35825 3.27 - 3.81: 70662 3.81 - 4.36: 85364 4.36 - 4.90: 135607 Nonbonded interactions: 329046 Sorted by model distance: nonbonded pdb=" OH TYR H 34 " pdb=" OE1 GLU H 107 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR A 34 " pdb=" OE1 GLU A 107 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR S 34 " pdb=" OE1 GLU S 107 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR C 34 " pdb=" OE1 GLU C 107 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR L 34 " pdb=" OE1 GLU L 107 " model vdw 2.188 3.040 ... (remaining 329041 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: 0.02 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' 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' 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: 4.940 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: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.660 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 0.022 34512 Z= 0.138 Angle : 0.565 7.094 46416 Z= 0.296 Chirality : 0.037 0.137 4848 Planarity : 0.004 0.034 6096 Dihedral : 18.734 89.041 13080 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.64 % Allowed : 20.34 % Favored : 78.02 % 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 are not related in a simple way. whole: 4.05 (0.13), residues: 4080 helix: 3.41 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -0.17 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 156 TYR 0.013 0.001 TYR B 137 PHE 0.015 0.002 PHE J 41 TRP 0.007 0.002 TRP S 93 HIS 0.003 0.001 HIS K 173 Details of bonding type rmsd covalent geometry : bond 0.00296 (34512) covalent geometry : angle 0.56452 (46416) hydrogen bonds : bond 0.09397 ( 2640) hydrogen bonds : angle 4.57660 ( 7920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 703 time to evaluate : 1.347 Fit side-chains REVERT: A 89 ASP cc_start: 0.7509 (m-30) cc_final: 0.7278 (m-30) REVERT: C 89 ASP cc_start: 0.7501 (m-30) cc_final: 0.7260 (m-30) REVERT: C 92 ASP cc_start: 0.8355 (t70) cc_final: 0.8133 (t70) REVERT: C 131 ASP cc_start: 0.8571 (t70) cc_final: 0.8355 (t70) REVERT: G 63 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7651 (ttm170) REVERT: G 89 ASP cc_start: 0.7542 (m-30) cc_final: 0.7293 (m-30) REVERT: G 92 ASP cc_start: 0.8374 (t70) cc_final: 0.8149 (t70) REVERT: H 89 ASP cc_start: 0.7566 (m-30) cc_final: 0.7331 (m-30) REVERT: H 92 ASP cc_start: 0.8311 (t70) cc_final: 0.8088 (t70) REVERT: H 131 ASP cc_start: 0.8566 (t70) cc_final: 0.8359 (t70) REVERT: I 89 ASP cc_start: 0.7496 (m-30) cc_final: 0.7253 (m-30) REVERT: I 92 ASP cc_start: 0.8378 (t70) cc_final: 0.8142 (t70) REVERT: J 83 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8620 (mm-40) REVERT: K 83 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8617 (mm-40) REVERT: K 89 ASP cc_start: 0.7576 (m-30) cc_final: 0.7338 (m-30) REVERT: K 92 ASP cc_start: 0.8302 (t70) cc_final: 0.8068 (t70) REVERT: L 89 ASP cc_start: 0.7491 (m-30) cc_final: 0.7258 (m-30) REVERT: M 89 ASP cc_start: 0.7539 (m-30) cc_final: 0.7306 (m-30) REVERT: M 92 ASP cc_start: 0.8330 (t70) cc_final: 0.8099 (t70) REVERT: N 89 ASP cc_start: 0.7498 (m-30) cc_final: 0.7237 (m-30) REVERT: N 92 ASP cc_start: 0.8282 (t70) cc_final: 0.7851 (t0) REVERT: O 89 ASP cc_start: 0.7519 (m-30) cc_final: 0.7280 (m-30) REVERT: P 89 ASP cc_start: 0.7442 (m-30) cc_final: 0.7180 (m-30) REVERT: Q 89 ASP cc_start: 0.7492 (m-30) cc_final: 0.7239 (m-30) REVERT: R 89 ASP cc_start: 0.7436 (m-30) cc_final: 0.7173 (m-30) REVERT: S 89 ASP cc_start: 0.7383 (m-30) cc_final: 0.7139 (m-30) REVERT: V 89 ASP cc_start: 0.7508 (m-30) cc_final: 0.7279 (m-30) REVERT: W 89 ASP cc_start: 0.7408 (m-30) cc_final: 0.7158 (m-30) REVERT: W 92 ASP cc_start: 0.8308 (t70) cc_final: 0.8073 (t70) REVERT: W 131 ASP cc_start: 0.8604 (t70) cc_final: 0.8398 (t70) REVERT: X 83 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8651 (mm-40) REVERT: X 89 ASP cc_start: 0.7479 (m-30) cc_final: 0.7236 (m-30) REVERT: Y 89 ASP cc_start: 0.7457 (m-30) cc_final: 0.7189 (m-30) outliers start: 60 outliers final: 30 residues processed: 751 average time/residue: 0.9296 time to fit residues: 804.6347 Evaluate side-chains 667 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 636 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN B 154 ASN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 11 ASN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN Q 75 GLN Q 154 ASN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN X 154 ASN Y 14 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.101629 restraints weight = 38792.185| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.24 r_work: 0.2897 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34512 Z= 0.116 Angle : 0.459 5.590 46416 Z= 0.242 Chirality : 0.034 0.116 4848 Planarity : 0.003 0.029 6096 Dihedral : 4.478 57.826 4556 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.25 % Allowed : 17.46 % Favored : 78.29 % 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 are not related in a simple way. whole: 5.05 (0.13), residues: 4080 helix: 4.16 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.01 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 90 TYR 0.013 0.001 TYR I 137 PHE 0.013 0.002 PHE W 41 TRP 0.008 0.002 TRP W 93 HIS 0.003 0.001 HIS S 173 Details of bonding type rmsd covalent geometry : bond 0.00261 (34512) covalent geometry : angle 0.45877 (46416) hydrogen bonds : bond 0.03730 ( 2640) hydrogen bonds : angle 3.27113 ( 7920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 906 time to evaluate : 1.670 Fit side-chains REVERT: A 63 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7780 (ttm170) REVERT: A 89 ASP cc_start: 0.7759 (m-30) cc_final: 0.7449 (m-30) REVERT: A 143 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8167 (ttmt) REVERT: B 63 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7857 (ttm170) REVERT: B 89 ASP cc_start: 0.7831 (m-30) cc_final: 0.7511 (m-30) REVERT: B 143 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8166 (ttmt) REVERT: C 63 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7862 (ttm170) REVERT: C 89 ASP cc_start: 0.7814 (m-30) cc_final: 0.7489 (m-30) REVERT: C 143 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8161 (ttmt) REVERT: D 89 ASP cc_start: 0.7723 (m-30) cc_final: 0.7403 (m-30) REVERT: D 143 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8215 (ttmt) REVERT: E 89 ASP cc_start: 0.7657 (m-30) cc_final: 0.7322 (m-30) REVERT: E 143 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8189 (ttmt) REVERT: F 89 ASP cc_start: 0.7837 (m-30) cc_final: 0.7532 (m-30) REVERT: F 143 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: G 89 ASP cc_start: 0.7774 (m-30) cc_final: 0.7454 (m-30) REVERT: G 143 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8162 (ttmt) REVERT: H 89 ASP cc_start: 0.7835 (m-30) cc_final: 0.7538 (m-30) REVERT: H 143 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8162 (ttmt) REVERT: I 63 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: I 89 ASP cc_start: 0.7822 (m-30) cc_final: 0.7492 (m-30) REVERT: I 143 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8163 (ttmt) REVERT: J 143 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8174 (ttmt) REVERT: K 89 ASP cc_start: 0.7881 (m-30) cc_final: 0.7575 (m-30) REVERT: K 143 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8168 (ttmt) REVERT: L 63 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: L 89 ASP cc_start: 0.7759 (m-30) cc_final: 0.7449 (m-30) REVERT: L 143 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: M 89 ASP cc_start: 0.7778 (m-30) cc_final: 0.7483 (m-30) REVERT: M 143 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8170 (ttmt) REVERT: N 89 ASP cc_start: 0.7769 (m-30) cc_final: 0.7444 (m-30) REVERT: N 143 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8173 (ttmt) REVERT: O 89 ASP cc_start: 0.7752 (m-30) cc_final: 0.7441 (m-30) REVERT: O 143 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8170 (ttmt) REVERT: P 89 ASP cc_start: 0.7788 (m-30) cc_final: 0.7454 (m-30) REVERT: P 143 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8177 (ttmt) REVERT: Q 89 ASP cc_start: 0.7765 (m-30) cc_final: 0.7441 (m-30) REVERT: Q 143 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8197 (ttmt) REVERT: R 89 ASP cc_start: 0.7721 (m-30) cc_final: 0.7398 (m-30) REVERT: R 143 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8159 (ttmt) REVERT: S 89 ASP cc_start: 0.7631 (m-30) cc_final: 0.7290 (m-30) REVERT: S 143 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8184 (ttmt) REVERT: T 89 ASP cc_start: 0.7826 (m-30) cc_final: 0.7495 (m-30) REVERT: T 143 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8175 (ttmt) REVERT: V 89 ASP cc_start: 0.7806 (m-30) cc_final: 0.7510 (m-30) REVERT: V 143 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8180 (ttmt) REVERT: W 89 ASP cc_start: 0.7596 (m-30) cc_final: 0.7269 (m-30) REVERT: W 143 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8183 (ttmt) REVERT: X 89 ASP cc_start: 0.7785 (m-30) cc_final: 0.7471 (m-30) REVERT: X 143 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8217 (ttmt) REVERT: Y 89 ASP cc_start: 0.7770 (m-30) cc_final: 0.7432 (m-30) REVERT: Y 143 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8183 (ttmt) outliers start: 155 outliers final: 25 residues processed: 1013 average time/residue: 1.0133 time to fit residues: 1171.6023 Evaluate side-chains 769 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 715 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 122 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 258 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 289 optimal weight: 7.9990 chunk 380 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 11 ASN O 14 GLN P 14 GLN Q 14 GLN Q 75 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 11 ASN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.097205 restraints weight = 39349.680| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.22 r_work: 0.2836 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 34512 Z= 0.253 Angle : 0.596 6.922 46416 Z= 0.305 Chirality : 0.041 0.138 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.225 15.865 4512 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.43 % Allowed : 15.87 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.60 (0.13), residues: 4080 helix: 3.75 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.25 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 76 TYR 0.016 0.002 TYR Q 137 PHE 0.018 0.002 PHE W 41 TRP 0.010 0.003 TRP O 93 HIS 0.003 0.001 HIS X 65 Details of bonding type rmsd covalent geometry : bond 0.00594 (34512) covalent geometry : angle 0.59648 (46416) hydrogen bonds : bond 0.05283 ( 2640) hydrogen bonds : angle 3.57586 ( 7920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 772 time to evaluate : 1.527 Fit side-chains REVERT: A 63 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7928 (ttm170) REVERT: A 89 ASP cc_start: 0.7746 (m-30) cc_final: 0.7328 (m-30) REVERT: A 147 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: B 63 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: B 83 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8684 (mm110) REVERT: B 89 ASP cc_start: 0.7760 (m-30) cc_final: 0.7365 (m-30) REVERT: C 63 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: C 89 ASP cc_start: 0.7761 (m-30) cc_final: 0.7362 (m-30) REVERT: C 92 ASP cc_start: 0.8451 (t70) cc_final: 0.8185 (t70) REVERT: C 147 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: D 63 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: D 89 ASP cc_start: 0.7701 (m-30) cc_final: 0.7295 (m-30) REVERT: E 63 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: E 89 ASP cc_start: 0.7608 (m-30) cc_final: 0.7192 (m-30) REVERT: F 63 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: F 89 ASP cc_start: 0.7779 (m-30) cc_final: 0.7401 (m-30) REVERT: F 143 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8230 (ttmt) REVERT: F 147 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: G 63 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7851 (ttm170) REVERT: G 89 ASP cc_start: 0.7766 (m-30) cc_final: 0.7362 (m-30) REVERT: G 92 ASP cc_start: 0.8442 (t70) cc_final: 0.8182 (t70) REVERT: G 143 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8215 (ttmt) REVERT: H 63 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7918 (ttm170) REVERT: H 89 ASP cc_start: 0.7797 (m-30) cc_final: 0.7423 (m-30) REVERT: H 92 ASP cc_start: 0.8427 (t70) cc_final: 0.8166 (t70) REVERT: I 63 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: I 89 ASP cc_start: 0.7756 (m-30) cc_final: 0.7356 (m-30) REVERT: I 92 ASP cc_start: 0.8445 (t70) cc_final: 0.8160 (t70) REVERT: I 143 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8228 (ttmt) REVERT: J 63 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7900 (ttm170) REVERT: J 83 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8686 (mm110) REVERT: J 89 ASP cc_start: 0.7783 (m-30) cc_final: 0.7435 (m-30) REVERT: K 83 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8676 (mm110) REVERT: K 89 ASP cc_start: 0.7838 (m-30) cc_final: 0.7453 (m-30) REVERT: K 92 ASP cc_start: 0.8431 (t70) cc_final: 0.8163 (t70) REVERT: K 147 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: L 63 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7920 (ttm170) REVERT: L 89 ASP cc_start: 0.7767 (m-30) cc_final: 0.7356 (m-30) REVERT: L 143 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8225 (ttmt) REVERT: M 63 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: M 89 ASP cc_start: 0.7754 (m-30) cc_final: 0.7370 (m-30) REVERT: M 92 ASP cc_start: 0.8440 (t70) cc_final: 0.8170 (t70) REVERT: N 89 ASP cc_start: 0.7748 (m-30) cc_final: 0.7342 (m-30) REVERT: O 89 ASP cc_start: 0.7738 (m-30) cc_final: 0.7338 (m-30) REVERT: O 143 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: O 147 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: P 89 ASP cc_start: 0.7759 (m-30) cc_final: 0.7352 (m-30) REVERT: P 147 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: Q 89 ASP cc_start: 0.7817 (m-30) cc_final: 0.7407 (m-30) REVERT: Q 143 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8240 (ttmt) REVERT: Q 147 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: R 70 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9106 (mtm) REVERT: R 89 ASP cc_start: 0.7704 (m-30) cc_final: 0.7287 (m-30) REVERT: S 89 ASP cc_start: 0.7595 (m-30) cc_final: 0.7168 (m-30) REVERT: S 147 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: T 89 ASP cc_start: 0.7770 (m-30) cc_final: 0.7358 (m-30) REVERT: V 89 ASP cc_start: 0.7775 (m-30) cc_final: 0.7396 (m-30) REVERT: V 143 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8216 (ttmt) REVERT: V 147 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: W 89 ASP cc_start: 0.7573 (m-30) cc_final: 0.7154 (m-30) REVERT: W 92 ASP cc_start: 0.8428 (t70) cc_final: 0.8171 (t70) REVERT: W 147 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: X 83 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8695 (mm110) REVERT: X 89 ASP cc_start: 0.7768 (m-30) cc_final: 0.7352 (m-30) REVERT: X 143 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: X 147 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: Y 89 ASP cc_start: 0.7718 (m-30) cc_final: 0.7279 (m-30) outliers start: 198 outliers final: 28 residues processed: 906 average time/residue: 0.9783 time to fit residues: 1020.5971 Evaluate side-chains 744 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 684 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 147 GLU Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 147 GLU Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 147 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 304 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 274 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 343 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN F 65 HIS G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN Q 75 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099315 restraints weight = 38829.236| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.23 r_work: 0.2858 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 34512 Z= 0.153 Angle : 0.509 6.169 46416 Z= 0.263 Chirality : 0.037 0.123 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.040 16.407 4512 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.69 % Allowed : 17.65 % Favored : 77.66 % 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 are not related in a simple way. whole: 4.75 (0.13), residues: 4080 helix: 3.90 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.00 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 90 TYR 0.014 0.002 TYR G 137 PHE 0.016 0.002 PHE J 41 TRP 0.009 0.002 TRP Q 93 HIS 0.002 0.001 HIS S 173 Details of bonding type rmsd covalent geometry : bond 0.00356 (34512) covalent geometry : angle 0.50883 (46416) hydrogen bonds : bond 0.04218 ( 2640) hydrogen bonds : angle 3.34980 ( 7920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 717 time to evaluate : 1.397 Fit side-chains REVERT: A 63 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7922 (ttm170) REVERT: A 89 ASP cc_start: 0.7745 (m-30) cc_final: 0.7322 (m-30) REVERT: A 147 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7934 (tt0) REVERT: B 63 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: B 89 ASP cc_start: 0.7745 (m-30) cc_final: 0.7325 (m-30) REVERT: C 63 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: C 89 ASP cc_start: 0.7755 (m-30) cc_final: 0.7339 (m-30) REVERT: C 92 ASP cc_start: 0.8427 (t70) cc_final: 0.8217 (t70) REVERT: C 147 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: D 63 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7907 (ttm170) REVERT: D 89 ASP cc_start: 0.7705 (m-30) cc_final: 0.7278 (m-30) REVERT: E 63 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7874 (ttm170) REVERT: E 89 ASP cc_start: 0.7623 (m-30) cc_final: 0.7183 (m-30) REVERT: F 63 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7882 (ttm170) REVERT: F 89 ASP cc_start: 0.7788 (m-30) cc_final: 0.7388 (m-30) REVERT: F 143 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8180 (ttmt) REVERT: F 147 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: G 63 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7834 (ttm170) REVERT: G 89 ASP cc_start: 0.7769 (m-30) cc_final: 0.7346 (m-30) REVERT: G 92 ASP cc_start: 0.8426 (t70) cc_final: 0.8187 (t70) REVERT: G 143 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8149 (ttmt) REVERT: H 63 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7894 (ttm170) REVERT: H 89 ASP cc_start: 0.7792 (m-30) cc_final: 0.7410 (m-30) REVERT: H 92 ASP cc_start: 0.8383 (t70) cc_final: 0.8133 (t70) REVERT: I 63 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: I 89 ASP cc_start: 0.7755 (m-30) cc_final: 0.7331 (m-30) REVERT: I 92 ASP cc_start: 0.8438 (t70) cc_final: 0.8184 (t70) REVERT: I 143 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8172 (ttmt) REVERT: J 63 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7904 (ttm170) REVERT: J 89 ASP cc_start: 0.7765 (m-30) cc_final: 0.7392 (m-30) REVERT: K 89 ASP cc_start: 0.7849 (m-30) cc_final: 0.7452 (m-30) REVERT: K 92 ASP cc_start: 0.8411 (t70) cc_final: 0.8153 (t70) REVERT: L 63 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: L 89 ASP cc_start: 0.7749 (m-30) cc_final: 0.7326 (m-30) REVERT: L 143 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: M 63 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7913 (ttm170) REVERT: M 89 ASP cc_start: 0.7745 (m-30) cc_final: 0.7353 (m-30) REVERT: M 92 ASP cc_start: 0.8430 (t70) cc_final: 0.8230 (t70) REVERT: N 89 ASP cc_start: 0.7763 (m-30) cc_final: 0.7342 (m-30) REVERT: O 89 ASP cc_start: 0.7746 (m-30) cc_final: 0.7325 (m-30) REVERT: O 143 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8172 (ttmt) REVERT: O 147 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: P 89 ASP cc_start: 0.7739 (m-30) cc_final: 0.7310 (m-30) REVERT: Q 89 ASP cc_start: 0.7790 (m-30) cc_final: 0.7362 (m-30) REVERT: Q 143 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: Q 147 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: R 89 ASP cc_start: 0.7713 (m-30) cc_final: 0.7280 (m-30) REVERT: S 89 ASP cc_start: 0.7625 (m-30) cc_final: 0.7179 (m-30) REVERT: S 147 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: T 89 ASP cc_start: 0.7731 (m-30) cc_final: 0.7309 (m-30) REVERT: V 89 ASP cc_start: 0.7759 (m-30) cc_final: 0.7362 (m-30) REVERT: V 143 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8170 (ttmt) REVERT: W 89 ASP cc_start: 0.7594 (m-30) cc_final: 0.7150 (m-30) REVERT: W 92 ASP cc_start: 0.8391 (t70) cc_final: 0.8151 (t70) REVERT: W 147 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: X 83 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8741 (mm-40) REVERT: X 89 ASP cc_start: 0.7749 (m-30) cc_final: 0.7334 (m-30) REVERT: X 143 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8167 (ttmt) REVERT: X 147 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: Y 89 ASP cc_start: 0.7746 (m-30) cc_final: 0.7296 (m-30) outliers start: 171 outliers final: 68 residues processed: 857 average time/residue: 0.9789 time to fit residues: 965.4071 Evaluate side-chains 764 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 668 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain O residue 147 GLU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain Q residue 147 GLU Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 147 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain X residue 147 GLU Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 39 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 372 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 336 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN Q 75 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.107735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098317 restraints weight = 39105.406| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.22 r_work: 0.2871 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34512 Z= 0.189 Angle : 0.544 6.509 46416 Z= 0.279 Chirality : 0.038 0.128 4848 Planarity : 0.004 0.029 6096 Dihedral : 4.129 16.472 4512 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.63 % Allowed : 17.74 % Favored : 77.63 % 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 are not related in a simple way. whole: 4.82 (0.13), residues: 4080 helix: 3.90 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.36 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 90 TYR 0.015 0.002 TYR C 137 PHE 0.017 0.002 PHE J 41 TRP 0.010 0.002 TRP S 93 HIS 0.002 0.001 HIS X 105 Details of bonding type rmsd covalent geometry : bond 0.00442 (34512) covalent geometry : angle 0.54357 (46416) hydrogen bonds : bond 0.04620 ( 2640) hydrogen bonds : angle 3.43856 ( 7920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 699 time to evaluate : 1.544 Fit side-chains REVERT: A 63 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7930 (ttm170) REVERT: A 89 ASP cc_start: 0.7760 (m-30) cc_final: 0.7324 (m-30) REVERT: B 63 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: B 83 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8680 (mm110) REVERT: B 89 ASP cc_start: 0.7746 (m-30) cc_final: 0.7321 (m-30) REVERT: C 63 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7917 (ttm170) REVERT: C 89 ASP cc_start: 0.7757 (m-30) cc_final: 0.7330 (m-30) REVERT: C 92 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (t70) REVERT: D 63 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (ttm170) REVERT: D 89 ASP cc_start: 0.7732 (m-30) cc_final: 0.7296 (m-30) REVERT: E 63 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: E 89 ASP cc_start: 0.7637 (m-30) cc_final: 0.7180 (m-30) REVERT: F 63 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: F 89 ASP cc_start: 0.7741 (m-30) cc_final: 0.7362 (m-30) REVERT: F 90 ARG cc_start: 0.7776 (ptp-170) cc_final: 0.7549 (ptp-170) REVERT: F 143 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8201 (ttmt) REVERT: G 63 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7813 (ttm170) REVERT: G 89 ASP cc_start: 0.7779 (m-30) cc_final: 0.7352 (m-30) REVERT: G 92 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8154 (t70) REVERT: G 143 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: H 63 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7900 (ttm170) REVERT: H 89 ASP cc_start: 0.7773 (m-30) cc_final: 0.7383 (m-30) REVERT: H 92 ASP cc_start: 0.8418 (t70) cc_final: 0.8169 (t70) REVERT: I 63 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: I 89 ASP cc_start: 0.7758 (m-30) cc_final: 0.7323 (m-30) REVERT: I 92 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8160 (t70) REVERT: I 143 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8197 (ttmt) REVERT: J 63 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7884 (ttm170) REVERT: J 83 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8669 (mm110) REVERT: J 89 ASP cc_start: 0.7787 (m-30) cc_final: 0.7386 (m-30) REVERT: K 83 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8669 (mm110) REVERT: K 89 ASP cc_start: 0.7828 (m-30) cc_final: 0.7424 (m-30) REVERT: K 92 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8169 (t70) REVERT: L 63 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: L 89 ASP cc_start: 0.7753 (m-30) cc_final: 0.7315 (m-30) REVERT: L 143 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8201 (ttmt) REVERT: M 63 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7904 (ttm170) REVERT: M 89 ASP cc_start: 0.7726 (m-30) cc_final: 0.7327 (m-30) REVERT: M 92 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (t70) REVERT: N 89 ASP cc_start: 0.7753 (m-30) cc_final: 0.7322 (m-30) REVERT: O 89 ASP cc_start: 0.7744 (m-30) cc_final: 0.7310 (m-30) REVERT: O 143 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8192 (ttmt) REVERT: P 89 ASP cc_start: 0.7707 (m-30) cc_final: 0.7299 (m-30) REVERT: P 90 ARG cc_start: 0.7792 (ptp-170) cc_final: 0.7559 (ptp-170) REVERT: Q 89 ASP cc_start: 0.7784 (m-30) cc_final: 0.7344 (m-30) REVERT: Q 143 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8217 (ttmt) REVERT: R 70 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9105 (mtp) REVERT: R 89 ASP cc_start: 0.7684 (m-30) cc_final: 0.7265 (m-30) REVERT: R 90 ARG cc_start: 0.7752 (ptp-170) cc_final: 0.7520 (ptp-170) REVERT: S 89 ASP cc_start: 0.7640 (m-30) cc_final: 0.7171 (m-30) REVERT: S 147 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: T 89 ASP cc_start: 0.7761 (m-30) cc_final: 0.7332 (m-30) REVERT: V 89 ASP cc_start: 0.7735 (m-30) cc_final: 0.7355 (m-30) REVERT: V 90 ARG cc_start: 0.7791 (ptp-170) cc_final: 0.7555 (ptp-170) REVERT: V 143 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: W 89 ASP cc_start: 0.7634 (m-30) cc_final: 0.7175 (m-30) REVERT: W 92 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8220 (t70) REVERT: W 147 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: X 89 ASP cc_start: 0.7739 (m-30) cc_final: 0.7312 (m-30) REVERT: X 143 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8183 (ttmt) REVERT: Y 89 ASP cc_start: 0.7724 (m-30) cc_final: 0.7293 (m-30) REVERT: Y 90 ARG cc_start: 0.7754 (ptp-170) cc_final: 0.7520 (ptp-170) outliers start: 169 outliers final: 91 residues processed: 823 average time/residue: 0.9982 time to fit residues: 943.7908 Evaluate side-chains 792 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 672 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 147 GLU Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 147 GLU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 70 optimal weight: 4.9990 chunk 211 optimal weight: 0.9990 chunk 385 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN H 154 ASN I 14 GLN I 154 ASN J 14 GLN J 154 ASN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN O 154 ASN P 14 GLN P 154 ASN Q 14 GLN Q 75 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN W 154 ASN X 14 GLN Y 14 GLN Y 154 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100615 restraints weight = 38963.715| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.24 r_work: 0.2890 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34512 Z= 0.123 Angle : 0.473 5.757 46416 Z= 0.247 Chirality : 0.035 0.117 4848 Planarity : 0.003 0.029 6096 Dihedral : 3.927 16.504 4512 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.80 % Allowed : 17.65 % Favored : 77.55 % 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 are not related in a simple way. whole: 5.06 (0.13), residues: 4080 helix: 4.12 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 90 TYR 0.013 0.001 TYR M 137 PHE 0.015 0.002 PHE J 41 TRP 0.009 0.002 TRP S 93 HIS 0.002 0.001 HIS K 105 Details of bonding type rmsd covalent geometry : bond 0.00281 (34512) covalent geometry : angle 0.47304 (46416) hydrogen bonds : bond 0.03783 ( 2640) hydrogen bonds : angle 3.25319 ( 7920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 773 time to evaluate : 1.133 Fit side-chains REVERT: A 63 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7906 (ttm170) REVERT: A 89 ASP cc_start: 0.7756 (m-30) cc_final: 0.7326 (m-30) REVERT: B 63 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7882 (ttm170) REVERT: B 89 ASP cc_start: 0.7753 (m-30) cc_final: 0.7338 (m-30) REVERT: C 63 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7879 (ttm170) REVERT: C 89 ASP cc_start: 0.7780 (m-30) cc_final: 0.7355 (m-30) REVERT: C 92 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8134 (t70) REVERT: D 63 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7809 (ttm170) REVERT: D 89 ASP cc_start: 0.7732 (m-30) cc_final: 0.7303 (m-30) REVERT: E 63 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: E 89 ASP cc_start: 0.7637 (m-30) cc_final: 0.7190 (m-30) REVERT: F 63 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7859 (ttm170) REVERT: F 89 ASP cc_start: 0.7750 (m-30) cc_final: 0.7377 (m-30) REVERT: F 90 ARG cc_start: 0.7733 (ptp-170) cc_final: 0.7487 (ptp-170) REVERT: F 143 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: G 63 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7816 (ttm170) REVERT: G 89 ASP cc_start: 0.7793 (m-30) cc_final: 0.7365 (m-30) REVERT: G 92 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8129 (t70) REVERT: G 143 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8158 (ttmt) REVERT: H 63 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7806 (ttm170) REVERT: H 89 ASP cc_start: 0.7791 (m-30) cc_final: 0.7406 (m-30) REVERT: H 92 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8113 (t70) REVERT: I 63 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7888 (ttm170) REVERT: I 89 ASP cc_start: 0.7771 (m-30) cc_final: 0.7342 (m-30) REVERT: I 92 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8129 (t70) REVERT: I 143 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8167 (ttmt) REVERT: J 63 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7797 (ttm170) REVERT: J 89 ASP cc_start: 0.7775 (m-30) cc_final: 0.7395 (m-30) REVERT: K 89 ASP cc_start: 0.7848 (m-30) cc_final: 0.7449 (m-30) REVERT: K 92 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8185 (t70) REVERT: L 63 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7808 (ttm170) REVERT: L 89 ASP cc_start: 0.7764 (m-30) cc_final: 0.7338 (m-30) REVERT: L 143 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: M 63 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7889 (ttm170) REVERT: M 89 ASP cc_start: 0.7752 (m-30) cc_final: 0.7358 (m-30) REVERT: M 92 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (t70) REVERT: N 89 ASP cc_start: 0.7767 (m-30) cc_final: 0.7344 (m-30) REVERT: O 89 ASP cc_start: 0.7736 (m-30) cc_final: 0.7304 (m-30) REVERT: O 143 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8189 (ttmt) REVERT: P 89 ASP cc_start: 0.7731 (m-30) cc_final: 0.7332 (m-30) REVERT: P 90 ARG cc_start: 0.7773 (ptp-170) cc_final: 0.7521 (ptp-170) REVERT: Q 89 ASP cc_start: 0.7785 (m-30) cc_final: 0.7360 (m-30) REVERT: Q 143 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8199 (ttmt) REVERT: R 89 ASP cc_start: 0.7695 (m-30) cc_final: 0.7288 (m-30) REVERT: R 90 ARG cc_start: 0.7707 (ptp-170) cc_final: 0.7458 (ptp-170) REVERT: S 89 ASP cc_start: 0.7629 (m-30) cc_final: 0.7174 (m-30) REVERT: T 89 ASP cc_start: 0.7760 (m-30) cc_final: 0.7336 (m-30) REVERT: V 89 ASP cc_start: 0.7705 (m-30) cc_final: 0.7347 (m-30) REVERT: V 90 ARG cc_start: 0.7770 (ptp-170) cc_final: 0.7507 (ptp-170) REVERT: V 143 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8169 (ttmt) REVERT: W 89 ASP cc_start: 0.7622 (m-30) cc_final: 0.7171 (m-30) REVERT: W 92 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8091 (t70) REVERT: X 83 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8692 (mm-40) REVERT: X 89 ASP cc_start: 0.7741 (m-30) cc_final: 0.7323 (m-30) REVERT: X 143 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8208 (ttmt) REVERT: Y 89 ASP cc_start: 0.7694 (m-30) cc_final: 0.7283 (m-30) REVERT: Y 90 ARG cc_start: 0.7734 (ptp-170) cc_final: 0.7471 (ptp-170) outliers start: 175 outliers final: 90 residues processed: 896 average time/residue: 0.9360 time to fit residues: 966.3114 Evaluate side-chains 794 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 677 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 87 LYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 370 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 273 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 383 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN D 154 ASN E 14 GLN F 14 GLN F 154 ASN G 14 GLN G 154 ASN H 14 GLN I 14 GLN J 14 GLN K 14 GLN K 154 ASN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.111873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.102346 restraints weight = 38835.882| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.24 r_work: 0.2919 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 34512 Z= 0.101 Angle : 0.446 5.397 46416 Z= 0.235 Chirality : 0.034 0.113 4848 Planarity : 0.003 0.028 6096 Dihedral : 3.793 16.266 4512 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.32 % Allowed : 19.16 % Favored : 77.52 % 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 are not related in a simple way. whole: 5.34 (0.13), residues: 4080 helix: 4.33 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.13 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 90 TYR 0.012 0.001 TYR G 137 PHE 0.014 0.002 PHE W 41 TRP 0.008 0.002 TRP Y 93 HIS 0.002 0.001 HIS O 105 Details of bonding type rmsd covalent geometry : bond 0.00224 (34512) covalent geometry : angle 0.44566 (46416) hydrogen bonds : bond 0.03320 ( 2640) hydrogen bonds : angle 3.15653 ( 7920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 730 time to evaluate : 1.461 Fit side-chains REVERT: A 63 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7846 (ttm170) REVERT: A 89 ASP cc_start: 0.7724 (m-30) cc_final: 0.7301 (m-30) REVERT: B 63 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7834 (ttm170) REVERT: B 89 ASP cc_start: 0.7734 (m-30) cc_final: 0.7311 (m-30) REVERT: C 63 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7849 (ttm170) REVERT: C 89 ASP cc_start: 0.7792 (m-30) cc_final: 0.7377 (m-30) REVERT: C 131 ASP cc_start: 0.8557 (t70) cc_final: 0.8322 (t70) REVERT: D 63 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7842 (ttm170) REVERT: D 89 ASP cc_start: 0.7695 (m-30) cc_final: 0.7277 (m-30) REVERT: E 63 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7823 (ttm170) REVERT: E 89 ASP cc_start: 0.7615 (m-30) cc_final: 0.7183 (m-30) REVERT: F 63 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7823 (ttm170) REVERT: F 89 ASP cc_start: 0.7704 (m-30) cc_final: 0.7344 (m-30) REVERT: F 90 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7443 (ptp-170) REVERT: F 143 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8165 (ttmt) REVERT: G 63 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7773 (ttm170) REVERT: G 89 ASP cc_start: 0.7774 (m-30) cc_final: 0.7344 (m-30) REVERT: G 143 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8170 (ttmt) REVERT: H 63 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7801 (ttm170) REVERT: H 89 ASP cc_start: 0.7769 (m-30) cc_final: 0.7398 (m-30) REVERT: H 92 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8093 (t70) REVERT: I 63 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7841 (ttm170) REVERT: I 89 ASP cc_start: 0.7800 (m-30) cc_final: 0.7377 (m-30) REVERT: I 143 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8154 (ttmt) REVERT: J 63 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7802 (ttm170) REVERT: J 89 ASP cc_start: 0.7787 (m-30) cc_final: 0.7411 (m-30) REVERT: K 89 ASP cc_start: 0.7817 (m-30) cc_final: 0.7433 (m-30) REVERT: K 92 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8075 (t70) REVERT: L 63 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7823 (ttm170) REVERT: L 89 ASP cc_start: 0.7738 (m-30) cc_final: 0.7316 (m-30) REVERT: L 143 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8174 (ttmt) REVERT: M 63 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7850 (ttm170) REVERT: M 89 ASP cc_start: 0.7731 (m-30) cc_final: 0.7342 (m-30) REVERT: N 89 ASP cc_start: 0.7755 (m-30) cc_final: 0.7331 (m-30) REVERT: O 89 ASP cc_start: 0.7713 (m-30) cc_final: 0.7294 (m-30) REVERT: O 143 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8157 (ttmt) REVERT: P 89 ASP cc_start: 0.7719 (m-30) cc_final: 0.7324 (m-30) REVERT: P 90 ARG cc_start: 0.7722 (ptp-170) cc_final: 0.7464 (ptp-170) REVERT: Q 89 ASP cc_start: 0.7747 (m-30) cc_final: 0.7339 (m-30) REVERT: Q 143 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8183 (ttmt) REVERT: R 89 ASP cc_start: 0.7658 (m-30) cc_final: 0.7275 (m-30) REVERT: R 90 ARG cc_start: 0.7724 (ptp-170) cc_final: 0.7466 (ptp-170) REVERT: S 89 ASP cc_start: 0.7607 (m-30) cc_final: 0.7164 (m-30) REVERT: T 89 ASP cc_start: 0.7722 (m-30) cc_final: 0.7289 (m-30) REVERT: T 131 ASP cc_start: 0.8571 (t70) cc_final: 0.8369 (t70) REVERT: V 89 ASP cc_start: 0.7687 (m-30) cc_final: 0.7331 (m-30) REVERT: V 90 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.7449 (ptp-170) REVERT: V 143 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8150 (ttmt) REVERT: W 89 ASP cc_start: 0.7572 (m-30) cc_final: 0.7135 (m-30) REVERT: W 92 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8071 (t70) REVERT: X 89 ASP cc_start: 0.7700 (m-30) cc_final: 0.7303 (m-30) REVERT: X 143 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8156 (ttmt) REVERT: Y 89 ASP cc_start: 0.7697 (m-30) cc_final: 0.7298 (m-30) REVERT: Y 90 ARG cc_start: 0.7695 (ptp-170) cc_final: 0.7429 (ptp-170) outliers start: 121 outliers final: 66 residues processed: 815 average time/residue: 0.9779 time to fit residues: 922.4518 Evaluate side-chains 759 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 670 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain I residue 165 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 126 ASP 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 87 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain V residue 165 MET Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain X residue 64 GLU Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 140 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 359 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Y 125 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.108708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099243 restraints weight = 38797.108| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.22 r_work: 0.2860 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34512 Z= 0.163 Angle : 0.520 6.044 46416 Z= 0.269 Chirality : 0.037 0.124 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.023 16.427 4512 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.85 % Allowed : 17.46 % Favored : 77.69 % 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 are not related in a simple way. whole: 5.01 (0.13), residues: 4080 helix: 4.05 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : 0.26 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 90 TYR 0.013 0.002 TYR G 137 PHE 0.016 0.002 PHE W 41 TRP 0.008 0.002 TRP Q 93 HIS 0.002 0.001 HIS T 105 Details of bonding type rmsd covalent geometry : bond 0.00380 (34512) covalent geometry : angle 0.51979 (46416) hydrogen bonds : bond 0.04253 ( 2640) hydrogen bonds : angle 3.34450 ( 7920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 692 time to evaluate : 1.439 Fit side-chains REVERT: A 63 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7941 (ttm170) REVERT: A 89 ASP cc_start: 0.7769 (m-30) cc_final: 0.7321 (m-30) REVERT: A 143 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8191 (ttmt) REVERT: B 63 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: B 89 ASP cc_start: 0.7750 (m-30) cc_final: 0.7328 (m-30) REVERT: B 143 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8205 (ttmt) REVERT: C 63 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: C 89 ASP cc_start: 0.7773 (m-30) cc_final: 0.7352 (m-30) REVERT: C 92 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8142 (t70) REVERT: C 143 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8184 (ttmt) REVERT: D 63 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: D 89 ASP cc_start: 0.7728 (m-30) cc_final: 0.7298 (m-30) REVERT: D 143 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8225 (ttmt) REVERT: E 63 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: E 89 ASP cc_start: 0.7657 (m-30) cc_final: 0.7208 (m-30) REVERT: E 143 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8225 (ttmt) REVERT: F 63 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7861 (ttm170) REVERT: F 90 ARG cc_start: 0.7761 (ptp-170) cc_final: 0.7492 (ptp-170) REVERT: F 143 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8228 (ttmt) REVERT: G 63 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7820 (ttm170) REVERT: G 89 ASP cc_start: 0.7786 (m-30) cc_final: 0.7355 (m-30) REVERT: G 92 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8134 (t70) REVERT: G 143 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8208 (ttmt) REVERT: H 63 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: H 89 ASP cc_start: 0.7788 (m-30) cc_final: 0.7384 (m-30) REVERT: H 92 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8111 (t70) REVERT: H 143 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8197 (ttmt) REVERT: I 63 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7920 (ttm170) REVERT: I 89 ASP cc_start: 0.7783 (m-30) cc_final: 0.7344 (m-30) REVERT: I 92 ASP cc_start: 0.8442 (t70) cc_final: 0.8134 (t70) REVERT: I 143 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8221 (ttmt) REVERT: J 63 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7913 (ttm170) REVERT: J 89 ASP cc_start: 0.7827 (m-30) cc_final: 0.7441 (m-30) REVERT: J 143 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8192 (ttmt) REVERT: K 89 ASP cc_start: 0.7833 (m-30) cc_final: 0.7418 (m-30) REVERT: K 92 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8127 (t70) REVERT: K 143 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8180 (ttmt) REVERT: L 63 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7918 (ttm170) REVERT: L 89 ASP cc_start: 0.7785 (m-30) cc_final: 0.7338 (m-30) REVERT: L 143 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8199 (ttmt) REVERT: M 63 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7895 (ttm170) REVERT: M 89 ASP cc_start: 0.7739 (m-30) cc_final: 0.7340 (m-30) REVERT: M 92 ASP cc_start: 0.8441 (t70) cc_final: 0.8148 (t70) REVERT: M 143 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8211 (ttmt) REVERT: N 89 ASP cc_start: 0.7765 (m-30) cc_final: 0.7317 (m-30) REVERT: N 92 ASP cc_start: 0.8389 (t70) cc_final: 0.7933 (t0) REVERT: N 143 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8202 (ttmt) REVERT: O 89 ASP cc_start: 0.7768 (m-30) cc_final: 0.7322 (m-30) REVERT: O 143 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8216 (ttmt) REVERT: P 89 ASP cc_start: 0.7736 (m-30) cc_final: 0.7309 (m-30) REVERT: P 90 ARG cc_start: 0.7802 (ptp-170) cc_final: 0.7541 (ptp-170) REVERT: P 143 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8205 (ttmt) REVERT: Q 89 ASP cc_start: 0.7796 (m-30) cc_final: 0.7361 (m-30) REVERT: Q 143 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8218 (ttmt) REVERT: R 89 ASP cc_start: 0.7744 (m-30) cc_final: 0.7296 (m-30) REVERT: R 90 ARG cc_start: 0.7746 (ptp-170) cc_final: 0.7485 (ptp-170) REVERT: R 92 ASP cc_start: 0.8410 (t70) cc_final: 0.8191 (t70) REVERT: R 143 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8205 (ttmt) REVERT: S 89 ASP cc_start: 0.7652 (m-30) cc_final: 0.7192 (m-30) REVERT: S 143 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8195 (ttmt) REVERT: T 89 ASP cc_start: 0.7722 (m-30) cc_final: 0.7287 (m-30) REVERT: T 143 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8191 (ttmt) REVERT: V 90 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7512 (ptp-170) REVERT: V 143 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8216 (ttmt) REVERT: W 89 ASP cc_start: 0.7640 (m-30) cc_final: 0.7180 (m-30) REVERT: W 92 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8102 (t70) REVERT: W 143 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8203 (ttmt) REVERT: X 89 ASP cc_start: 0.7757 (m-30) cc_final: 0.7318 (m-30) REVERT: X 143 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8199 (ttmt) REVERT: Y 90 ARG cc_start: 0.7755 (ptp-170) cc_final: 0.7490 (ptp-170) REVERT: Y 143 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8223 (ttmt) outliers start: 177 outliers final: 84 residues processed: 813 average time/residue: 0.9498 time to fit residues: 891.7368 Evaluate side-chains 826 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 701 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 125 optimal weight: 7.9990 chunk 297 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 241 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 14 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN R 14 GLN S 14 GLN T 14 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.108596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099110 restraints weight = 38929.966| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.23 r_work: 0.2859 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34512 Z= 0.171 Angle : 0.536 6.214 46416 Z= 0.277 Chirality : 0.038 0.126 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.093 16.483 4512 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.71 % Allowed : 17.76 % Favored : 77.52 % 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 are not related in a simple way. whole: 5.04 (0.13), residues: 4080 helix: 4.01 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.62 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 90 TYR 0.014 0.002 TYR W 137 PHE 0.016 0.002 PHE W 41 TRP 0.008 0.002 TRP S 93 HIS 0.002 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00400 (34512) covalent geometry : angle 0.53644 (46416) hydrogen bonds : bond 0.04343 ( 2640) hydrogen bonds : angle 3.38292 ( 7920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 701 time to evaluate : 1.439 Fit side-chains REVERT: A 63 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: A 89 ASP cc_start: 0.7760 (m-30) cc_final: 0.7302 (m-30) REVERT: A 143 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8167 (ttmt) REVERT: B 63 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7896 (ttm170) REVERT: B 89 ASP cc_start: 0.7784 (m-30) cc_final: 0.7307 (m-30) REVERT: B 143 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8189 (ttmt) REVERT: C 63 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: C 89 ASP cc_start: 0.7767 (m-30) cc_final: 0.7330 (m-30) REVERT: C 143 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8148 (ttmt) REVERT: D 63 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: D 89 ASP cc_start: 0.7725 (m-30) cc_final: 0.7271 (m-30) REVERT: D 143 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8225 (ttmt) REVERT: E 63 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7885 (ttm170) REVERT: E 89 ASP cc_start: 0.7660 (m-30) cc_final: 0.7190 (m-30) REVERT: E 143 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8178 (ttmt) REVERT: F 63 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7862 (ttm170) REVERT: F 90 ARG cc_start: 0.7757 (ptp-170) cc_final: 0.7480 (ptp-170) REVERT: F 143 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8208 (ttmt) REVERT: G 63 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7835 (ttm170) REVERT: G 89 ASP cc_start: 0.7802 (m-30) cc_final: 0.7299 (m-30) REVERT: G 92 ASP cc_start: 0.8426 (t70) cc_final: 0.8147 (t70) REVERT: G 143 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8163 (ttmt) REVERT: H 63 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7901 (ttm170) REVERT: H 89 ASP cc_start: 0.7803 (m-30) cc_final: 0.7350 (m-30) REVERT: H 92 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8129 (t70) REVERT: H 143 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8151 (ttmt) REVERT: I 63 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: I 89 ASP cc_start: 0.7769 (m-30) cc_final: 0.7326 (m-30) REVERT: I 92 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8145 (t70) REVERT: I 143 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8186 (ttmt) REVERT: J 63 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7903 (ttm170) REVERT: J 83 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8648 (mm-40) REVERT: J 89 ASP cc_start: 0.7806 (m-30) cc_final: 0.7403 (m-30) REVERT: J 143 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8161 (ttmt) REVERT: K 89 ASP cc_start: 0.7855 (m-30) cc_final: 0.7393 (m-30) REVERT: K 92 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8126 (t70) REVERT: K 143 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8155 (ttmt) REVERT: L 63 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7900 (ttm170) REVERT: L 89 ASP cc_start: 0.7773 (m-30) cc_final: 0.7315 (m-30) REVERT: L 143 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8176 (ttmt) REVERT: M 63 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: M 89 ASP cc_start: 0.7763 (m-30) cc_final: 0.7290 (m-30) REVERT: M 92 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8149 (t70) REVERT: M 143 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8174 (ttmt) REVERT: N 89 ASP cc_start: 0.7764 (m-30) cc_final: 0.7319 (m-30) REVERT: N 143 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8177 (ttmt) REVERT: O 89 ASP cc_start: 0.7757 (m-30) cc_final: 0.7304 (m-30) REVERT: O 143 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: P 90 ARG cc_start: 0.7765 (ptp-170) cc_final: 0.7495 (ptp-170) REVERT: P 143 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8191 (ttmt) REVERT: Q 89 ASP cc_start: 0.7830 (m-30) cc_final: 0.7328 (m-30) REVERT: Q 143 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8208 (ttmt) REVERT: R 90 ARG cc_start: 0.7745 (ptp-170) cc_final: 0.7475 (ptp-170) REVERT: R 143 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8190 (ttmt) REVERT: S 89 ASP cc_start: 0.7645 (m-30) cc_final: 0.7160 (m-30) REVERT: S 143 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8178 (ttmt) REVERT: T 89 ASP cc_start: 0.7780 (m-30) cc_final: 0.7313 (m-30) REVERT: T 143 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8172 (ttmt) REVERT: V 90 ARG cc_start: 0.7777 (ptp-170) cc_final: 0.7503 (ptp-170) REVERT: V 143 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: W 89 ASP cc_start: 0.7633 (m-30) cc_final: 0.7158 (m-30) REVERT: W 92 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8154 (t70) REVERT: W 143 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8164 (ttmt) REVERT: X 89 ASP cc_start: 0.7812 (m-30) cc_final: 0.7346 (m-30) REVERT: X 143 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8177 (ttmt) REVERT: Y 90 ARG cc_start: 0.7757 (ptp-170) cc_final: 0.7467 (ptp-170) REVERT: Y 143 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8196 (ttmt) outliers start: 172 outliers final: 93 residues processed: 829 average time/residue: 0.9635 time to fit residues: 922.7624 Evaluate side-chains 812 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 678 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 398 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 54 optimal weight: 0.0770 chunk 167 optimal weight: 6.9990 chunk 356 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 75 GLN C 14 GLN D 14 GLN E 14 GLN F 14 GLN F 75 GLN G 14 GLN H 14 GLN I 14 GLN J 14 GLN J 75 GLN K 14 GLN L 14 GLN M 14 GLN N 14 GLN O 14 GLN P 14 GLN Q 14 GLN Q 75 GLN R 14 GLN S 14 GLN T 14 GLN T 75 GLN V 14 GLN W 14 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.108729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099256 restraints weight = 38843.332| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.23 r_work: 0.2854 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34512 Z= 0.175 Angle : 0.546 6.201 46416 Z= 0.282 Chirality : 0.038 0.126 4848 Planarity : 0.004 0.030 6096 Dihedral : 4.121 16.491 4512 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.02 % Allowed : 17.52 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.99 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.64 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 90 TYR 0.014 0.002 TYR G 137 PHE 0.016 0.002 PHE W 41 TRP 0.008 0.002 TRP K 93 HIS 0.002 0.001 HIS Q 105 Details of bonding type rmsd covalent geometry : bond 0.00408 (34512) covalent geometry : angle 0.54570 (46416) hydrogen bonds : bond 0.04355 ( 2640) hydrogen bonds : angle 3.39289 ( 7920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 697 time to evaluate : 1.414 Fit side-chains REVERT: A 63 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7926 (ttm170) REVERT: A 89 ASP cc_start: 0.7772 (m-30) cc_final: 0.7330 (m-30) REVERT: A 143 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8167 (ttmt) REVERT: B 63 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7907 (ttm170) REVERT: B 89 ASP cc_start: 0.7779 (m-30) cc_final: 0.7293 (m-30) REVERT: B 143 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8169 (ttmt) REVERT: C 63 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: C 89 ASP cc_start: 0.7775 (m-30) cc_final: 0.7337 (m-30) REVERT: C 92 ASP cc_start: 0.8464 (t70) cc_final: 0.8192 (t70) REVERT: C 143 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8166 (ttmt) REVERT: D 63 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: D 89 ASP cc_start: 0.7733 (m-30) cc_final: 0.7298 (m-30) REVERT: D 143 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8209 (ttmt) REVERT: E 63 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: E 89 ASP cc_start: 0.7653 (m-30) cc_final: 0.7190 (m-30) REVERT: E 143 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: F 63 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7846 (ttm170) REVERT: F 90 ARG cc_start: 0.7759 (ptp-170) cc_final: 0.7479 (ptp-170) REVERT: F 143 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8196 (ttmt) REVERT: G 63 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7846 (ttm170) REVERT: G 89 ASP cc_start: 0.7815 (m-30) cc_final: 0.7320 (m-30) REVERT: G 92 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8163 (t70) REVERT: G 143 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8169 (ttmt) REVERT: H 63 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: H 89 ASP cc_start: 0.7815 (m-30) cc_final: 0.7365 (m-30) REVERT: H 92 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8145 (t70) REVERT: H 143 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8159 (ttmt) REVERT: I 63 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: I 89 ASP cc_start: 0.7773 (m-30) cc_final: 0.7335 (m-30) REVERT: I 92 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8152 (t70) REVERT: I 143 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8193 (ttmt) REVERT: J 63 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (ttm170) REVERT: J 89 ASP cc_start: 0.7788 (m-30) cc_final: 0.7394 (m-30) REVERT: J 143 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8168 (ttmt) REVERT: K 89 ASP cc_start: 0.7853 (m-30) cc_final: 0.7385 (m-30) REVERT: K 92 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8181 (t70) REVERT: K 143 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8195 (ttmt) REVERT: L 63 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: L 89 ASP cc_start: 0.7795 (m-30) cc_final: 0.7301 (m-30) REVERT: L 143 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: M 63 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7904 (ttm170) REVERT: M 89 ASP cc_start: 0.7773 (m-30) cc_final: 0.7309 (m-30) REVERT: M 92 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8157 (t70) REVERT: M 143 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8185 (ttmt) REVERT: N 89 ASP cc_start: 0.7752 (m-30) cc_final: 0.7299 (m-30) REVERT: N 143 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8199 (ttmt) REVERT: O 89 ASP cc_start: 0.7761 (m-30) cc_final: 0.7323 (m-30) REVERT: O 143 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8180 (ttmt) REVERT: P 90 ARG cc_start: 0.7785 (ptp-170) cc_final: 0.7515 (ptp-170) REVERT: P 143 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8173 (ttmt) REVERT: Q 89 ASP cc_start: 0.7818 (m-30) cc_final: 0.7313 (m-30) REVERT: Q 143 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8215 (ttmt) REVERT: R 90 ARG cc_start: 0.7761 (ptp-170) cc_final: 0.7468 (ptp-170) REVERT: R 143 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8183 (ttmt) REVERT: S 89 ASP cc_start: 0.7645 (m-30) cc_final: 0.7176 (m-30) REVERT: S 143 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: T 89 ASP cc_start: 0.7780 (m-30) cc_final: 0.7300 (m-30) REVERT: T 143 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8188 (ttmt) REVERT: V 90 ARG cc_start: 0.7779 (ptp-170) cc_final: 0.7491 (ptp-170) REVERT: V 143 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8177 (ttmt) REVERT: W 89 ASP cc_start: 0.7673 (m-30) cc_final: 0.7184 (m-30) REVERT: W 92 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8157 (t70) REVERT: W 143 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8175 (ttmt) REVERT: X 89 ASP cc_start: 0.7806 (m-30) cc_final: 0.7317 (m-30) REVERT: X 143 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8198 (ttmt) REVERT: Y 90 ARG cc_start: 0.7760 (ptp-170) cc_final: 0.7464 (ptp-170) REVERT: Y 143 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8183 (ttmt) outliers start: 183 outliers final: 100 residues processed: 836 average time/residue: 0.9389 time to fit residues: 905.1319 Evaluate side-chains 824 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 682 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 143 LYS Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 63 ARG Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 143 LYS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 63 ARG Chi-restraints excluded: chain H residue 87 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 63 ARG Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 122 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 143 LYS Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 63 ARG Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 139 SER Chi-restraints excluded: chain J residue 143 LYS Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 122 THR Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 126 ASP Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 143 LYS Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 63 ARG Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 143 LYS Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 126 ASP Chi-restraints excluded: chain N residue 139 SER Chi-restraints excluded: chain N residue 143 LYS Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 122 THR Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain P residue 126 ASP Chi-restraints excluded: chain P residue 139 SER Chi-restraints excluded: chain P residue 143 LYS Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 143 LYS Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain S residue 126 ASP Chi-restraints excluded: chain S residue 139 SER Chi-restraints excluded: chain S residue 143 LYS Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 87 LYS Chi-restraints excluded: chain T residue 126 ASP Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 143 LYS Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 87 LYS Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 126 ASP Chi-restraints excluded: chain V residue 139 SER Chi-restraints excluded: chain V residue 143 LYS Chi-restraints excluded: chain W residue 8 VAL Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 122 THR Chi-restraints excluded: chain W residue 139 SER Chi-restraints excluded: chain W residue 143 LYS Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 143 LYS Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 126 ASP Chi-restraints excluded: chain Y residue 139 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 108 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 314 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 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 B 14 GLN B 75 GLN C 14 GLN C 75 GLN D 14 GLN E 14 GLN E 75 GLN F 14 GLN F 75 GLN G 14 GLN G 75 GLN H 14 GLN I 14 GLN J 14 GLN J 75 GLN K 14 GLN L 14 GLN M 14 GLN M 75 GLN N 14 GLN N 75 GLN O 14 GLN O 75 GLN P 14 GLN Q 14 GLN Q 75 GLN R 14 GLN S 14 GLN S 75 GLN T 14 GLN T 75 GLN V 14 GLN W 14 GLN W 75 GLN X 14 GLN Y 14 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.107991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.098579 restraints weight = 38836.759| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.22 r_work: 0.2845 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 34512 Z= 0.200 Angle : 0.576 6.375 46416 Z= 0.297 Chirality : 0.040 0.129 4848 Planarity : 0.004 0.031 6096 Dihedral : 4.210 16.574 4512 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.96 % Allowed : 17.60 % Favored : 77.44 % 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 are not related in a simple way. whole: 4.86 (0.13), residues: 4080 helix: 3.86 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : 0.66 (0.24), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 90 TYR 0.015 0.002 TYR G 137 PHE 0.017 0.003 PHE W 41 TRP 0.008 0.002 TRP S 93 HIS 0.003 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00469 (34512) covalent geometry : angle 0.57559 (46416) hydrogen bonds : bond 0.04622 ( 2640) hydrogen bonds : angle 3.45564 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15436.87 seconds wall clock time: 263 minutes 13.50 seconds (15793.50 seconds total)