Starting phenix.real_space_refine on Sat Feb 7 19:19:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k85_62161/02_2026/9k85_62161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k85_62161/02_2026/9k85_62161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k85_62161/02_2026/9k85_62161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k85_62161/02_2026/9k85_62161.map" model { file = "/net/cci-nas-00/data/ceres_data/9k85_62161/02_2026/9k85_62161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k85_62161/02_2026/9k85_62161.cif" } resolution = 2.59 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= 0.016 sd= 0.216 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 Zn 42 6.06 5 S 84 5.16 5 C 23310 2.51 5 N 5838 2.21 5 O 6531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35805 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "B" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "C" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "F" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "G" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "H" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "I" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "J" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "K" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "M" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "N" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "O" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "P" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "Q" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "R" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "S" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "T" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "U" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.54, per 1000 atoms: 0.24 Number of scatterers: 35805 At special positions: 0 Unit cell: (124.967, 124.967, 184.218, 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) Zn 42 29.99 S 84 16.00 O 6531 8.00 N 5838 7.00 C 23310 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS K 47 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 124 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 207 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS B 75 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 47 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS J 124 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS I 47 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 124 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS D 75 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 207 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS L 124 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 207 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS A 75 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS M 47 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 124 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS G 47 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 124 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 207 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS F 75 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 47 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS N 124 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 207 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS C 75 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS O 47 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 124 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS E 47 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 124 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS F 207 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS H 75 " pdb=" ZN F 303 " pdb="ZN ZN F 303 " - pdb=" NE2 HIS F 47 " pdb="ZN ZN F 303 " - pdb=" NE2 HIS P 124 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 207 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS E 75 " pdb=" ZN G 302 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS Q 47 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS G 124 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS C 47 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 124 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 207 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS J 75 " pdb=" ZN H 303 " pdb="ZN ZN H 303 " - pdb=" NE2 HIS H 47 " pdb="ZN ZN H 303 " - pdb=" NE2 HIS R 124 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 207 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS G 75 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS S 47 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS I 124 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 207 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS L 75 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS J 47 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS T 124 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 207 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS I 75 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS U 47 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS K 124 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS L 207 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS N 75 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 207 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS K 75 " pdb=" ZN M 302 " pdb="ZN ZN M 302 " - pdb=" NE2 HIS M 124 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 207 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS P 75 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS O 207 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS M 75 " pdb=" ZN O 302 " pdb="ZN ZN O 302 " - pdb=" NE2 HIS O 124 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 207 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS R 75 " pdb=" ZN Q 301 " pdb="ZN ZN Q 301 " - pdb=" NE2 HIS Q 207 " pdb="ZN ZN Q 301 " - pdb=" NE2 HIS O 75 " pdb=" ZN Q 302 " pdb="ZN ZN Q 302 " - pdb=" NE2 HIS Q 124 " pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 207 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS T 75 " pdb=" ZN S 301 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS S 207 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS Q 75 " pdb=" ZN S 302 " pdb="ZN ZN S 302 " - pdb=" NE2 HIS S 124 " pdb=" ZN U 301 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS U 207 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS S 75 " pdb=" ZN U 302 " pdb="ZN ZN U 302 " - pdb=" NE2 HIS U 124 " pdb=" ZN U 303 " pdb="ZN ZN U 303 " - pdb=" NE2 HIS U 75 " 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8526 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 6 through 26 Processing helix chain 'A' and resid 30 through 51 Processing helix chain 'A' and resid 58 through 80 removed outlier: 3.755A pdb=" N GLY A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.506A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 159 through 182 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 186 through 213 Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.822A pdb=" N LYS B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 51 Processing helix chain 'B' and resid 58 through 80 removed outlier: 3.786A pdb=" N GLY B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.508A pdb=" N LEU B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 159 through 182 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 213 Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.862A pdb=" N LYS C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 51 Processing helix chain 'C' and resid 58 through 80 removed outlier: 3.784A pdb=" N GLY C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.506A pdb=" N LEU C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 159 through 182 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 186 through 213 Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.797A pdb=" N LYS D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 58 through 80 removed outlier: 3.740A pdb=" N GLY D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 105 Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.550A pdb=" N LEU D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 159 through 182 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 186 through 213 Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.824A pdb=" N LYS E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 51 Processing helix chain 'E' and resid 58 through 80 removed outlier: 3.804A pdb=" N GLY E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 108 through 131 removed outlier: 3.640A pdb=" N LEU E 112 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 159 through 182 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 186 through 213 Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.867A pdb=" N LYS F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 51 Processing helix chain 'F' and resid 58 through 80 removed outlier: 3.796A pdb=" N GLY F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 105 Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.521A pdb=" N LEU F 112 " --> pdb=" O SER F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 159 through 182 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 186 through 213 Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.902A pdb=" N LYS G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 52 Processing helix chain 'G' and resid 58 through 80 removed outlier: 3.813A pdb=" N GLY G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 105 Processing helix chain 'G' and resid 108 through 131 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 159 through 182 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 186 through 213 Processing helix chain 'H' and resid 7 through 27 removed outlier: 3.835A pdb=" N LYS H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 51 Processing helix chain 'H' and resid 58 through 80 removed outlier: 3.796A pdb=" N GLY H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 105 Processing helix chain 'H' and resid 108 through 131 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 159 through 182 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 186 through 213 Processing helix chain 'I' and resid 7 through 27 removed outlier: 3.807A pdb=" N LYS I 27 " --> pdb=" O GLU I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 51 Processing helix chain 'I' and resid 58 through 80 removed outlier: 3.790A pdb=" N GLY I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 108 through 131 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 159 through 182 Processing helix chain 'I' and resid 183 through 185 No H-bonds generated for 'chain 'I' and resid 183 through 185' Processing helix chain 'I' and resid 186 through 213 Processing helix chain 'J' and resid 7 through 27 removed outlier: 3.862A pdb=" N LYS J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 51 Processing helix chain 'J' and resid 58 through 80 removed outlier: 3.824A pdb=" N GLY J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 105 Processing helix chain 'J' and resid 108 through 131 removed outlier: 3.502A pdb=" N LEU J 112 " --> pdb=" O SER J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 159 through 182 Processing helix chain 'J' and resid 183 through 185 No H-bonds generated for 'chain 'J' and resid 183 through 185' Processing helix chain 'J' and resid 186 through 213 Processing helix chain 'K' and resid 7 through 27 removed outlier: 3.822A pdb=" N LYS K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 51 Processing helix chain 'K' and resid 58 through 80 removed outlier: 3.777A pdb=" N GLY K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 Processing helix chain 'K' and resid 108 through 131 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 159 through 182 Processing helix chain 'K' and resid 183 through 185 No H-bonds generated for 'chain 'K' and resid 183 through 185' Processing helix chain 'K' and resid 186 through 213 Processing helix chain 'L' and resid 7 through 27 removed outlier: 3.816A pdb=" N LYS L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 51 Processing helix chain 'L' and resid 58 through 80 removed outlier: 3.848A pdb=" N GLY L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 105 Processing helix chain 'L' and resid 108 through 131 removed outlier: 3.502A pdb=" N LEU L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 159 through 182 Processing helix chain 'L' and resid 183 through 185 No H-bonds generated for 'chain 'L' and resid 183 through 185' Processing helix chain 'L' and resid 186 through 213 Processing helix chain 'M' and resid 7 through 27 removed outlier: 3.816A pdb=" N LYS M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 51 Processing helix chain 'M' and resid 58 through 80 removed outlier: 3.812A pdb=" N GLY M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 105 Processing helix chain 'M' and resid 108 through 131 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 159 through 182 Processing helix chain 'M' and resid 183 through 185 No H-bonds generated for 'chain 'M' and resid 183 through 185' Processing helix chain 'M' and resid 186 through 213 Processing helix chain 'N' and resid 7 through 27 removed outlier: 3.908A pdb=" N LYS N 27 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 51 Processing helix chain 'N' and resid 58 through 80 removed outlier: 3.794A pdb=" N GLY N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 105 Processing helix chain 'N' and resid 108 through 131 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 159 through 182 Processing helix chain 'N' and resid 183 through 185 No H-bonds generated for 'chain 'N' and resid 183 through 185' Processing helix chain 'N' and resid 186 through 213 Processing helix chain 'O' and resid 7 through 27 removed outlier: 3.872A pdb=" N LYS O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 51 Processing helix chain 'O' and resid 58 through 80 removed outlier: 3.796A pdb=" N GLY O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 105 Processing helix chain 'O' and resid 108 through 131 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 159 through 182 Processing helix chain 'O' and resid 183 through 185 No H-bonds generated for 'chain 'O' and resid 183 through 185' Processing helix chain 'O' and resid 186 through 213 Processing helix chain 'P' and resid 7 through 27 removed outlier: 3.820A pdb=" N LYS P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 51 Processing helix chain 'P' and resid 58 through 80 removed outlier: 3.843A pdb=" N GLY P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 105 Processing helix chain 'P' and resid 108 through 131 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 159 through 182 Processing helix chain 'P' and resid 183 through 185 No H-bonds generated for 'chain 'P' and resid 183 through 185' Processing helix chain 'P' and resid 186 through 213 Processing helix chain 'Q' and resid 7 through 27 removed outlier: 3.850A pdb=" N LYS Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 51 Processing helix chain 'Q' and resid 58 through 80 removed outlier: 3.845A pdb=" N GLY Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 105 Processing helix chain 'Q' and resid 108 through 131 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 159 through 182 Processing helix chain 'Q' and resid 183 through 185 No H-bonds generated for 'chain 'Q' and resid 183 through 185' Processing helix chain 'Q' and resid 186 through 213 Processing helix chain 'R' and resid 7 through 27 removed outlier: 3.866A pdb=" N LYS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 51 Processing helix chain 'R' and resid 58 through 80 removed outlier: 3.824A pdb=" N GLY R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 105 Processing helix chain 'R' and resid 108 through 131 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 159 through 182 Processing helix chain 'R' and resid 183 through 185 No H-bonds generated for 'chain 'R' and resid 183 through 185' Processing helix chain 'R' and resid 186 through 213 Processing helix chain 'S' and resid 7 through 27 removed outlier: 3.867A pdb=" N LYS S 27 " --> pdb=" O GLU S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 51 Processing helix chain 'S' and resid 58 through 80 removed outlier: 3.838A pdb=" N GLY S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 105 Processing helix chain 'S' and resid 108 through 131 removed outlier: 3.512A pdb=" N LEU S 112 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 159 through 182 Processing helix chain 'S' and resid 183 through 185 No H-bonds generated for 'chain 'S' and resid 183 through 185' Processing helix chain 'S' and resid 186 through 213 Processing helix chain 'T' and resid 7 through 27 removed outlier: 3.838A pdb=" N LYS T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 51 Processing helix chain 'T' and resid 58 through 80 removed outlier: 3.814A pdb=" N GLY T 80 " --> pdb=" O ALA T 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 105 Processing helix chain 'T' and resid 108 through 131 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 159 through 182 Processing helix chain 'T' and resid 183 through 185 No H-bonds generated for 'chain 'T' and resid 183 through 185' Processing helix chain 'T' and resid 186 through 213 Processing helix chain 'U' and resid 7 through 27 removed outlier: 3.802A pdb=" N LYS U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 51 Processing helix chain 'U' and resid 58 through 80 removed outlier: 3.823A pdb=" N GLY U 80 " --> pdb=" O ALA U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 105 Processing helix chain 'U' and resid 108 through 131 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 159 through 182 Processing helix chain 'U' and resid 183 through 185 No H-bonds generated for 'chain 'U' and resid 183 through 185' Processing helix chain 'U' and resid 186 through 213 3248 hydrogen bonds defined for protein. 9744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 4.17 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: 11822 1.34 - 1.46: 2995 1.46 - 1.57: 21282 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 36267 Sorted by residual: bond pdb=" CG ARG T 110 " pdb=" CD ARG T 110 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" CG ARG A 110 " pdb=" CD ARG A 110 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG ARG B 110 " pdb=" CD ARG B 110 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CG ARG G 110 " pdb=" CD ARG G 110 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" CG ARG C 110 " pdb=" CD ARG C 110 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 36262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 48297 1.86 - 3.72: 582 3.72 - 5.58: 29 5.58 - 7.44: 20 7.44 - 9.30: 2 Bond angle restraints: 48930 Sorted by residual: angle pdb=" N GLY T 80 " pdb=" CA GLY T 80 " pdb=" C GLY T 80 " ideal model delta sigma weight residual 111.63 116.04 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N GLY C 80 " pdb=" CA GLY C 80 " pdb=" C GLY C 80 " ideal model delta sigma weight residual 111.63 115.95 -4.32 1.15e+00 7.56e-01 1.41e+01 angle pdb=" CG ARG S 110 " pdb=" CD ARG S 110 " pdb=" NE ARG S 110 " ideal model delta sigma weight residual 112.00 118.32 -6.32 2.20e+00 2.07e-01 8.26e+00 angle pdb=" CG ARG O 110 " pdb=" CD ARG O 110 " pdb=" NE ARG O 110 " ideal model delta sigma weight residual 112.00 117.86 -5.86 2.20e+00 2.07e-01 7.10e+00 angle pdb=" CA LEU R 51 " pdb=" CB LEU R 51 " pdb=" CG LEU R 51 " ideal model delta sigma weight residual 116.30 125.60 -9.30 3.50e+00 8.16e-02 7.06e+00 ... (remaining 48925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 18828 17.67 - 35.35: 2604 35.35 - 53.02: 984 53.02 - 70.69: 180 70.69 - 88.37: 42 Dihedral angle restraints: 22638 sinusoidal: 9744 harmonic: 12894 Sorted by residual: dihedral pdb=" CB GLU H 56 " pdb=" CG GLU H 56 " pdb=" CD GLU H 56 " pdb=" OE1 GLU H 56 " ideal model delta sinusoidal sigma weight residual 0.00 -88.37 88.37 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU P 172 " pdb=" CG GLU P 172 " pdb=" CD GLU P 172 " pdb=" OE1 GLU P 172 " ideal model delta sinusoidal sigma weight residual 0.00 -87.04 87.04 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU B 56 " pdb=" CG GLU B 56 " pdb=" CD GLU B 56 " pdb=" OE1 GLU B 56 " ideal model delta sinusoidal sigma weight residual 0.00 86.05 -86.05 1 3.00e+01 1.11e-03 9.93e+00 ... (remaining 22635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3771 0.027 - 0.053: 1502 0.053 - 0.080: 460 0.080 - 0.107: 109 0.107 - 0.133: 80 Chirality restraints: 5922 Sorted by residual: chirality pdb=" CG LEU C 88 " pdb=" CB LEU C 88 " pdb=" CD1 LEU C 88 " pdb=" CD2 LEU C 88 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CB VAL M 115 " pdb=" CA VAL M 115 " pdb=" CG1 VAL M 115 " pdb=" CG2 VAL M 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO D 83 " pdb=" N PRO D 83 " pdb=" C PRO D 83 " pdb=" CB PRO D 83 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 5919 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 110 " -0.143 9.50e-02 1.11e+02 6.45e-02 3.23e+00 pdb=" NE ARG U 110 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG U 110 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG U 110 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG U 110 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 110 " 0.141 9.50e-02 1.11e+02 6.39e-02 3.16e+00 pdb=" NE ARG C 110 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 110 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 110 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 110 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 110 " 0.141 9.50e-02 1.11e+02 6.36e-02 3.10e+00 pdb=" NE ARG A 110 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 110 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 110 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 110 " 0.001 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 161 2.51 - 3.11: 24745 3.11 - 3.70: 55587 3.70 - 4.30: 77832 4.30 - 4.90: 135394 Nonbonded interactions: 293719 Sorted by model distance: nonbonded pdb=" OD2 ASP U 43 " pdb="ZN ZN K 302 " model vdw 1.911 2.230 nonbonded pdb=" OD2 ASP H 43 " pdb="ZN ZN H 303 " model vdw 1.916 2.230 nonbonded pdb=" OD2 ASP G 43 " pdb="ZN ZN D 301 " model vdw 1.929 2.230 nonbonded pdb=" OD2 ASP B 43 " pdb="ZN ZN B 303 " model vdw 1.935 2.230 nonbonded pdb=" OD2 ASP S 43 " pdb="ZN ZN I 302 " model vdw 1.949 2.230 ... (remaining 293714 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 213) selection = (chain 'B' and resid 6 through 213) selection = (chain 'C' and resid 6 through 213) selection = (chain 'D' and resid 6 through 213) selection = (chain 'E' and resid 6 through 213) selection = (chain 'F' and resid 6 through 213) selection = (chain 'G' and resid 6 through 213) selection = (chain 'H' and resid 6 through 213) selection = (chain 'I' and resid 6 through 213) selection = (chain 'J' and resid 6 through 213) selection = (chain 'K' and resid 6 through 213) selection = (chain 'L' and resid 6 through 213) selection = (chain 'M' and resid 6 through 213) selection = (chain 'N' and resid 6 through 213) selection = (chain 'O' and resid 6 through 213) selection = (chain 'P' and resid 6 through 213) selection = (chain 'Q' and resid 6 through 213) selection = (chain 'R' and resid 6 through 213) selection = (chain 'S' and resid 6 through 213) selection = chain 'T' selection = (chain 'U' and resid 6 through 213) } 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: 0.920 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: 0.510 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 36.790 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.004 0.034 36345 Z= 0.156 Angle : 0.494 9.301 48930 Z= 0.263 Chirality : 0.034 0.133 5922 Planarity : 0.005 0.064 6216 Dihedral : 18.512 88.369 14112 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 2.03 % Allowed : 24.31 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.83 (0.12), residues: 4326 helix: 3.56 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 110 TYR 0.005 0.001 TYR L 198 PHE 0.008 0.001 PHE M 167 HIS 0.003 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00356 (36267) covalent geometry : angle 0.49383 (48930) hydrogen bonds : bond 0.10036 ( 3248) hydrogen bonds : angle 3.32526 ( 9744) metal coordination : bond 0.00198 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 440 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 35 MET cc_start: 0.9020 (mtt) cc_final: 0.8721 (mtp) outliers start: 81 outliers final: 68 residues processed: 514 average time/residue: 1.0867 time to fit residues: 633.3594 Evaluate side-chains 499 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 431 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 180 LYS Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 151 ARG Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 151 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 151 ARG Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 151 ARG Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 151 ARG Chi-restraints excluded: chain R residue 151 ARG Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 151 ARG Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 180 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN O 55 ASN Q 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105256 restraints weight = 33209.553| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.69 r_work: 0.2990 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 36345 Z= 0.179 Angle : 0.490 5.047 48930 Z= 0.254 Chirality : 0.036 0.139 5922 Planarity : 0.005 0.040 6216 Dihedral : 7.420 84.681 4840 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.58 % Allowed : 22.08 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.79 (0.12), residues: 4326 helix: 3.56 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -0.60 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 110 TYR 0.006 0.001 TYR D 198 PHE 0.009 0.002 PHE M 153 HIS 0.003 0.001 HIS P 207 Details of bonding type rmsd covalent geometry : bond 0.00433 (36267) covalent geometry : angle 0.48969 (48930) hydrogen bonds : bond 0.07392 ( 3248) hydrogen bonds : angle 3.07831 ( 9744) metal coordination : bond 0.00282 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 441 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8534 (mtpp) REVERT: A 151 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8335 (tpt90) REVERT: B 39 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8438 (mtpt) REVERT: B 51 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 117 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 121 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 151 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8081 (tpt90) REVERT: D 51 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7433 (tt) REVERT: E 51 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8049 (tp) REVERT: F 39 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8306 (mtpp) REVERT: G 51 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7470 (tt) REVERT: G 151 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8021 (tpt90) REVERT: I 51 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8010 (tt) REVERT: K 51 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7763 (tt) REVERT: K 107 THR cc_start: 0.8725 (m) cc_final: 0.8305 (p) REVERT: M 51 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7533 (tt) REVERT: M 151 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8189 (tpt170) REVERT: N 55 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8392 (p0) REVERT: N 151 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8208 (ttt90) REVERT: O 51 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7411 (tt) REVERT: P 95 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: P 151 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8313 (ttt90) REVERT: P 206 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: R 51 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8353 (tt) REVERT: S 8 LEU cc_start: 0.8748 (tp) cc_final: 0.8493 (tm) REVERT: S 51 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7733 (tt) outliers start: 143 outliers final: 44 residues processed: 563 average time/residue: 1.0708 time to fit residues: 681.8236 Evaluate side-chains 489 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 423 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 151 ARG Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 151 ARG Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 151 ARG Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 151 ARG Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 174 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 300 optimal weight: 20.0000 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 405 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN O 55 ASN Q 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.139437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107483 restraints weight = 33318.757| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.69 r_work: 0.3047 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36345 Z= 0.138 Angle : 0.442 4.353 48930 Z= 0.231 Chirality : 0.034 0.129 5922 Planarity : 0.004 0.038 6216 Dihedral : 5.996 82.972 4747 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.31 % Allowed : 22.46 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4326 helix: 3.68 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -0.63 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 110 TYR 0.005 0.001 TYR J 198 PHE 0.008 0.001 PHE M 167 HIS 0.002 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00307 (36267) covalent geometry : angle 0.44185 (48930) hydrogen bonds : bond 0.06166 ( 3248) hydrogen bonds : angle 2.95021 ( 9744) metal coordination : bond 0.00178 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 438 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8482 (mtpp) REVERT: B 39 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8409 (mtpt) REVERT: B 51 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7738 (tp) REVERT: B 121 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 151 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8216 (tmt-80) REVERT: D 51 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7391 (tt) REVERT: E 51 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7985 (tp) REVERT: F 39 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8306 (mtpp) REVERT: G 51 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7606 (tt) REVERT: I 51 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7936 (tt) REVERT: I 95 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: I 151 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8318 (tmt-80) REVERT: K 51 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7668 (tt) REVERT: K 107 THR cc_start: 0.8791 (m) cc_final: 0.8405 (p) REVERT: K 184 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7153 (mt-10) REVERT: M 51 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7501 (tt) REVERT: N 13 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7610 (mtm110) REVERT: N 35 MET cc_start: 0.9020 (mtt) cc_final: 0.8733 (mtp) REVERT: N 55 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8728 (p0) REVERT: O 51 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7364 (tt) REVERT: P 95 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: P 151 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8267 (ttt90) REVERT: P 206 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: Q 95 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: R 107 THR cc_start: 0.8760 (m) cc_final: 0.8472 (p) REVERT: S 8 LEU cc_start: 0.8724 (tp) cc_final: 0.8466 (tm) REVERT: S 51 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7580 (tt) REVERT: U 13 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7732 (mtm-85) outliers start: 132 outliers final: 45 residues processed: 554 average time/residue: 1.0646 time to fit residues: 667.6448 Evaluate side-chains 489 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 424 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 180 LYS Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 55 ASN Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 78 ARG Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 151 ARG Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 125 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 232 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111133 restraints weight = 33416.665| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.69 r_work: 0.3095 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 36345 Z= 0.109 Angle : 0.405 5.150 48930 Z= 0.211 Chirality : 0.033 0.123 5922 Planarity : 0.004 0.036 6216 Dihedral : 5.079 78.943 4704 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.76 % Allowed : 23.11 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.30 (0.12), residues: 4326 helix: 3.88 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 110 TYR 0.004 0.001 TYR J 198 PHE 0.008 0.001 PHE O 167 HIS 0.002 0.000 HIS G 47 Details of bonding type rmsd covalent geometry : bond 0.00220 (36267) covalent geometry : angle 0.40459 (48930) hydrogen bonds : bond 0.04840 ( 3248) hydrogen bonds : angle 2.81830 ( 9744) metal coordination : bond 0.00107 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 476 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: C 51 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7402 (tp) REVERT: D 51 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (tt) REVERT: E 51 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7696 (tt) REVERT: F 39 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8261 (mtpp) REVERT: F 117 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8094 (mt-10) REVERT: G 44 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7737 (mm-30) REVERT: G 51 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7570 (tt) REVERT: I 95 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: K 44 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8071 (mt-10) REVERT: K 107 THR cc_start: 0.8816 (m) cc_final: 0.8437 (p) REVERT: K 184 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7133 (mt-10) REVERT: M 51 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7451 (tt) REVERT: N 13 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7573 (mtm110) REVERT: N 35 MET cc_start: 0.8943 (mtt) cc_final: 0.8654 (mtp) REVERT: N 55 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8496 (p0) REVERT: O 51 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7278 (tt) REVERT: P 206 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: R 95 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: R 107 THR cc_start: 0.8826 (m) cc_final: 0.8621 (p) REVERT: S 8 LEU cc_start: 0.8525 (tp) cc_final: 0.8288 (tm) REVERT: S 51 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7516 (tt) REVERT: U 13 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7699 (mtm-85) REVERT: U 119 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8610 (tp) outliers start: 110 outliers final: 28 residues processed: 570 average time/residue: 0.9466 time to fit residues: 618.4101 Evaluate side-chains 478 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 437 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 25 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 329 optimal weight: 8.9990 chunk 377 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.137616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105623 restraints weight = 32794.855| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.67 r_work: 0.3016 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 36345 Z= 0.166 Angle : 0.471 5.874 48930 Z= 0.244 Chirality : 0.035 0.136 5922 Planarity : 0.005 0.045 6216 Dihedral : 4.724 54.400 4678 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.36 % Allowed : 22.53 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.96 (0.12), residues: 4326 helix: 3.68 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -0.61 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 110 TYR 0.006 0.001 TYR D 198 PHE 0.009 0.001 PHE I 153 HIS 0.002 0.001 HIS P 207 Details of bonding type rmsd covalent geometry : bond 0.00398 (36267) covalent geometry : angle 0.47094 (48930) hydrogen bonds : bond 0.06864 ( 3248) hydrogen bonds : angle 2.95830 ( 9744) metal coordination : bond 0.00236 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 434 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8499 (mtpp) REVERT: A 179 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9002 (mt) REVERT: B 39 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8406 (mtpt) REVERT: D 51 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7517 (tt) REVERT: E 51 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7898 (tt) REVERT: F 21 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7875 (tpm-80) REVERT: F 39 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8315 (mtpp) REVERT: H 21 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7396 (mmm160) REVERT: I 95 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: J 21 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7743 (mmm160) REVERT: K 107 THR cc_start: 0.8897 (m) cc_final: 0.8528 (p) REVERT: K 184 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7227 (mt-10) REVERT: N 13 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7615 (mtm110) REVERT: N 21 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8159 (tpt-90) REVERT: N 55 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8593 (p0) REVERT: P 95 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: P 206 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: Q 95 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: Q 119 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8342 (tp) REVERT: R 95 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: R 184 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6967 (mt-10) REVERT: S 8 LEU cc_start: 0.8580 (tp) cc_final: 0.8348 (tm) REVERT: S 21 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7436 (mmp-170) REVERT: S 95 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: U 21 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7336 (mmp-170) REVERT: U 119 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8601 (tp) REVERT: U 129 ILE cc_start: 0.9188 (mm) cc_final: 0.8984 (mt) outliers start: 134 outliers final: 56 residues processed: 549 average time/residue: 0.9826 time to fit residues: 614.5752 Evaluate side-chains 497 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 420 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 21 ARG Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 143 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 88 LEU Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 216 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 296 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108248 restraints weight = 32983.188| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.68 r_work: 0.3048 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36345 Z= 0.128 Angle : 0.438 6.094 48930 Z= 0.228 Chirality : 0.034 0.126 5922 Planarity : 0.005 0.047 6216 Dihedral : 4.543 56.384 4676 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.33 % Allowed : 22.48 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.17 (0.12), residues: 4326 helix: 3.80 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 110 TYR 0.005 0.001 TYR J 198 PHE 0.008 0.001 PHE M 167 HIS 0.002 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00280 (36267) covalent geometry : angle 0.43813 (48930) hydrogen bonds : bond 0.05666 ( 3248) hydrogen bonds : angle 2.85601 ( 9744) metal coordination : bond 0.00147 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 437 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: B 39 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8392 (mtpt) REVERT: C 51 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7574 (tt) REVERT: D 51 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7492 (tt) REVERT: E 51 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7848 (tt) REVERT: F 21 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7876 (tpm-80) REVERT: F 39 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8297 (mtpp) REVERT: G 51 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7654 (tt) REVERT: H 21 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7374 (mmm160) REVERT: I 51 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7830 (tt) REVERT: I 95 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: J 136 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7588 (ttp80) REVERT: K 55 ASN cc_start: 0.8684 (p0) cc_final: 0.8481 (p0) REVERT: K 107 THR cc_start: 0.8863 (m) cc_final: 0.8495 (p) REVERT: K 184 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7174 (mt-10) REVERT: L 21 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7686 (mmm160) REVERT: L 119 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8487 (tp) REVERT: N 13 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7572 (mtm110) REVERT: N 21 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8148 (tpt-90) REVERT: N 35 MET cc_start: 0.8947 (mtt) cc_final: 0.8626 (mtp) REVERT: N 44 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7889 (mt-10) REVERT: N 55 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8496 (p0) REVERT: O 51 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7362 (tt) REVERT: P 95 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: P 206 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: Q 21 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7827 (mmp-170) REVERT: Q 95 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: R 21 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7685 (mmm160) REVERT: R 95 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: R 143 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8304 (mp) REVERT: R 184 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6928 (mt-10) REVERT: S 8 LEU cc_start: 0.8553 (tp) cc_final: 0.8314 (tm) REVERT: S 21 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7337 (mmp-170) REVERT: S 95 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7945 (tp30) REVERT: S 119 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8451 (tp) REVERT: U 13 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7732 (mtm-85) REVERT: U 21 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7180 (mmp-170) REVERT: U 119 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8578 (tp) outliers start: 133 outliers final: 62 residues processed: 549 average time/residue: 0.9935 time to fit residues: 621.0616 Evaluate side-chains 515 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 425 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 21 ARG Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 81 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 342 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 390 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN M 55 ASN Q 55 ASN T 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106106 restraints weight = 32888.057| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.68 r_work: 0.3025 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 36345 Z= 0.155 Angle : 0.468 6.118 48930 Z= 0.242 Chirality : 0.035 0.133 5922 Planarity : 0.005 0.052 6216 Dihedral : 4.627 55.614 4674 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.61 % Allowed : 22.28 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4326 helix: 3.72 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -0.68 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 110 TYR 0.006 0.001 TYR D 198 PHE 0.008 0.001 PHE M 167 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00365 (36267) covalent geometry : angle 0.46819 (48930) hydrogen bonds : bond 0.06540 ( 3248) hydrogen bonds : angle 2.92458 ( 9744) metal coordination : bond 0.00209 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 439 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8492 (mtpp) REVERT: B 39 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8410 (mtpt) REVERT: D 51 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7609 (tt) REVERT: E 51 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7888 (tt) REVERT: F 21 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7868 (tpm-80) REVERT: F 39 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8316 (mtpp) REVERT: G 51 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7663 (tt) REVERT: H 21 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7375 (mmm160) REVERT: I 51 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7833 (tt) REVERT: I 95 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: J 21 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7747 (mmm160) REVERT: J 136 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7709 (ttp80) REVERT: K 107 THR cc_start: 0.8882 (m) cc_final: 0.8510 (p) REVERT: K 184 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7224 (mt-10) REVERT: L 21 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7680 (mmm160) REVERT: L 119 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8513 (tp) REVERT: N 13 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7615 (mtm110) REVERT: N 21 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8192 (tpt-90) REVERT: N 55 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8521 (p0) REVERT: N 151 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8072 (ttt90) REVERT: O 51 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7403 (tt) REVERT: P 95 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: P 206 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: Q 21 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7821 (mmp-170) REVERT: Q 95 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: Q 119 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8334 (tp) REVERT: R 21 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7691 (mmm160) REVERT: R 95 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: R 143 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8367 (mp) REVERT: R 184 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6915 (mt-10) REVERT: S 8 LEU cc_start: 0.8591 (tp) cc_final: 0.8357 (tm) REVERT: S 21 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7473 (mmp-170) REVERT: S 95 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: S 119 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8553 (tp) REVERT: S 136 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7684 (ttp80) REVERT: T 151 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8221 (tpt170) REVERT: U 21 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7276 (mmp-170) REVERT: U 119 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8591 (tp) outliers start: 144 outliers final: 68 residues processed: 563 average time/residue: 1.0028 time to fit residues: 642.6941 Evaluate side-chains 523 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 422 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 151 ARG Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain S residue 21 ARG Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 55 ASN Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 151 ARG Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 232 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 296 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 323 optimal weight: 0.8980 chunk 348 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN M 55 ASN Q 55 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.137934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105919 restraints weight = 32757.715| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.68 r_work: 0.3021 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36345 Z= 0.161 Angle : 0.479 6.189 48930 Z= 0.248 Chirality : 0.035 0.135 5922 Planarity : 0.005 0.058 6216 Dihedral : 4.665 55.887 4672 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.36 % Allowed : 22.81 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.97 (0.12), residues: 4326 helix: 3.68 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -0.62 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 110 TYR 0.006 0.001 TYR D 198 PHE 0.008 0.001 PHE I 153 HIS 0.002 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00384 (36267) covalent geometry : angle 0.47862 (48930) hydrogen bonds : bond 0.06677 ( 3248) hydrogen bonds : angle 2.93919 ( 9744) metal coordination : bond 0.00222 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 423 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8499 (mtpp) REVERT: B 39 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8408 (mtpt) REVERT: D 51 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7631 (tt) REVERT: E 51 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7875 (tt) REVERT: F 21 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7862 (tpm-80) REVERT: F 39 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8316 (mtpp) REVERT: G 51 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7636 (tt) REVERT: H 21 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7388 (mmm160) REVERT: I 95 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: J 21 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7748 (mmm160) REVERT: J 136 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7725 (ttp80) REVERT: K 107 THR cc_start: 0.8886 (m) cc_final: 0.8516 (p) REVERT: K 184 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7220 (mt-10) REVERT: L 21 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7681 (mmm160) REVERT: L 119 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8515 (tp) REVERT: N 13 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7618 (mtm110) REVERT: N 21 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8166 (tpt-90) REVERT: N 55 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8511 (p0) REVERT: N 151 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8057 (ttt90) REVERT: O 51 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7428 (tt) REVERT: P 95 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: P 206 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: Q 21 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7847 (mmp-170) REVERT: Q 95 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: Q 119 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8344 (tp) REVERT: R 21 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7691 (mmm160) REVERT: R 95 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: R 143 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8377 (mp) REVERT: S 8 LEU cc_start: 0.8595 (tp) cc_final: 0.8361 (tm) REVERT: S 21 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7476 (mmp-170) REVERT: S 95 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: S 119 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8526 (tp) REVERT: S 136 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7707 (ttp80) REVERT: T 151 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8233 (tpt170) REVERT: U 21 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7267 (mmp-170) REVERT: U 119 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8593 (tp) outliers start: 134 outliers final: 73 residues processed: 538 average time/residue: 1.0508 time to fit residues: 641.6768 Evaluate side-chains 523 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 418 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 151 ARG Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain S residue 21 ARG Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 151 ARG Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 325 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 400 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 411 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 55 ASN T 55 ASN U 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105846 restraints weight = 32898.941| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.68 r_work: 0.3005 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36345 Z= 0.168 Angle : 0.495 6.576 48930 Z= 0.256 Chirality : 0.035 0.135 5922 Planarity : 0.005 0.062 6216 Dihedral : 4.717 55.636 4672 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 3.46 % Allowed : 22.86 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.94 (0.12), residues: 4326 helix: 3.66 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -0.62 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 110 TYR 0.006 0.001 TYR D 198 PHE 0.009 0.001 PHE I 153 HIS 0.002 0.001 HIS P 207 Details of bonding type rmsd covalent geometry : bond 0.00404 (36267) covalent geometry : angle 0.49460 (48930) hydrogen bonds : bond 0.06827 ( 3248) hydrogen bonds : angle 2.95458 ( 9744) metal coordination : bond 0.00232 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 424 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8490 (mtpp) REVERT: B 39 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8404 (mtpt) REVERT: D 51 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7659 (tt) REVERT: E 51 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7825 (tt) REVERT: E 111 GLU cc_start: 0.8225 (mp0) cc_final: 0.7894 (mp0) REVERT: F 21 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7840 (tpm-80) REVERT: F 39 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8313 (mtpp) REVERT: F 117 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8068 (mt-10) REVERT: G 51 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7645 (tt) REVERT: H 21 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7374 (mmm160) REVERT: I 95 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: J 21 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7755 (mmm160) REVERT: J 55 ASN cc_start: 0.8388 (p0) cc_final: 0.8110 (p0) REVERT: J 136 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7693 (ttp80) REVERT: K 107 THR cc_start: 0.8877 (m) cc_final: 0.8502 (p) REVERT: K 184 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7206 (mt-10) REVERT: L 21 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7701 (mmm160) REVERT: L 119 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8538 (tp) REVERT: N 13 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7617 (mtm110) REVERT: N 21 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8167 (tpt-90) REVERT: N 55 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8455 (p0) REVERT: N 151 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8045 (ttt90) REVERT: O 24 GLU cc_start: 0.7902 (tt0) cc_final: 0.7673 (tm-30) REVERT: P 95 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: P 206 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: Q 21 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7822 (mmp-170) REVERT: Q 95 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: Q 119 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8377 (tp) REVERT: R 21 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7680 (mmm160) REVERT: R 95 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: R 143 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8380 (mp) REVERT: S 8 LEU cc_start: 0.8594 (tp) cc_final: 0.8357 (tm) REVERT: S 21 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7488 (mmp-170) REVERT: S 95 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: S 119 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8521 (tp) REVERT: S 136 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7735 (ttp80) REVERT: T 151 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8248 (tpt170) REVERT: U 21 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7333 (mmp-170) REVERT: U 119 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8584 (tp) outliers start: 138 outliers final: 73 residues processed: 540 average time/residue: 1.1117 time to fit residues: 680.6344 Evaluate side-chains 525 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 421 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 151 ARG Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain S residue 21 ARG Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 55 ASN Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 151 ARG Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 41 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 chunk 412 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 295 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 ASN F 55 ASN M 55 ASN Q 55 ASN T 55 ASN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107036 restraints weight = 33111.402| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.69 r_work: 0.3036 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36345 Z= 0.147 Angle : 0.475 5.990 48930 Z= 0.247 Chirality : 0.034 0.130 5922 Planarity : 0.005 0.060 6216 Dihedral : 4.660 56.391 4672 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.86 % Allowed : 23.61 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 4326 helix: 3.73 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -0.60 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG U 110 TYR 0.006 0.001 TYR G 198 PHE 0.008 0.001 PHE M 167 HIS 0.002 0.001 HIS T 207 Details of bonding type rmsd covalent geometry : bond 0.00340 (36267) covalent geometry : angle 0.47550 (48930) hydrogen bonds : bond 0.06238 ( 3248) hydrogen bonds : angle 2.90883 ( 9744) metal coordination : bond 0.00188 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 425 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8411 (mtpt) REVERT: D 51 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7653 (tt) REVERT: E 51 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7787 (tt) REVERT: F 21 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7847 (tpm-80) REVERT: F 39 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8294 (mtpp) REVERT: F 117 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8053 (mt-10) REVERT: G 51 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7635 (tt) REVERT: H 21 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7374 (mmm160) REVERT: I 95 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: J 21 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7753 (mmm160) REVERT: J 136 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7596 (ttp80) REVERT: K 107 THR cc_start: 0.8784 (m) cc_final: 0.8415 (p) REVERT: K 184 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7180 (mt-10) REVERT: L 21 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7711 (mmm160) REVERT: L 119 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8512 (tp) REVERT: N 13 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7610 (mtm110) REVERT: N 21 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8179 (tpt-90) REVERT: N 55 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8429 (p0) REVERT: O 51 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7409 (tt) REVERT: P 95 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: P 206 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7700 (tm-30) REVERT: Q 21 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7824 (mmp-170) REVERT: Q 95 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: Q 119 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8385 (tp) REVERT: R 21 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7671 (mmm160) REVERT: R 95 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: R 143 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8334 (mp) REVERT: S 8 LEU cc_start: 0.8584 (tp) cc_final: 0.8343 (tm) REVERT: S 21 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7366 (mmp-170) REVERT: S 95 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: S 119 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8540 (tp) REVERT: S 136 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7666 (ttp80) REVERT: T 151 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8188 (tpt90) REVERT: U 21 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7280 (mmp-170) REVERT: U 119 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8569 (tp) outliers start: 114 outliers final: 67 residues processed: 522 average time/residue: 1.1209 time to fit residues: 662.4378 Evaluate side-chains 515 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 418 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 39 LYS Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 21 ARG Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 189 THR Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 182 LEU Chi-restraints excluded: chain M residue 35 MET Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 55 ASN Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 51 LEU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 119 LEU Chi-restraints excluded: chain O residue 189 THR Chi-restraints excluded: chain P residue 18 VAL Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain Q residue 21 ARG Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 51 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain S residue 21 ARG Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain S residue 119 LEU Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain S residue 206 GLU Chi-restraints excluded: chain T residue 39 LYS Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 55 ASN Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 151 ARG Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 119 LEU Chi-restraints excluded: chain U residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 374 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107112 restraints weight = 32850.993| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.68 r_work: 0.3052 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36345 Z= 0.147 Angle : 0.479 6.401 48930 Z= 0.248 Chirality : 0.034 0.130 5922 Planarity : 0.005 0.069 6216 Dihedral : 4.652 56.488 4672 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.98 % Allowed : 23.56 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 5.08 (0.12), residues: 4326 helix: 3.75 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 110 TYR 0.005 0.001 TYR J 198 PHE 0.008 0.001 PHE M 167 HIS 0.002 0.001 HIS T 207 Details of bonding type rmsd covalent geometry : bond 0.00340 (36267) covalent geometry : angle 0.47936 (48930) hydrogen bonds : bond 0.06232 ( 3248) hydrogen bonds : angle 2.90884 ( 9744) metal coordination : bond 0.00186 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14304.55 seconds wall clock time: 243 minutes 20.97 seconds (14600.97 seconds total)