Starting phenix.real_space_refine on Sat Feb 7 18:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k86_62162/02_2026/9k86_62162_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k86_62162/02_2026/9k86_62162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k86_62162/02_2026/9k86_62162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k86_62162/02_2026/9k86_62162.map" model { file = "/net/cci-nas-00/data/ceres_data/9k86_62162/02_2026/9k86_62162_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k86_62162/02_2026/9k86_62162_neut.cif" } resolution = 2.76 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= 0.019 sd= 0.224 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 42 5.16 5 C 23394 2.51 5 N 5628 2.21 5 O 6321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 276 residue(s): 0.04s 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: 35427 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "B" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "D" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "F" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "G" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "H" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "I" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "J" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "L" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "M" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "N" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "O" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "P" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "Q" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "R" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "S" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "T" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "U" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain: "A" 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: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" 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: "O" 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: "P" 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: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "U" 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} Time building chain proxies: 9.26, per 1000 atoms: 0.26 Number of scatterers: 35427 At special positions: 0 Unit cell: (122.812, 126.044, 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 42 16.00 O 6321 8.00 N 5628 7.00 C 23394 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: 3.67 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 C 207 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 75 " 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 A 207 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 75 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 207 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS D 75 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS M 47 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 124 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS E 207 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 75 " 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 F 75 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 207 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS O 47 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 124 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS G 207 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 75 " 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 G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS Q 47 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 124 " pdb=" ZN G 302 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS I 207 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS G 75 " 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 I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS S 47 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 124 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS K 207 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS I 75 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS A 47 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 124 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS J 207 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS L 75 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS U 47 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 124 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS M 207 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS K 75 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS L 124 " pdb=" ZN L 302 " pdb="ZN ZN L 302 " - pdb=" NE2 HIS L 207 " pdb="ZN ZN L 302 " - pdb=" NE2 HIS N 75 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 124 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS D 47 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 124 " pdb=" ZN N 302 " pdb="ZN ZN N 302 " - pdb=" NE2 HIS N 207 " pdb="ZN ZN N 302 " - 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 303 " pdb="ZN ZN O 303 " - pdb=" NE2 HIS O 75 " pdb="ZN ZN O 303 " - pdb=" NE2 HIS Q 207 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS F 47 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 124 " pdb=" ZN P 302 " pdb="ZN ZN P 302 " - pdb=" NE2 HIS P 207 " pdb="ZN ZN P 302 " - pdb=" NE2 HIS R 75 " pdb=" ZN Q 302 " pdb="ZN ZN Q 302 " - pdb=" NE2 HIS S 207 " pdb="ZN ZN Q 302 " - pdb=" NE2 HIS Q 75 " pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS H 47 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 124 " pdb=" ZN R 302 " pdb="ZN ZN R 302 " - pdb=" NE2 HIS R 207 " pdb="ZN ZN R 302 " - pdb=" NE2 HIS T 75 " pdb=" ZN S 301 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS S 124 " pdb=" ZN S 302 " pdb="ZN ZN S 302 " - pdb=" NE2 HIS U 207 " pdb="ZN ZN S 302 " - pdb=" NE2 HIS S 75 " pdb=" ZN T 301 " pdb="ZN ZN T 301 " - pdb=" NE2 HIS J 47 " pdb="ZN ZN T 301 " - pdb=" NE2 HIS T 124 " pdb=" ZN U 301 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS U 124 " pdb=" ZN U 302 " pdb="ZN ZN U 302 " - 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: 8484 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 0 sheets defined 93.7% 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 27 Processing helix chain 'A' and resid 30 through 52 removed outlier: 3.748A pdb=" N LEU A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 4.311A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 108 through 131 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 removed outlier: 3.588A pdb=" N ILE A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 27 Processing helix chain 'B' and resid 30 through 52 removed outlier: 3.858A pdb=" N LEU B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 79 removed outlier: 4.335A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 108 through 131 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 removed outlier: 3.612A pdb=" N ILE B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 Processing helix chain 'C' and resid 30 through 52 removed outlier: 3.916A pdb=" N LEU C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 79 removed outlier: 4.329A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 Processing helix chain 'C' and resid 108 through 131 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 removed outlier: 3.726A pdb=" N ILE C 191 " --> pdb=" O PRO C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.789A pdb=" N LEU D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 79 removed outlier: 4.318A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 105 Processing helix chain 'D' and resid 108 through 131 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 Processing helix chain 'E' and resid 30 through 52 removed outlier: 3.774A pdb=" N LEU E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 79 removed outlier: 4.271A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 108 through 131 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 removed outlier: 3.799A pdb=" N ILE E 191 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 Processing helix chain 'F' and resid 30 through 52 removed outlier: 3.840A pdb=" N LEU F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 4.299A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 105 Processing helix chain 'F' and resid 108 through 131 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 Processing helix chain 'G' and resid 30 through 52 removed outlier: 3.752A pdb=" N LEU G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 79 removed outlier: 4.299A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE G 61 " --> pdb=" O GLU G 57 " (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 removed outlier: 3.506A pdb=" N GLY G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 27 Processing helix chain 'H' and resid 30 through 52 removed outlier: 3.803A pdb=" N LEU H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 79 removed outlier: 4.259A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE H 61 " --> pdb=" O GLU H 57 " (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 Processing helix chain 'I' and resid 30 through 52 removed outlier: 3.733A pdb=" N LEU I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 79 removed outlier: 4.340A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE I 61 " --> pdb=" O GLU I 57 " (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 Processing helix chain 'J' and resid 30 through 52 removed outlier: 3.855A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 79 removed outlier: 4.351A pdb=" N LEU J 60 " --> pdb=" O PRO J 56 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 105 Processing helix chain 'J' and resid 108 through 131 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 Processing helix chain 'K' and resid 30 through 52 removed outlier: 3.891A pdb=" N LEU K 36 " --> pdb=" O GLU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 79 removed outlier: 4.329A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE K 61 " --> pdb=" O GLU K 57 " (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 Processing helix chain 'L' and resid 30 through 52 removed outlier: 3.834A pdb=" N LEU L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 79 removed outlier: 4.320A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 105 removed outlier: 3.513A pdb=" N GLY L 105 " --> pdb=" O LEU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 131 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 Processing helix chain 'M' and resid 30 through 52 removed outlier: 3.900A pdb=" N LEU M 36 " --> pdb=" O GLU M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 79 removed outlier: 4.309A pdb=" N LEU M 60 " --> pdb=" O PRO M 56 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE M 61 " --> pdb=" O GLU M 57 " (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 removed outlier: 3.705A pdb=" N GLY M 213 " --> pdb=" O LEU M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 27 Processing helix chain 'N' and resid 31 through 52 removed outlier: 3.883A pdb=" N LEU N 36 " --> pdb=" O GLU N 32 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 79 removed outlier: 4.307A pdb=" N LEU N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE N 61 " --> pdb=" O GLU N 57 " (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 removed outlier: 3.592A pdb=" N ILE N 191 " --> pdb=" O PRO N 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 27 Processing helix chain 'O' and resid 30 through 52 removed outlier: 3.921A pdb=" N LEU O 36 " --> pdb=" O GLU O 32 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS O 37 " --> pdb=" O GLU O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 79 removed outlier: 4.278A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE O 61 " --> pdb=" O GLU O 57 " (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 Processing helix chain 'P' and resid 31 through 52 removed outlier: 3.821A pdb=" N LEU P 36 " --> pdb=" O GLU P 32 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS P 37 " --> pdb=" O GLU P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 79 removed outlier: 4.293A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE P 61 " --> pdb=" O GLU P 57 " (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 Processing helix chain 'Q' and resid 30 through 52 removed outlier: 3.774A pdb=" N LEU Q 36 " --> pdb=" O GLU Q 32 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Q 52 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 79 removed outlier: 4.322A pdb=" N LEU Q 60 " --> pdb=" O PRO Q 56 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE Q 61 " --> pdb=" O GLU Q 57 " (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 Processing helix chain 'R' and resid 31 through 52 removed outlier: 3.816A pdb=" N LEU R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS R 37 " --> pdb=" O GLU R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 79 removed outlier: 4.286A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE R 61 " --> pdb=" O GLU R 57 " (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 removed outlier: 3.719A pdb=" N ILE R 191 " --> pdb=" O PRO R 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 27 Processing helix chain 'S' and resid 30 through 52 removed outlier: 3.739A pdb=" N LEU S 36 " --> pdb=" O GLU S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 79 removed outlier: 4.281A pdb=" N LEU S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE S 61 " --> pdb=" O GLU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 105 Processing helix chain 'S' and resid 108 through 131 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 Processing helix chain 'T' and resid 31 through 52 removed outlier: 3.863A pdb=" N LEU T 36 " --> pdb=" O GLU T 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS T 37 " --> pdb=" O GLU T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 79 removed outlier: 4.346A pdb=" N LEU T 60 " --> pdb=" O PRO T 56 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE T 61 " --> pdb=" O GLU T 57 " (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 removed outlier: 3.611A pdb=" N ILE T 191 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 27 Processing helix chain 'U' and resid 31 through 52 removed outlier: 3.880A pdb=" N LEU U 36 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS U 37 " --> pdb=" O GLU U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 79 removed outlier: 4.277A pdb=" N LEU U 60 " --> pdb=" O PRO U 56 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE U 61 " --> pdb=" O GLU U 57 " (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 removed outlier: 3.685A pdb=" N ILE U 191 " --> pdb=" O PRO U 187 " (cutoff:3.500A) 3273 hydrogen bonds defined for protein. 9819 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: 6.87 Time building geometry restraints manager: 4.63 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: 10075 1.34 - 1.45: 3446 1.45 - 1.57: 22241 1.57 - 1.69: 1 1.69 - 1.81: 84 Bond restraints: 35847 Sorted by residual: bond pdb=" C VAL U 185 " pdb=" O VAL U 185 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.19e-02 7.06e+03 2.57e+00 bond pdb=" CB PRO G 53 " pdb=" CG PRO G 53 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.53e+00 bond pdb=" C VAL M 185 " pdb=" O VAL M 185 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.37e+00 bond pdb=" C VAL N 185 " pdb=" O VAL N 185 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.19e-02 7.06e+03 2.33e+00 bond pdb=" CB PRO R 53 " pdb=" CG PRO R 53 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 ... (remaining 35842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 47027 1.61 - 3.22: 1097 3.22 - 4.83: 201 4.83 - 6.44: 47 6.44 - 8.05: 12 Bond angle restraints: 48384 Sorted by residual: angle pdb=" N LYS Q 13 " pdb=" CA LYS Q 13 " pdb=" C LYS Q 13 " ideal model delta sigma weight residual 111.07 106.32 4.75 1.07e+00 8.73e-01 1.97e+01 angle pdb=" N ILE P 31 " pdb=" CA ILE P 31 " pdb=" C ILE P 31 " ideal model delta sigma weight residual 110.72 114.52 -3.80 1.01e+00 9.80e-01 1.42e+01 angle pdb=" N GLY D 80 " pdb=" CA GLY D 80 " pdb=" C GLY D 80 " ideal model delta sigma weight residual 111.72 116.45 -4.73 1.31e+00 5.83e-01 1.30e+01 angle pdb=" CA GLU J 113 " pdb=" CB GLU J 113 " pdb=" CG GLU J 113 " ideal model delta sigma weight residual 114.10 121.30 -7.20 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA GLU Q 113 " pdb=" CB GLU Q 113 " pdb=" CG GLU Q 113 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 ... (remaining 48379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 18107 17.91 - 35.81: 2822 35.81 - 53.72: 1110 53.72 - 71.62: 164 71.62 - 89.53: 36 Dihedral angle restraints: 22239 sinusoidal: 9387 harmonic: 12852 Sorted by residual: dihedral pdb=" CA ASN D 186 " pdb=" C ASN D 186 " pdb=" N PRO D 187 " pdb=" CA PRO D 187 " ideal model delta harmonic sigma weight residual -180.00 -162.16 -17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " pdb=" NE ARG A 92 " pdb=" CZ ARG A 92 " ideal model delta sinusoidal sigma weight residual -90.00 -39.91 -50.09 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CG ARG H 92 " pdb=" CD ARG H 92 " pdb=" NE ARG H 92 " pdb=" CZ ARG H 92 " ideal model delta sinusoidal sigma weight residual -90.00 -39.93 -50.07 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 22236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 4618 0.039 - 0.077: 1273 0.077 - 0.116: 141 0.116 - 0.155: 14 0.155 - 0.194: 23 Chirality restraints: 6069 Sorted by residual: chirality pdb=" CA PRO P 187 " pdb=" N PRO P 187 " pdb=" C PRO P 187 " pdb=" CB PRO P 187 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA PRO D 187 " pdb=" N PRO D 187 " pdb=" C PRO D 187 " pdb=" CB PRO D 187 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA PRO I 187 " pdb=" N PRO I 187 " pdb=" C PRO I 187 " pdb=" CB PRO I 187 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 6066 not shown) Planarity restraints: 5859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 52 " -0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO L 53 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO L 53 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 53 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 52 " -0.048 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO G 53 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU I 17 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" CD GLU I 17 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU I 17 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU I 17 " -0.017 2.00e-02 2.50e+03 ... (remaining 5856 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 183 2.51 - 3.10: 25214 3.10 - 3.70: 55071 3.70 - 4.30: 78289 4.30 - 4.90: 133163 Nonbonded interactions: 291920 Sorted by model distance: nonbonded pdb=" OD2 ASP A 203 " pdb="ZN ZN B 302 " model vdw 1.907 2.230 nonbonded pdb=" OD2 ASP R 203 " pdb="ZN ZN R 302 " model vdw 1.919 2.230 nonbonded pdb=" OD2 ASP U 203 " pdb="ZN ZN S 302 " model vdw 1.922 2.230 nonbonded pdb=" OD2 ASP E 203 " pdb="ZN ZN C 302 " model vdw 1.928 2.230 nonbonded pdb=" OD2 ASP M 203 " pdb="ZN ZN K 302 " model vdw 1.930 2.230 ... (remaining 291915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 301) selection = (chain 'B' and resid 6 through 301) selection = (chain 'C' and resid 6 through 301) selection = (chain 'D' and resid 6 through 301) selection = (chain 'E' and resid 6 through 301) selection = (chain 'F' and resid 6 through 301) selection = (chain 'G' and resid 6 through 301) selection = (chain 'H' and resid 6 through 301) selection = (chain 'I' and resid 6 through 301) selection = (chain 'J' and resid 6 through 301) selection = (chain 'K' and resid 6 through 301) selection = (chain 'L' and resid 6 through 301) selection = chain 'M' selection = (chain 'N' and resid 6 through 301) selection = (chain 'O' and resid 6 through 301) selection = (chain 'P' and resid 6 through 301) selection = (chain 'Q' and resid 6 through 301) selection = (chain 'R' and resid 6 through 301) selection = (chain 'S' and resid 6 through 301) selection = chain 'T' selection = (chain 'U' and resid 6 through 301) } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.110 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.080 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.010 0.700 35923 Z= 0.369 Angle : 0.624 8.055 48384 Z= 0.359 Chirality : 0.036 0.194 6069 Planarity : 0.006 0.072 5859 Dihedral : 19.727 89.527 13755 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.49 % Allowed : 1.69 % Favored : 97.83 % Rotamer: Outliers : 2.69 % Allowed : 31.41 % Favored : 65.90 % 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: 3.31 (0.12), residues: 4326 helix: 2.49 (0.08), residues: 3948 sheet: None (None), residues: 0 loop : -1.31 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 92 TYR 0.017 0.002 TYR T 198 PHE 0.012 0.002 PHE G 145 TRP 0.014 0.001 TRP A 63 HIS 0.005 0.001 HIS H 47 Details of bonding type rmsd covalent geometry : bond 0.00418 (35847) covalent geometry : angle 0.62370 (48384) hydrogen bonds : bond 0.11687 ( 3273) hydrogen bonds : angle 4.15371 ( 9819) metal coordination : bond 0.20923 ( 76) *********************** 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 691 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 586 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 99 ASN cc_start: 0.8225 (m-40) cc_final: 0.7933 (m-40) REVERT: H 19 GLU cc_start: 0.7626 (mp0) cc_final: 0.7110 (mp0) REVERT: H 131 ARG cc_start: 0.8892 (mtt180) cc_final: 0.8684 (ttm170) REVERT: I 184 ARG cc_start: 0.8814 (ptp-170) cc_final: 0.8545 (ptp-170) REVERT: J 84 GLU cc_start: 0.8517 (mp0) cc_final: 0.8309 (mp0) REVERT: L 117 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7953 (ttmp) REVERT: N 19 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: O 40 GLU cc_start: 0.7952 (pt0) cc_final: 0.7614 (pt0) REVERT: O 113 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7358 (tm-30) REVERT: R 33 GLU cc_start: 0.6368 (mm-30) cc_final: 0.5458 (mm-30) REVERT: R 113 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7121 (tm-30) REVERT: S 188 GLU cc_start: 0.8693 (mp0) cc_final: 0.8261 (mp0) outliers start: 105 outliers final: 83 residues processed: 679 average time/residue: 0.8051 time to fit residues: 638.7780 Evaluate side-chains 643 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 559 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 154 LYS Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 107 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 186 ASN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN I 47 HIS J 189 GLN N 75 HIS O 75 HIS P 186 ASN P 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.101006 restraints weight = 29879.468| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.53 r_work: 0.2805 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.517 35923 Z= 0.265 Angle : 0.602 10.713 48384 Z= 0.307 Chirality : 0.036 0.156 6069 Planarity : 0.005 0.060 5859 Dihedral : 7.166 70.101 4644 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.49 % Allowed : 1.64 % Favored : 97.87 % Rotamer: Outliers : 4.35 % Allowed : 27.83 % Favored : 67.82 % 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: 3.42 (0.12), residues: 4326 helix: 2.56 (0.08), residues: 3948 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.015 0.002 TYR T 198 PHE 0.014 0.002 PHE C 145 TRP 0.014 0.002 TRP R 63 HIS 0.004 0.001 HIS H 47 Details of bonding type rmsd covalent geometry : bond 0.00526 (35847) covalent geometry : angle 0.60243 (48384) hydrogen bonds : bond 0.07498 ( 3273) hydrogen bonds : angle 3.72323 ( 9819) metal coordination : bond 0.10052 ( 76) *********************** 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 776 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 606 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8377 (mm) cc_final: 0.8162 (mm) REVERT: A 33 GLU cc_start: 0.7209 (tp30) cc_final: 0.6664 (tp30) REVERT: A 48 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7352 (mm-30) REVERT: A 84 GLU cc_start: 0.8487 (mp0) cc_final: 0.8147 (mp0) REVERT: A 113 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: A 198 TYR cc_start: 0.9056 (m-10) cc_final: 0.8571 (m-10) REVERT: B 20 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7629 (mppt) REVERT: B 113 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 113 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7182 (tm-30) REVERT: D 20 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7599 (ttpp) REVERT: D 99 ASN cc_start: 0.8201 (m-40) cc_final: 0.7912 (m-40) REVERT: D 113 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: E 113 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: F 39 LEU cc_start: 0.8641 (mt) cc_final: 0.8312 (mt) REVERT: F 92 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7840 (mmm160) REVERT: F 113 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7411 (tm-30) REVERT: G 17 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: H 12 LEU cc_start: 0.8234 (mm) cc_final: 0.8001 (mm) REVERT: I 113 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7284 (tm-30) REVERT: J 17 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: J 113 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7483 (tm-30) REVERT: J 169 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7531 (mmmt) REVERT: K 12 LEU cc_start: 0.8096 (mm) cc_final: 0.7766 (mm) REVERT: K 113 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7505 (tm-30) REVERT: L 20 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7897 (mppt) REVERT: L 40 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: L 117 LYS cc_start: 0.8311 (mtpp) cc_final: 0.8049 (ttpt) REVERT: L 161 GLU cc_start: 0.7493 (tp30) cc_final: 0.7221 (tp30) REVERT: M 40 GLU cc_start: 0.8073 (tp30) cc_final: 0.7762 (tt0) REVERT: M 106 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7607 (ttp) REVERT: M 195 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8448 (mt-10) REVERT: M 206 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7201 (ttpt) REVERT: N 19 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: N 21 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7073 (mtp180) REVERT: N 33 GLU cc_start: 0.5517 (mm-30) cc_final: 0.5070 (mm-30) REVERT: N 92 ARG cc_start: 0.8237 (mtp85) cc_final: 0.8019 (mmm160) REVERT: O 20 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8082 (mppt) REVERT: O 40 GLU cc_start: 0.8225 (pt0) cc_final: 0.7949 (pt0) REVERT: P 33 GLU cc_start: 0.5963 (mm-30) cc_final: 0.4334 (pp20) REVERT: P 40 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: Q 19 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6845 (tp30) REVERT: Q 20 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8007 (mppt) REVERT: Q 113 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7562 (tm-30) REVERT: Q 188 GLU cc_start: 0.8621 (mp0) cc_final: 0.8072 (mp0) REVERT: R 33 GLU cc_start: 0.6425 (mm-30) cc_final: 0.4624 (mm-30) REVERT: R 113 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7235 (tm-30) REVERT: S 12 LEU cc_start: 0.8275 (mm) cc_final: 0.8054 (mm) REVERT: S 113 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: S 188 GLU cc_start: 0.8735 (mp0) cc_final: 0.8194 (mp0) outliers start: 170 outliers final: 75 residues processed: 721 average time/residue: 0.8101 time to fit residues: 677.1498 Evaluate side-chains 664 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 570 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 179 GLU Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 206 LYS Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 159 GLU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain S residue 29 GLU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 209 LEU Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 99 ASN Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 7 optimal weight: 0.9990 chunk 328 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 368 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 297 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 189 GLN D 189 GLN F 99 ASN F 186 ASN I 189 GLN L 189 GLN M 186 ASN N 99 ASN O 75 HIS O 186 ASN Q 189 GLN R 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109695 restraints weight = 30506.779| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.56 r_work: 0.2945 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.525 35923 Z= 0.169 Angle : 0.470 9.433 48384 Z= 0.246 Chirality : 0.033 0.141 6069 Planarity : 0.004 0.051 5859 Dihedral : 5.827 69.030 4574 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.32 % Favored : 98.22 % Rotamer: Outliers : 3.56 % Allowed : 27.85 % Favored : 68.59 % 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: 4.28 (0.12), residues: 4326 helix: 3.12 (0.08), residues: 3948 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.005 0.001 TYR S 198 PHE 0.011 0.001 PHE T 112 TRP 0.011 0.001 TRP B 63 HIS 0.006 0.001 HIS L 207 Details of bonding type rmsd covalent geometry : bond 0.00228 (35847) covalent geometry : angle 0.47018 (48384) hydrogen bonds : bond 0.04666 ( 3273) hydrogen bonds : angle 3.34299 ( 9819) metal coordination : bond 0.07905 ( 76) *********************** 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 779 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 640 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8319 (mm) cc_final: 0.8073 (mm) REVERT: A 48 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7259 (mm-30) REVERT: A 113 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 198 TYR cc_start: 0.9004 (m-10) cc_final: 0.8539 (m-10) REVERT: B 113 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 117 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8243 (mtpp) REVERT: B 151 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8048 (ttpt) REVERT: C 113 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7002 (tm-30) REVERT: D 113 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: F 19 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: F 39 LEU cc_start: 0.8557 (mt) cc_final: 0.8266 (mt) REVERT: F 92 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7814 (mmm160) REVERT: F 113 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7214 (tm-30) REVERT: G 96 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8279 (mtmm) REVERT: G 195 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8291 (mt-10) REVERT: H 12 LEU cc_start: 0.8111 (mm) cc_final: 0.7883 (mm) REVERT: H 19 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: H 103 MET cc_start: 0.7755 (ttm) cc_final: 0.7513 (ttm) REVERT: I 17 GLU cc_start: 0.7532 (mp0) cc_final: 0.7285 (mp0) REVERT: I 113 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7323 (tm-30) REVERT: J 9 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7983 (mp0) REVERT: J 17 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: J 113 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7348 (tm-30) REVERT: K 12 LEU cc_start: 0.8098 (mm) cc_final: 0.7842 (mm) REVERT: K 19 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: K 113 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7322 (tm-30) REVERT: L 20 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7755 (mppt) REVERT: L 40 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: L 113 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7348 (tm-30) REVERT: L 161 GLU cc_start: 0.7493 (tp30) cc_final: 0.7129 (tp30) REVERT: L 209 LEU cc_start: 0.6552 (mm) cc_final: 0.5953 (tt) REVERT: M 106 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7528 (ttp) REVERT: M 113 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7394 (tm-30) REVERT: M 184 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (ptp-170) REVERT: N 19 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: N 172 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7413 (mt-10) REVERT: O 20 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8070 (mppt) REVERT: O 40 GLU cc_start: 0.8275 (pt0) cc_final: 0.7987 (pt0) REVERT: O 209 LEU cc_start: 0.6443 (mm) cc_final: 0.5748 (tt) REVERT: P 21 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: P 24 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6813 (pt0) REVERT: P 33 GLU cc_start: 0.5738 (mm-30) cc_final: 0.4721 (mm-30) REVERT: Q 113 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7285 (tm-30) REVERT: Q 117 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7905 (mtmm) REVERT: Q 137 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7632 (mm-30) REVERT: Q 188 GLU cc_start: 0.8477 (mp0) cc_final: 0.7980 (mp0) REVERT: R 33 GLU cc_start: 0.6365 (mm-30) cc_final: 0.5454 (mm-30) REVERT: R 113 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7155 (tm-30) REVERT: S 12 LEU cc_start: 0.8218 (mm) cc_final: 0.7971 (mm) REVERT: S 19 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: S 113 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: S 131 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8406 (mtt180) REVERT: T 21 ARG cc_start: 0.7813 (mmp-170) cc_final: 0.7413 (mmp-170) REVERT: U 137 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7922 (mp0) outliers start: 139 outliers final: 25 residues processed: 735 average time/residue: 0.8502 time to fit residues: 719.8235 Evaluate side-chains 619 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 576 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 186 ASN Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 179 GLU Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 21 ARG Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain U residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 177 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 375 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 189 GLN B 99 ASN F 99 ASN K 189 GLN O 75 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.100120 restraints weight = 30481.652| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.57 r_work: 0.2788 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.517 35923 Z= 0.246 Angle : 0.596 8.294 48384 Z= 0.305 Chirality : 0.037 0.163 6069 Planarity : 0.005 0.059 5859 Dihedral : 4.976 59.827 4521 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.44 % Allowed : 1.69 % Favored : 97.87 % Rotamer: Outliers : 3.66 % Allowed : 28.01 % Favored : 68.33 % 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: 3.73 (0.12), residues: 4326 helix: 2.72 (0.07), residues: 3969 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.009 0.002 TYR L 198 PHE 0.015 0.002 PHE C 145 TRP 0.014 0.002 TRP F 63 HIS 0.009 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00563 (35847) covalent geometry : angle 0.59563 (48384) hydrogen bonds : bond 0.07594 ( 3273) hydrogen bonds : angle 3.64248 ( 9819) metal coordination : bond 0.05931 ( 76) *********************** 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 750 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 607 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8334 (mm) cc_final: 0.8083 (mm) REVERT: A 84 GLU cc_start: 0.8498 (mp0) cc_final: 0.8134 (mp0) REVERT: A 113 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 198 TYR cc_start: 0.9056 (m-10) cc_final: 0.8662 (m-10) REVERT: B 20 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7642 (mppt) REVERT: B 84 GLU cc_start: 0.8479 (mp0) cc_final: 0.8265 (mp0) REVERT: B 113 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 151 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8129 (ttpt) REVERT: C 113 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7192 (tm-30) REVERT: D 20 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7637 (ttpp) REVERT: D 113 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: D 184 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8194 (ptp-170) REVERT: D 206 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7139 (tttm) REVERT: E 113 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: F 19 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: F 39 LEU cc_start: 0.8654 (mt) cc_final: 0.8308 (mt) REVERT: F 113 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7380 (tm-30) REVERT: F 131 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.6878 (mtm180) REVERT: F 184 ARG cc_start: 0.8770 (ptp-170) cc_final: 0.8537 (ptp-170) REVERT: G 17 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: G 33 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7041 (mp0) REVERT: G 92 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7783 (mtm180) REVERT: G 96 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (mtmm) REVERT: H 12 LEU cc_start: 0.8196 (mm) cc_final: 0.7958 (mm) REVERT: H 92 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8161 (mtm180) REVERT: I 17 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: I 113 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7355 (tm-30) REVERT: I 137 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8178 (mm-30) REVERT: I 184 ARG cc_start: 0.8769 (ptp-170) cc_final: 0.8403 (ptp-170) REVERT: J 17 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: J 113 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7398 (tm-30) REVERT: J 169 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7451 (mmmt) REVERT: K 12 LEU cc_start: 0.8170 (mm) cc_final: 0.7877 (mm) REVERT: K 19 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: K 113 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7543 (tm-30) REVERT: K 120 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8366 (mm-30) REVERT: L 19 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7312 (mp0) REVERT: L 20 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7834 (mppt) REVERT: L 33 GLU cc_start: 0.8441 (pt0) cc_final: 0.8207 (pt0) REVERT: L 40 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: L 113 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7543 (tm-30) REVERT: L 117 LYS cc_start: 0.8339 (mtpp) cc_final: 0.8074 (ttpt) REVERT: L 161 GLU cc_start: 0.7571 (tp30) cc_final: 0.7241 (tp30) REVERT: M 106 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7639 (ttp) REVERT: M 113 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7574 (tm-30) REVERT: M 135 GLU cc_start: 0.8419 (mp0) cc_final: 0.8156 (mt-10) REVERT: M 206 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7241 (ttpt) REVERT: N 19 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: N 33 GLU cc_start: 0.5923 (mm-30) cc_final: 0.4570 (mm-30) REVERT: N 48 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7422 (mm-30) REVERT: N 113 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7610 (tm-30) REVERT: O 20 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8052 (mppt) REVERT: O 40 GLU cc_start: 0.8232 (pt0) cc_final: 0.7958 (pt0) REVERT: O 137 GLU cc_start: 0.8348 (mp0) cc_final: 0.7846 (mm-30) REVERT: P 24 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7256 (tt0) REVERT: P 33 GLU cc_start: 0.6307 (mm-30) cc_final: 0.4219 (pp20) REVERT: Q 20 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (mppt) REVERT: Q 113 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7543 (tm-30) REVERT: Q 188 GLU cc_start: 0.8622 (mp0) cc_final: 0.8091 (mp0) REVERT: R 20 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7928 (mppt) REVERT: R 33 GLU cc_start: 0.6370 (mm-30) cc_final: 0.4633 (mm-30) REVERT: R 113 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7269 (tm-30) REVERT: S 12 LEU cc_start: 0.8285 (mm) cc_final: 0.8008 (mm) REVERT: S 19 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: S 113 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: S 188 GLU cc_start: 0.8769 (mp0) cc_final: 0.8324 (mp0) REVERT: T 33 GLU cc_start: 0.5138 (mm-30) cc_final: 0.3967 (mm-30) REVERT: U 131 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8281 (mtm180) outliers start: 143 outliers final: 62 residues processed: 701 average time/residue: 0.8865 time to fit residues: 716.8155 Evaluate side-chains 669 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 581 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 20 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 104 VAL Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 186 ASN Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 206 LYS Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 20 LYS Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 106 MET Chi-restraints excluded: chain T residue 107 VAL Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 131 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 406 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 186 ASN A 189 GLN B 99 ASN B 189 GLN F 99 ASN G 186 ASN G 189 GLN I 189 GLN N 99 ASN N 189 GLN P 189 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105004 restraints weight = 30229.652| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.54 r_work: 0.2863 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35923 Z= 0.144 Angle : 0.501 8.612 48384 Z= 0.261 Chirality : 0.033 0.143 6069 Planarity : 0.004 0.053 5859 Dihedral : 4.796 59.332 4519 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.41 % Favored : 98.20 % Rotamer: Outliers : 3.12 % Allowed : 28.83 % Favored : 68.05 % 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: 4.11 (0.12), residues: 4326 helix: 3.02 (0.07), residues: 3948 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 92 TYR 0.007 0.001 TYR L 198 PHE 0.011 0.002 PHE C 145 TRP 0.011 0.001 TRP Q 63 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00311 (35847) covalent geometry : angle 0.50070 (48384) hydrogen bonds : bond 0.05790 ( 3273) hydrogen bonds : angle 3.44544 ( 9819) metal coordination : bond 0.00158 ( 76) *********************** 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 716 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 594 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8398 (mm) cc_final: 0.8153 (mm) REVERT: A 48 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 113 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 198 TYR cc_start: 0.8975 (m-10) cc_final: 0.8583 (m-10) REVERT: B 113 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 131 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7698 (mtm180) REVERT: B 151 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8043 (ttpt) REVERT: C 113 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7179 (tm-30) REVERT: D 169 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8152 (mmmt) REVERT: D 206 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7066 (tttm) REVERT: F 19 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: F 21 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7031 (mmm160) REVERT: F 39 LEU cc_start: 0.8636 (mt) cc_final: 0.8327 (mt) REVERT: F 113 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7295 (tm-30) REVERT: F 131 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7340 (mtm180) REVERT: F 135 GLU cc_start: 0.8262 (mp0) cc_final: 0.7902 (mt-10) REVERT: F 184 ARG cc_start: 0.8749 (ptp-170) cc_final: 0.8498 (ptp-170) REVERT: G 92 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7661 (mtm180) REVERT: G 96 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8372 (mtmm) REVERT: G 184 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7668 (ptp-170) REVERT: H 103 MET cc_start: 0.7842 (ttm) cc_final: 0.7514 (ttm) REVERT: I 17 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: I 113 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7349 (tm-30) REVERT: I 188 GLU cc_start: 0.8389 (mp0) cc_final: 0.8093 (mp0) REVERT: J 17 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: J 113 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7364 (tm-30) REVERT: K 12 LEU cc_start: 0.8100 (mm) cc_final: 0.7863 (mm) REVERT: K 19 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: K 113 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7500 (tm-30) REVERT: K 120 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8342 (mm-30) REVERT: L 20 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7779 (mppt) REVERT: L 33 GLU cc_start: 0.8371 (pt0) cc_final: 0.8092 (pt0) REVERT: L 40 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: L 113 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7438 (tm-30) REVERT: L 117 LYS cc_start: 0.8262 (mtpp) cc_final: 0.7993 (ttpt) REVERT: L 161 GLU cc_start: 0.7509 (tp30) cc_final: 0.7126 (tp30) REVERT: M 106 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7612 (ttp) REVERT: M 113 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7553 (tm-30) REVERT: M 137 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7436 (mm-30) REVERT: N 19 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: N 33 GLU cc_start: 0.5574 (mm-30) cc_final: 0.5212 (mm-30) REVERT: O 20 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8056 (mppt) REVERT: O 40 GLU cc_start: 0.8174 (pt0) cc_final: 0.7885 (pt0) REVERT: P 33 GLU cc_start: 0.6308 (mm-30) cc_final: 0.4306 (pp20) REVERT: P 40 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7790 (tt0) REVERT: Q 20 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8027 (mppt) REVERT: Q 113 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7475 (tm-30) REVERT: Q 137 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7771 (mm-30) REVERT: Q 188 GLU cc_start: 0.8558 (mp0) cc_final: 0.8022 (mp0) REVERT: R 20 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7845 (mppt) REVERT: R 33 GLU cc_start: 0.6334 (mm-30) cc_final: 0.4617 (mm-30) REVERT: R 113 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7205 (tm-30) REVERT: S 12 LEU cc_start: 0.8283 (mm) cc_final: 0.8012 (mm) REVERT: S 113 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: T 33 GLU cc_start: 0.5193 (mm-30) cc_final: 0.4361 (mm-30) REVERT: U 113 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7356 (tm-30) REVERT: U 131 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8650 (ttm170) outliers start: 122 outliers final: 46 residues processed: 674 average time/residue: 0.8810 time to fit residues: 684.7246 Evaluate side-chains 631 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 563 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 131 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 12 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 361 optimal weight: 10.0000 chunk 419 optimal weight: 0.9980 chunk 280 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 189 GLN B 189 GLN F 99 ASN G 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105693 restraints weight = 30234.567| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.54 r_work: 0.2875 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35923 Z= 0.138 Angle : 0.495 8.064 48384 Z= 0.258 Chirality : 0.033 0.148 6069 Planarity : 0.004 0.052 5859 Dihedral : 4.617 59.781 4514 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.90 % Favored : 97.71 % Rotamer: Outliers : 2.84 % Allowed : 29.24 % Favored : 67.92 % 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: 4.27 (0.12), residues: 4326 helix: 3.12 (0.07), residues: 3948 sheet: None (None), residues: 0 loop : -1.09 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 92 TYR 0.005 0.001 TYR D 198 PHE 0.011 0.001 PHE G 145 TRP 0.014 0.001 TRP O 63 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00295 (35847) covalent geometry : angle 0.49539 (48384) hydrogen bonds : bond 0.05564 ( 3273) hydrogen bonds : angle 3.39089 ( 9819) metal coordination : bond 0.00123 ( 76) *********************** 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 691 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 580 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8398 (mm) cc_final: 0.8164 (mm) REVERT: A 48 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 113 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 198 TYR cc_start: 0.8997 (m-10) cc_final: 0.8642 (m-10) REVERT: B 20 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7645 (mtpt) REVERT: B 113 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7333 (tm-30) REVERT: B 131 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7956 (mtm180) REVERT: D 169 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8145 (mmmt) REVERT: D 206 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7098 (tttm) REVERT: F 19 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: F 21 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7058 (mmm160) REVERT: F 39 LEU cc_start: 0.8631 (mt) cc_final: 0.8324 (mt) REVERT: F 92 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7788 (mtm110) REVERT: F 113 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7332 (tm-30) REVERT: F 131 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.7432 (mtm180) REVERT: F 135 GLU cc_start: 0.8251 (mp0) cc_final: 0.7895 (mt-10) REVERT: F 184 ARG cc_start: 0.8742 (ptp-170) cc_final: 0.8503 (ptp-170) REVERT: G 17 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: G 96 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8310 (mtmm) REVERT: G 184 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7488 (ptp-170) REVERT: H 12 LEU cc_start: 0.8108 (mm) cc_final: 0.7871 (mm) REVERT: H 19 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: H 103 MET cc_start: 0.7819 (ttm) cc_final: 0.7526 (ttm) REVERT: H 206 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7478 (ttpt) REVERT: I 17 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: I 113 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7369 (tm-30) REVERT: I 188 GLU cc_start: 0.8377 (mp0) cc_final: 0.8011 (mp0) REVERT: J 17 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: J 84 GLU cc_start: 0.8407 (mp0) cc_final: 0.8182 (mp0) REVERT: J 113 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7374 (tm-30) REVERT: K 12 LEU cc_start: 0.8070 (mm) cc_final: 0.7867 (mm) REVERT: K 19 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: K 113 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7491 (tm-30) REVERT: K 120 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8348 (mm-30) REVERT: K 209 LEU cc_start: 0.6519 (mm) cc_final: 0.5797 (tt) REVERT: L 19 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7301 (mp0) REVERT: L 20 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7771 (mppt) REVERT: L 33 GLU cc_start: 0.8377 (pt0) cc_final: 0.8110 (pt0) REVERT: L 40 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: L 113 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7420 (tm-30) REVERT: L 117 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7939 (ttpt) REVERT: L 161 GLU cc_start: 0.7485 (tp30) cc_final: 0.7085 (tp30) REVERT: L 209 LEU cc_start: 0.6672 (mm) cc_final: 0.6079 (tt) REVERT: M 106 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7602 (ttp) REVERT: M 113 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7431 (tm-30) REVERT: M 137 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7430 (mm-30) REVERT: N 19 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: N 33 GLU cc_start: 0.5461 (mm-30) cc_final: 0.5179 (mm-30) REVERT: O 20 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8049 (mppt) REVERT: O 40 GLU cc_start: 0.8161 (pt0) cc_final: 0.7871 (pt0) REVERT: O 209 LEU cc_start: 0.6255 (mm) cc_final: 0.5577 (tt) REVERT: P 33 GLU cc_start: 0.6254 (mm-30) cc_final: 0.4255 (pp20) REVERT: Q 20 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8042 (mppt) REVERT: Q 113 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7373 (tm-30) REVERT: Q 117 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7876 (mtmm) REVERT: Q 137 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7744 (mm-30) REVERT: Q 188 GLU cc_start: 0.8532 (mp0) cc_final: 0.8016 (mp0) REVERT: R 20 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7840 (mppt) REVERT: R 33 GLU cc_start: 0.6270 (mm-30) cc_final: 0.4618 (mm-30) REVERT: R 113 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7190 (tm-30) REVERT: S 12 LEU cc_start: 0.8298 (mm) cc_final: 0.8051 (mm) REVERT: S 113 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: S 131 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8474 (mtt180) REVERT: T 21 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6905 (mmp-170) REVERT: T 33 GLU cc_start: 0.5105 (mm-30) cc_final: 0.4282 (mm-30) REVERT: T 40 GLU cc_start: 0.8258 (pt0) cc_final: 0.7904 (pp20) REVERT: T 117 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7959 (ttpt) REVERT: U 113 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7353 (tm-30) outliers start: 111 outliers final: 47 residues processed: 662 average time/residue: 0.8574 time to fit residues: 654.0822 Evaluate side-chains 641 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 567 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 179 GLU Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 21 ARG Chi-restraints excluded: chain T residue 117 LYS Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 184 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 299 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 262 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 chunk 400 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 189 GLN B 99 ASN B 189 GLN F 99 ASN K 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104315 restraints weight = 30343.651| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.54 r_work: 0.2857 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35923 Z= 0.153 Angle : 0.513 7.668 48384 Z= 0.267 Chirality : 0.034 0.146 6069 Planarity : 0.004 0.053 5859 Dihedral : 4.640 59.136 4514 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.94 % Favored : 97.67 % Rotamer: Outliers : 3.02 % Allowed : 29.31 % Favored : 67.67 % 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: 4.19 (0.12), residues: 4326 helix: 3.07 (0.07), residues: 3990 sheet: None (None), residues: 0 loop : -1.66 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 92 TYR 0.006 0.001 TYR L 198 PHE 0.012 0.002 PHE T 145 TRP 0.012 0.001 TRP O 63 HIS 0.006 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (35847) covalent geometry : angle 0.51348 (48384) hydrogen bonds : bond 0.05929 ( 3273) hydrogen bonds : angle 3.42439 ( 9819) metal coordination : bond 0.00153 ( 76) *********************** 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 699 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 581 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8398 (mm) cc_final: 0.8168 (mm) REVERT: A 113 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7192 (tm-30) REVERT: A 198 TYR cc_start: 0.8969 (m-10) cc_final: 0.8606 (m-10) REVERT: B 20 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7637 (mtpt) REVERT: B 113 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 131 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7830 (mtm180) REVERT: B 151 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8050 (ttpt) REVERT: C 113 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7181 (tm-30) REVERT: D 113 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7400 (tm-30) REVERT: D 169 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8205 (mmmt) REVERT: D 206 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7118 (tttm) REVERT: E 113 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7599 (tm-30) REVERT: F 19 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: F 21 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7068 (mmm160) REVERT: F 39 LEU cc_start: 0.8621 (mt) cc_final: 0.8289 (mt) REVERT: F 113 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7378 (tm-30) REVERT: F 131 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7364 (mtm180) REVERT: F 135 GLU cc_start: 0.8257 (mp0) cc_final: 0.7894 (mt-10) REVERT: G 17 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: G 92 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7708 (mmm160) REVERT: G 96 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (mtmm) REVERT: H 12 LEU cc_start: 0.8063 (mm) cc_final: 0.7763 (mm) REVERT: H 19 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: H 103 MET cc_start: 0.7851 (ttm) cc_final: 0.7518 (ttm) REVERT: H 206 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7398 (ttpt) REVERT: I 17 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: I 113 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7387 (tm-30) REVERT: J 17 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: J 113 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7390 (tm-30) REVERT: K 12 LEU cc_start: 0.8123 (mm) cc_final: 0.7891 (mm) REVERT: K 19 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: K 113 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7518 (tm-30) REVERT: K 120 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8352 (mm-30) REVERT: K 209 LEU cc_start: 0.6506 (mm) cc_final: 0.5776 (tt) REVERT: L 19 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7295 (mp0) REVERT: L 20 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7783 (mppt) REVERT: L 33 GLU cc_start: 0.8369 (pt0) cc_final: 0.8090 (pt0) REVERT: L 40 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: L 48 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7301 (mm-30) REVERT: L 113 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7455 (tm-30) REVERT: L 117 LYS cc_start: 0.8279 (mtpp) cc_final: 0.8007 (ttpt) REVERT: L 161 GLU cc_start: 0.7508 (tp30) cc_final: 0.7101 (tp30) REVERT: L 209 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6074 (tt) REVERT: M 106 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7619 (ttp) REVERT: M 113 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7464 (tm-30) REVERT: M 137 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7439 (mm-30) REVERT: N 19 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: N 33 GLU cc_start: 0.5493 (mm-30) cc_final: 0.5128 (mm-30) REVERT: O 20 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8049 (mppt) REVERT: O 40 GLU cc_start: 0.8195 (pt0) cc_final: 0.7887 (pt0) REVERT: O 209 LEU cc_start: 0.6291 (mm) cc_final: 0.5615 (tt) REVERT: P 33 GLU cc_start: 0.6361 (mm-30) cc_final: 0.4304 (pp20) REVERT: Q 19 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7398 (mm-30) REVERT: Q 20 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8045 (mppt) REVERT: Q 92 ARG cc_start: 0.8329 (mtm110) cc_final: 0.8083 (mtm180) REVERT: Q 113 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7423 (tm-30) REVERT: Q 117 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7890 (mtmm) REVERT: Q 188 GLU cc_start: 0.8564 (mp0) cc_final: 0.8049 (mp0) REVERT: R 20 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7843 (mppt) REVERT: R 33 GLU cc_start: 0.6309 (mm-30) cc_final: 0.4578 (mm-30) REVERT: R 113 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7216 (tm-30) REVERT: S 12 LEU cc_start: 0.8330 (mm) cc_final: 0.8085 (mm) REVERT: S 19 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: S 113 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: S 131 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8464 (mtt180) REVERT: T 21 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6888 (mmp-170) REVERT: T 33 GLU cc_start: 0.5184 (mm-30) cc_final: 0.4252 (mm-30) REVERT: T 40 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7912 (pp20) REVERT: T 117 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: U 113 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7369 (tm-30) outliers start: 118 outliers final: 54 residues processed: 662 average time/residue: 0.8952 time to fit residues: 681.3925 Evaluate side-chains 647 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 564 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 209 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 179 GLU Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 21 ARG Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 117 LYS Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 184 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 176 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 186 ASN A 189 GLN B 99 ASN B 189 GLN F 99 ASN F 189 GLN I 189 GLN O 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102483 restraints weight = 30727.192| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.59 r_work: 0.2837 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 35923 Z= 0.165 Angle : 0.531 7.737 48384 Z= 0.275 Chirality : 0.035 0.156 6069 Planarity : 0.004 0.058 5859 Dihedral : 4.665 60.250 4513 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.99 % Favored : 97.62 % Rotamer: Outliers : 2.84 % Allowed : 29.54 % Favored : 67.61 % 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: 4.11 (0.12), residues: 4326 helix: 3.01 (0.07), residues: 3990 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 92 TYR 0.006 0.001 TYR D 198 PHE 0.012 0.002 PHE T 145 TRP 0.013 0.001 TRP G 63 HIS 0.006 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (35847) covalent geometry : angle 0.53124 (48384) hydrogen bonds : bond 0.06268 ( 3273) hydrogen bonds : angle 3.46536 ( 9819) metal coordination : bond 0.00173 ( 76) *********************** 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 683 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 572 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7218 (tm-30) REVERT: A 198 TYR cc_start: 0.8979 (m-10) cc_final: 0.8611 (m-10) REVERT: B 113 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 131 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7764 (mtm180) REVERT: B 151 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8076 (ttpt) REVERT: D 21 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6923 (mmp-170) REVERT: D 113 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7353 (tm-30) REVERT: D 169 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8214 (mmmt) REVERT: D 206 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7125 (tttm) REVERT: E 113 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7615 (tm-30) REVERT: E 188 GLU cc_start: 0.8625 (mp0) cc_final: 0.8281 (mp0) REVERT: F 19 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: F 21 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7069 (mmm160) REVERT: F 39 LEU cc_start: 0.8631 (mt) cc_final: 0.8299 (mt) REVERT: F 113 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7364 (tm-30) REVERT: F 120 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8165 (mm-30) REVERT: F 131 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7258 (mtm180) REVERT: F 135 GLU cc_start: 0.8296 (mp0) cc_final: 0.7919 (mt-10) REVERT: G 92 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7714 (mtm180) REVERT: H 12 LEU cc_start: 0.8059 (mm) cc_final: 0.7741 (mm) REVERT: H 19 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: H 103 MET cc_start: 0.7864 (ttm) cc_final: 0.7553 (ttm) REVERT: H 206 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7407 (tttm) REVERT: I 17 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: I 113 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7409 (tm-30) REVERT: I 188 GLU cc_start: 0.8413 (mp0) cc_final: 0.8211 (mp0) REVERT: I 195 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8127 (mt-10) REVERT: J 113 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7372 (tm-30) REVERT: K 12 LEU cc_start: 0.8134 (mm) cc_final: 0.7894 (mm) REVERT: K 19 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: K 113 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7537 (tm-30) REVERT: K 120 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8354 (mm-30) REVERT: K 209 LEU cc_start: 0.6582 (mm) cc_final: 0.5829 (tt) REVERT: L 19 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7310 (mp0) REVERT: L 20 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7787 (mppt) REVERT: L 33 GLU cc_start: 0.8374 (pt0) cc_final: 0.8092 (pt0) REVERT: L 40 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: L 113 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7448 (tm-30) REVERT: L 117 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8003 (ttpt) REVERT: L 161 GLU cc_start: 0.7532 (tp30) cc_final: 0.7129 (tp30) REVERT: L 209 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6000 (tt) REVERT: M 106 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7667 (ttp) REVERT: M 113 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7545 (tm-30) REVERT: M 137 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7506 (mm-30) REVERT: N 13 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8045 (ptmm) REVERT: N 19 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: N 33 GLU cc_start: 0.5625 (mm-30) cc_final: 0.5125 (mm-30) REVERT: O 20 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8048 (mppt) REVERT: O 40 GLU cc_start: 0.8237 (pt0) cc_final: 0.7948 (pt0) REVERT: O 137 GLU cc_start: 0.8300 (mp0) cc_final: 0.7766 (mm-30) REVERT: P 33 GLU cc_start: 0.6447 (mm-30) cc_final: 0.4337 (pp20) REVERT: P 40 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: Q 19 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7410 (mm-30) REVERT: Q 20 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8019 (mppt) REVERT: Q 92 ARG cc_start: 0.8360 (mtm110) cc_final: 0.8118 (mtm180) REVERT: Q 113 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7509 (tm-30) REVERT: Q 188 GLU cc_start: 0.8583 (mp0) cc_final: 0.8049 (mp0) REVERT: R 20 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7846 (mppt) REVERT: R 33 GLU cc_start: 0.6208 (mm-30) cc_final: 0.4592 (mm-30) REVERT: R 113 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7239 (tm-30) REVERT: S 12 LEU cc_start: 0.8310 (mm) cc_final: 0.8063 (mm) REVERT: S 113 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: S 131 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8469 (mtt180) REVERT: T 21 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6879 (mmp-170) REVERT: T 33 GLU cc_start: 0.4925 (mm-30) cc_final: 0.3957 (mm-30) REVERT: T 40 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7921 (pp20) REVERT: T 117 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8024 (ttpt) REVERT: U 113 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7390 (tm-30) outliers start: 111 outliers final: 57 residues processed: 650 average time/residue: 0.8353 time to fit residues: 626.5208 Evaluate side-chains 646 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 562 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 209 LEU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 21 ARG Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 117 LYS Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 VAL Chi-restraints excluded: chain U residue 184 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 61 optimal weight: 9.9990 chunk 350 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 326 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 417 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 189 GLN B 82 ASN B 99 ASN B 189 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN I 189 GLN R 99 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099497 restraints weight = 30481.878| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.58 r_work: 0.2788 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35923 Z= 0.221 Angle : 0.603 8.103 48384 Z= 0.309 Chirality : 0.037 0.161 6069 Planarity : 0.005 0.058 5859 Dihedral : 4.661 59.008 4510 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.92 % Favored : 97.69 % Rotamer: Outliers : 2.74 % Allowed : 29.54 % Favored : 67.72 % 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: 3.79 (0.12), residues: 4326 helix: 2.75 (0.07), residues: 4011 sheet: None (None), residues: 0 loop : -1.29 (0.29), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 92 TYR 0.009 0.002 TYR D 198 PHE 0.015 0.002 PHE C 145 TRP 0.014 0.002 TRP A 63 HIS 0.008 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00543 (35847) covalent geometry : angle 0.60257 (48384) hydrogen bonds : bond 0.07455 ( 3273) hydrogen bonds : angle 3.61618 ( 9819) metal coordination : bond 0.00243 ( 76) *********************** 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 675 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 568 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.9060 (m-10) cc_final: 0.8646 (m-10) REVERT: B 20 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7667 (mtpt) REVERT: B 113 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 131 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7664 (mtm180) REVERT: B 151 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8137 (ttpt) REVERT: C 113 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 21 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6955 (mmp-170) REVERT: D 113 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 169 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8265 (mmmt) REVERT: D 206 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7214 (tttm) REVERT: E 113 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7647 (tm-30) REVERT: F 9 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7142 (pp20) REVERT: F 19 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: F 21 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7094 (mmm160) REVERT: F 39 LEU cc_start: 0.8668 (mt) cc_final: 0.8293 (mt) REVERT: F 92 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7904 (mtp85) REVERT: F 113 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7388 (tm-30) REVERT: F 120 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8166 (mm-30) REVERT: F 131 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.6965 (mtm180) REVERT: G 17 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: G 33 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7032 (mp0) REVERT: G 92 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7795 (mtm180) REVERT: G 96 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8298 (mtmm) REVERT: H 12 LEU cc_start: 0.8086 (mm) cc_final: 0.7753 (mm) REVERT: H 19 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: H 206 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7420 (tttm) REVERT: I 17 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: I 113 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7376 (tm-30) REVERT: J 17 GLU cc_start: 0.7646 (mp0) cc_final: 0.7270 (tp30) REVERT: J 113 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7431 (tm-30) REVERT: K 113 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7602 (tm-30) REVERT: K 120 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8331 (mm-30) REVERT: L 20 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7816 (mppt) REVERT: L 33 GLU cc_start: 0.8399 (pt0) cc_final: 0.8112 (pt0) REVERT: L 40 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: L 113 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7502 (tm-30) REVERT: L 117 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8075 (ttpt) REVERT: L 161 GLU cc_start: 0.7512 (tp30) cc_final: 0.7126 (tp30) REVERT: M 106 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7717 (ttp) REVERT: M 113 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7611 (tm-30) REVERT: M 135 GLU cc_start: 0.8364 (mp0) cc_final: 0.8095 (mt-10) REVERT: N 13 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8102 (ptmm) REVERT: N 19 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: N 21 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7093 (mtp180) REVERT: N 33 GLU cc_start: 0.5775 (mm-30) cc_final: 0.4538 (mm-30) REVERT: N 48 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7403 (mm-30) REVERT: N 113 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7627 (tm-30) REVERT: O 20 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8043 (mppt) REVERT: O 40 GLU cc_start: 0.8263 (pt0) cc_final: 0.7972 (pt0) REVERT: O 137 GLU cc_start: 0.8417 (mp0) cc_final: 0.7848 (mm-30) REVERT: P 33 GLU cc_start: 0.6245 (mm-30) cc_final: 0.4082 (pp20) REVERT: Q 19 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7476 (mm-30) REVERT: Q 20 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8026 (mppt) REVERT: Q 113 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7546 (tm-30) REVERT: Q 188 GLU cc_start: 0.8613 (mp0) cc_final: 0.8076 (mp0) REVERT: R 20 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7948 (mppt) REVERT: R 33 GLU cc_start: 0.6408 (mm-30) cc_final: 0.4564 (mm-30) REVERT: R 113 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7336 (tm-30) REVERT: S 12 LEU cc_start: 0.8344 (mm) cc_final: 0.8116 (mm) REVERT: S 19 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: S 113 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: S 131 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8486 (mtt180) REVERT: S 188 GLU cc_start: 0.8658 (mp0) cc_final: 0.8249 (mp0) REVERT: T 21 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6946 (mmp-170) REVERT: T 33 GLU cc_start: 0.5158 (mm-30) cc_final: 0.3834 (mm-30) REVERT: T 40 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7932 (pp20) REVERT: T 117 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8040 (ttpt) REVERT: U 113 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7480 (tm-30) outliers start: 107 outliers final: 54 residues processed: 643 average time/residue: 0.8730 time to fit residues: 645.6120 Evaluate side-chains 635 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 551 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 21 ARG Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 117 LYS Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 366 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 302 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 240 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 189 GLN B 82 ASN B 99 ASN B 189 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 189 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102008 restraints weight = 30711.729| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.59 r_work: 0.2827 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35923 Z= 0.169 Angle : 0.553 8.113 48384 Z= 0.286 Chirality : 0.035 0.150 6069 Planarity : 0.004 0.055 5859 Dihedral : 4.550 61.191 4510 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.85 % Favored : 97.76 % Rotamer: Outliers : 2.23 % Allowed : 30.29 % Favored : 67.49 % 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: 3.96 (0.12), residues: 4326 helix: 2.92 (0.07), residues: 3990 sheet: None (None), residues: 0 loop : -1.72 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 92 TYR 0.008 0.001 TYR D 198 PHE 0.012 0.002 PHE T 145 TRP 0.012 0.001 TRP O 63 HIS 0.006 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00387 (35847) covalent geometry : angle 0.55321 (48384) hydrogen bonds : bond 0.06399 ( 3273) hydrogen bonds : angle 3.52080 ( 9819) metal coordination : bond 0.00170 ( 76) ********************** 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 645 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 558 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7219 (tm-30) REVERT: A 198 TYR cc_start: 0.9008 (m-10) cc_final: 0.8578 (m-10) REVERT: B 113 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 131 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7698 (mtm180) REVERT: B 151 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8070 (ttpt) REVERT: D 113 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 169 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8233 (mmmt) REVERT: D 188 GLU cc_start: 0.8654 (mp0) cc_final: 0.8255 (mp0) REVERT: D 206 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7179 (tttm) REVERT: E 113 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7605 (tm-30) REVERT: F 19 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: F 21 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7065 (mmm160) REVERT: F 39 LEU cc_start: 0.8647 (mt) cc_final: 0.8295 (mt) REVERT: F 92 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7867 (mtp85) REVERT: F 113 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7365 (tm-30) REVERT: F 120 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8170 (mm-30) REVERT: F 131 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7275 (mtm180) REVERT: F 135 GLU cc_start: 0.8360 (mp0) cc_final: 0.8023 (mt-10) REVERT: G 92 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7707 (mtm180) REVERT: G 96 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8264 (mtmm) REVERT: H 12 LEU cc_start: 0.8125 (mm) cc_final: 0.7807 (mm) REVERT: H 19 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: H 206 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7384 (tttm) REVERT: I 17 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: I 113 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7358 (tm-30) REVERT: I 195 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8185 (mt-10) REVERT: J 17 GLU cc_start: 0.7671 (mp0) cc_final: 0.7302 (tp30) REVERT: J 113 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7370 (tm-30) REVERT: K 113 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7555 (tm-30) REVERT: K 120 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8353 (mm-30) REVERT: L 20 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7774 (mppt) REVERT: L 33 GLU cc_start: 0.8374 (pt0) cc_final: 0.8112 (pt0) REVERT: L 40 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: L 113 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7451 (tm-30) REVERT: L 117 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7995 (ttpt) REVERT: L 161 GLU cc_start: 0.7531 (tp30) cc_final: 0.7108 (tp30) REVERT: M 106 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7673 (ttp) REVERT: M 113 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7546 (tm-30) REVERT: M 206 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7294 (ttpt) REVERT: N 19 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: N 21 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7033 (mtp180) REVERT: N 33 GLU cc_start: 0.5802 (mm-30) cc_final: 0.4569 (mm-30) REVERT: N 113 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7609 (tm-30) REVERT: O 20 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8063 (mppt) REVERT: O 40 GLU cc_start: 0.8229 (pt0) cc_final: 0.7924 (pt0) REVERT: P 33 GLU cc_start: 0.6115 (mm-30) cc_final: 0.4055 (pp20) REVERT: Q 19 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7390 (mm-30) REVERT: Q 20 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8024 (mppt) REVERT: Q 113 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7508 (tm-30) REVERT: Q 188 GLU cc_start: 0.8586 (mp0) cc_final: 0.8056 (mp0) REVERT: R 20 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7866 (mppt) REVERT: R 33 GLU cc_start: 0.6285 (mm-30) cc_final: 0.4580 (mm-30) REVERT: R 113 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7312 (tm-30) REVERT: S 12 LEU cc_start: 0.8313 (mm) cc_final: 0.8100 (mm) REVERT: S 113 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: S 131 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8463 (mtt180) REVERT: T 21 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6921 (mmp-170) REVERT: T 33 GLU cc_start: 0.5077 (mm-30) cc_final: 0.3989 (mm-30) REVERT: T 40 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7921 (pp20) REVERT: T 117 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8018 (ttpt) REVERT: U 113 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7444 (tm-30) REVERT: U 172 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7374 (mt-10) outliers start: 87 outliers final: 55 residues processed: 619 average time/residue: 0.8960 time to fit residues: 638.9637 Evaluate side-chains 634 residues out of total 3906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 554 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain F residue 9 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 186 ASN Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain K residue 88 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 20 LYS Chi-restraints excluded: chain L residue 40 GLU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 169 LYS Chi-restraints excluded: chain M residue 186 ASN Chi-restraints excluded: chain M residue 206 LYS Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 21 ARG Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 156 LEU Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 184 ARG Chi-restraints excluded: chain O residue 186 ASN Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain Q residue 20 LYS Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain S residue 131 ARG Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain T residue 21 ARG Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 40 GLU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 117 LYS Chi-restraints excluded: chain T residue 186 ASN Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 130 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 142 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 305 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 336 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 189 GLN B 189 GLN F 99 ASN O 75 HIS O 82 ASN U 189 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.148368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108418 restraints weight = 30443.704| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.55 r_work: 0.2921 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.318 35923 Z= 0.138 Angle : 0.503 7.367 48384 Z= 0.261 Chirality : 0.034 0.145 6069 Planarity : 0.004 0.052 5859 Dihedral : 4.347 63.396 4510 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.55 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 30.93 % Favored : 67.46 % 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: 4.46 (0.12), residues: 4326 helix: 3.44 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -2.19 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 92 TYR 0.009 0.001 TYR S 198 PHE 0.010 0.001 PHE T 145 TRP 0.009 0.001 TRP O 63 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00259 (35847) covalent geometry : angle 0.50259 (48384) hydrogen bonds : bond 0.04884 ( 3273) hydrogen bonds : angle 3.33409 ( 9819) metal coordination : bond 0.03649 ( 76) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13679.01 seconds wall clock time: 232 minutes 59.61 seconds (13979.61 seconds total)