Starting phenix.real_space_refine on Sat Feb 7 16:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k83_62159/02_2026/9k83_62159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k83_62159/02_2026/9k83_62159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k83_62159/02_2026/9k83_62159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k83_62159/02_2026/9k83_62159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k83_62159/02_2026/9k83_62159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k83_62159/02_2026/9k83_62159.map" } resolution = 3.64 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= 0.018 sd= 0.099 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: 4 Type Number sf(0) Gaussians Zn 42 6.06 5 C 22197 2.51 5 N 5628 2.21 5 O 6510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 309 residue(s): 0.03s 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: 34377 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "C" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "F" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "G" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "I" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "M" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "N" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "O" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "P" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "Q" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "R" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "S" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "T" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "U" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1635 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.31, per 1000 atoms: 0.21 Number of scatterers: 34377 At special positions: 0 Unit cell: (124.967, 122.812, 183.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) Zn 42 29.99 O 6510 8.00 N 5628 7.00 C 22197 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: 3.28 Conformation dependent library (CDL) restraints added in 1.1 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 B 75 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 207 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 47 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS J 124 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS I 47 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 124 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS D 75 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 207 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS L 124 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 207 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS M 47 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 124 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS E 207 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 75 " pdb=" ZN C 304 " pdb="ZN ZN C 304 " - pdb=" NE2 HIS C 47 " pdb="ZN ZN C 304 " - pdb=" NE2 HIS H 124 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS G 47 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 124 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS F 75 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 207 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 47 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS N 124 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS 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 E 303 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 47 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS F 124 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS H 75 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 207 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS F 47 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS P 124 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 75 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS I 207 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 207 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS J 75 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 47 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS R 124 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS L 75 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 207 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS J 47 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS T 124 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS I 75 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 207 " 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 L 207 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS N 75 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 124 " pdb=" ZN M 302 " pdb="ZN ZN M 302 " - pdb=" NE2 HIS O 207 " pdb="ZN ZN M 302 " - pdb=" NE2 HIS M 75 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS P 75 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 207 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS O 124 " pdb=" ZN O 302 " pdb="ZN ZN O 302 " - pdb=" NE2 HIS O 75 " pdb="ZN ZN O 302 " - pdb=" NE2 HIS Q 207 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS R 75 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 207 " pdb=" ZN Q 301 " pdb="ZN ZN Q 301 " - pdb=" NE2 HIS Q 47 " pdb="ZN ZN Q 301 " - pdb=" NE2 HIS G 124 " pdb=" ZN Q 302 " pdb="ZN ZN Q 302 " - pdb=" NE2 HIS Q 124 " pdb=" ZN Q 303 " pdb="ZN ZN Q 303 " - pdb=" NE2 HIS Q 75 " pdb="ZN ZN Q 303 " - pdb=" NE2 HIS S 207 " pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS T 75 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 207 " pdb=" ZN S 301 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS S 47 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS I 124 " pdb=" ZN S 302 " pdb="ZN ZN S 302 " - pdb=" NE2 HIS S 124 " pdb=" ZN S 303 " pdb="ZN ZN S 303 " - pdb=" NE2 HIS U 207 " pdb="ZN ZN S 303 " - pdb=" NE2 HIS S 75 " pdb=" ZN U 301 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS U 47 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS K 124 " pdb=" ZN U 302 " pdb="ZN ZN U 302 " - pdb=" NE2 HIS U 124 " 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: 8568 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 0 sheets defined 92.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.519A pdb=" N LYS A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 52 removed outlier: 3.848A pdb=" N ALA A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 79 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.778A pdb=" N GLU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 159 through 182 removed outlier: 3.709A pdb=" N ILE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 186 through 213 Processing helix chain 'B' and resid 7 through 28 removed outlier: 3.567A pdb=" N SER B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 removed outlier: 3.660A pdb=" N ALA B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.777A pdb=" N GLU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 159 through 182 removed outlier: 3.643A pdb=" N ILE B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 213 Processing helix chain 'C' and resid 7 through 28 removed outlier: 3.581A pdb=" N SER C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 52 removed outlier: 3.780A pdb=" N ALA C 34 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 79 Processing helix chain 'C' and resid 82 through 105 Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.818A pdb=" N GLU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 159 through 182 removed outlier: 3.682A pdb=" N ILE C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 186 through 213 Processing helix chain 'D' and resid 7 through 28 removed outlier: 3.572A pdb=" N SER D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 52 removed outlier: 3.784A pdb=" N ALA D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 79 Processing helix chain 'D' and resid 82 through 105 Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.736A pdb=" N GLU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 159 through 182 removed outlier: 3.711A pdb=" N ILE D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) 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 28 Processing helix chain 'E' and resid 30 through 52 removed outlier: 3.648A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 79 Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 108 through 131 removed outlier: 3.859A pdb=" N GLU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 159 through 182 removed outlier: 3.716A pdb=" N ILE E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 186 through 213 Processing helix chain 'F' and resid 7 through 28 removed outlier: 3.605A pdb=" N SER F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 52 removed outlier: 3.684A pdb=" N ALA F 34 " --> pdb=" O ASN F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 79 Processing helix chain 'F' and resid 82 through 105 Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.796A pdb=" N GLU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 159 through 182 removed outlier: 3.659A pdb=" N ILE F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) 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 28 removed outlier: 3.610A pdb=" N SER G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 52 removed outlier: 3.735A pdb=" N ALA G 34 " --> pdb=" O ASN G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 79 Processing helix chain 'G' and resid 82 through 105 Processing helix chain 'G' and resid 108 through 131 removed outlier: 3.784A pdb=" N GLU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 159 through 182 removed outlier: 3.646A pdb=" N ILE G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 186 through 213 Processing helix chain 'H' and resid 7 through 28 removed outlier: 3.539A pdb=" N SER H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 52 removed outlier: 3.598A pdb=" N ALA H 34 " --> pdb=" O ASN H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 79 Processing helix chain 'H' and resid 82 through 105 Processing helix chain 'H' and resid 108 through 131 removed outlier: 3.800A pdb=" N GLU H 112 " --> pdb=" O ASN H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 159 through 182 removed outlier: 3.706A pdb=" N ILE H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) 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 28 removed outlier: 3.592A pdb=" N SER I 28 " --> pdb=" O GLU I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 52 removed outlier: 3.788A pdb=" N ALA I 34 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 79 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 108 through 131 removed outlier: 3.765A pdb=" N GLU I 112 " --> pdb=" O ASN I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 159 through 182 removed outlier: 3.728A pdb=" N ILE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) 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 28 removed outlier: 3.557A pdb=" N SER J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 52 removed outlier: 3.745A pdb=" N ALA J 34 " --> pdb=" O ASN J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 79 Processing helix chain 'J' and resid 82 through 105 Processing helix chain 'J' and resid 108 through 131 removed outlier: 3.935A pdb=" N GLU J 112 " --> pdb=" O ASN J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 159 through 182 removed outlier: 3.609A pdb=" N ILE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) 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 28 removed outlier: 3.560A pdb=" N SER K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 52 removed outlier: 3.655A pdb=" N ALA K 34 " --> pdb=" O ASN K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 79 Processing helix chain 'K' and resid 82 through 105 Processing helix chain 'K' and resid 108 through 131 removed outlier: 3.837A pdb=" N GLU K 112 " --> pdb=" O ASN K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 159 through 182 removed outlier: 3.645A pdb=" N ILE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) 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 28 Processing helix chain 'L' and resid 30 through 52 removed outlier: 3.781A pdb=" N ALA L 34 " --> pdb=" O ASN L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 79 Processing helix chain 'L' and resid 82 through 105 Processing helix chain 'L' and resid 108 through 131 removed outlier: 3.779A pdb=" N GLU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 159 through 182 removed outlier: 3.761A pdb=" N ILE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) 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 28 removed outlier: 3.591A pdb=" N SER M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 52 removed outlier: 3.697A pdb=" N ALA M 34 " --> pdb=" O ASN M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 79 Processing helix chain 'M' and resid 82 through 105 Processing helix chain 'M' and resid 108 through 131 removed outlier: 3.811A pdb=" N GLU M 112 " --> pdb=" O ASN M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 159 through 182 removed outlier: 3.803A pdb=" N ILE M 163 " --> pdb=" O SER M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 185 No H-bonds generated for 'chain 'M' and resid 183 through 185' Processing helix chain 'M' and resid 186 through 213 Processing helix chain 'N' and resid 7 through 28 removed outlier: 3.532A pdb=" N SER N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 52 removed outlier: 3.675A pdb=" N ALA N 34 " --> pdb=" O ASN N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 79 Processing helix chain 'N' and resid 82 through 105 Processing helix chain 'N' and resid 108 through 131 removed outlier: 3.781A pdb=" N GLU N 112 " --> pdb=" O ASN N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 159 through 182 removed outlier: 3.665A pdb=" N ILE N 163 " --> pdb=" O SER N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 185 No H-bonds generated for 'chain 'N' and resid 183 through 185' Processing helix chain 'N' and resid 186 through 213 Processing helix chain 'O' and resid 7 through 28 removed outlier: 3.608A pdb=" N SER O 28 " --> pdb=" O GLU O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 52 removed outlier: 3.847A pdb=" N ALA O 34 " --> pdb=" O ASN O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 79 Processing helix chain 'O' and resid 82 through 105 Processing helix chain 'O' and resid 108 through 131 removed outlier: 3.774A pdb=" N GLU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 159 through 182 removed outlier: 3.744A pdb=" N ILE O 163 " --> pdb=" O SER O 159 " (cutoff:3.500A) 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 28 Processing helix chain 'P' and resid 30 through 52 removed outlier: 3.660A pdb=" N ALA P 34 " --> pdb=" O ASN P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 79 Processing helix chain 'P' and resid 82 through 105 Processing helix chain 'P' and resid 108 through 131 removed outlier: 3.779A pdb=" N GLU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 159 through 182 removed outlier: 3.712A pdb=" N ILE P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) 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 28 removed outlier: 3.618A pdb=" N SER Q 28 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 52 removed outlier: 3.539A pdb=" N ALA Q 34 " --> pdb=" O ASN Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 79 Processing helix chain 'Q' and resid 82 through 105 Processing helix chain 'Q' and resid 108 through 131 removed outlier: 3.764A pdb=" N GLU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 159 through 182 removed outlier: 3.727A pdb=" N ILE Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) 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 28 removed outlier: 3.520A pdb=" N SER R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 52 removed outlier: 3.670A pdb=" N ALA R 34 " --> pdb=" O ASN R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 79 Processing helix chain 'R' and resid 82 through 105 Processing helix chain 'R' and resid 108 through 131 removed outlier: 3.765A pdb=" N GLU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 159 through 182 removed outlier: 3.644A pdb=" N ILE R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 185 No H-bonds generated for 'chain 'R' and resid 183 through 185' Processing helix chain 'R' and resid 186 through 213 Processing helix chain 'S' and resid 7 through 28 Processing helix chain 'S' and resid 30 through 52 removed outlier: 3.557A pdb=" N ALA S 34 " --> pdb=" O ASN S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 58 through 79 Processing helix chain 'S' and resid 82 through 105 Processing helix chain 'S' and resid 108 through 131 removed outlier: 3.790A pdb=" N GLU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 159 through 182 removed outlier: 3.678A pdb=" N ILE S 163 " --> pdb=" O SER S 159 " (cutoff:3.500A) 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 28 removed outlier: 3.519A pdb=" N SER T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 52 removed outlier: 3.784A pdb=" N ALA T 34 " --> pdb=" O ASN T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 79 Processing helix chain 'T' and resid 82 through 105 Processing helix chain 'T' and resid 108 through 131 removed outlier: 3.810A pdb=" N GLU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 159 through 182 removed outlier: 3.769A pdb=" N ILE T 163 " --> pdb=" O SER T 159 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 185 No H-bonds generated for 'chain 'T' and resid 183 through 185' Processing helix chain 'T' and resid 186 through 213 Processing helix chain 'U' and resid 7 through 28 removed outlier: 3.512A pdb=" N SER U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 52 removed outlier: 3.751A pdb=" N ALA U 34 " --> pdb=" O ASN U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 79 Processing helix chain 'U' and resid 82 through 105 Processing helix chain 'U' and resid 108 through 131 removed outlier: 3.714A pdb=" N GLU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 159 through 182 removed outlier: 3.661A pdb=" N ILE U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) 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 3238 hydrogen bonds defined for protein. 9714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 6069 1.29 - 1.35: 5314 1.35 - 1.42: 1490 1.42 - 1.49: 5488 1.49 - 1.56: 16373 Bond restraints: 34734 Sorted by residual: bond pdb=" C ALA U 77 " pdb=" N ARG U 78 " ideal model delta sigma weight residual 1.335 1.299 0.036 1.38e-02 5.25e+03 6.84e+00 bond pdb=" C ALA A 77 " pdb=" N ARG A 78 " ideal model delta sigma weight residual 1.335 1.303 0.032 1.38e-02 5.25e+03 5.31e+00 bond pdb=" C ALA Q 77 " pdb=" N ARG Q 78 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.46e-02 4.69e+03 4.62e+00 bond pdb=" N HIS J 207 " pdb=" CA HIS J 207 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.20e-02 6.94e+03 4.48e+00 bond pdb=" C ALA B 77 " pdb=" N ARG B 78 " ideal model delta sigma weight residual 1.335 1.307 0.029 1.38e-02 5.25e+03 4.27e+00 ... (remaining 34729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 45476 2.04 - 4.08: 1255 4.08 - 6.12: 243 6.12 - 8.15: 56 8.15 - 10.19: 10 Bond angle restraints: 47040 Sorted by residual: angle pdb=" CB ARG J 131 " pdb=" CG ARG J 131 " pdb=" CD ARG J 131 " ideal model delta sigma weight residual 111.30 121.01 -9.71 2.30e+00 1.89e-01 1.78e+01 angle pdb=" N HIS O 207 " pdb=" CA HIS O 207 " pdb=" C HIS O 207 " ideal model delta sigma weight residual 111.14 106.70 4.44 1.08e+00 8.57e-01 1.69e+01 angle pdb=" N THR P 98 " pdb=" CA THR P 98 " pdb=" C THR P 98 " ideal model delta sigma weight residual 111.07 106.71 4.36 1.07e+00 8.73e-01 1.66e+01 angle pdb=" N HIS J 207 " pdb=" CA HIS J 207 " pdb=" C HIS J 207 " ideal model delta sigma weight residual 111.14 106.79 4.35 1.08e+00 8.57e-01 1.62e+01 angle pdb=" C ASN P 30 " pdb=" CA ASN P 30 " pdb=" CB ASN P 30 " ideal model delta sigma weight residual 112.27 119.32 -7.05 1.75e+00 3.27e-01 1.62e+01 ... (remaining 47035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18456 17.92 - 35.83: 2570 35.83 - 53.75: 526 53.75 - 71.67: 167 71.67 - 89.59: 100 Dihedral angle restraints: 21819 sinusoidal: 8883 harmonic: 12936 Sorted by residual: dihedral pdb=" CA LYS O 211 " pdb=" C LYS O 211 " pdb=" N TYR O 212 " pdb=" CA TYR O 212 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LYS J 211 " pdb=" C LYS J 211 " pdb=" N TYR J 212 " pdb=" CA TYR J 212 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS G 211 " pdb=" C LYS G 211 " pdb=" N TYR G 212 " pdb=" CA TYR G 212 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 21816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4818 0.052 - 0.103: 1034 0.103 - 0.155: 111 0.155 - 0.207: 19 0.207 - 0.258: 3 Chirality restraints: 5985 Sorted by residual: chirality pdb=" CG LEU B 198 " pdb=" CB LEU B 198 " pdb=" CD1 LEU B 198 " pdb=" CD2 LEU B 198 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CG LEU E 198 " pdb=" CB LEU E 198 " pdb=" CD1 LEU E 198 " pdb=" CD2 LEU E 198 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU F 38 " pdb=" CB LEU F 38 " pdb=" CD1 LEU F 38 " pdb=" CD2 LEU F 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 5982 not shown) Planarity restraints: 5901 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 149 " -0.018 2.00e-02 2.50e+03 1.99e-02 6.95e+00 pdb=" CG PHE K 149 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE K 149 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE K 149 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 149 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE K 149 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 149 " -0.015 2.00e-02 2.50e+03 1.80e-02 5.65e+00 pdb=" CG PHE H 149 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE H 149 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE H 149 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 149 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE H 149 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE H 149 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 194 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C LEU P 194 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU P 194 " 0.013 2.00e-02 2.50e+03 pdb=" N SER P 195 " 0.012 2.00e-02 2.50e+03 ... (remaining 5898 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 353 2.47 - 3.08: 26947 3.08 - 3.69: 58779 3.69 - 4.29: 75663 4.29 - 4.90: 123802 Nonbonded interactions: 285544 Sorted by model distance: nonbonded pdb=" OD2 ASP N 173 " pdb="ZN ZN D 303 " model vdw 1.863 2.230 nonbonded pdb=" OD2 ASP D 173 " pdb="ZN ZN D 301 " model vdw 1.888 2.230 nonbonded pdb=" OD2 ASP K 173 " pdb="ZN ZN U 301 " model vdw 1.889 2.230 nonbonded pdb=" OD2 ASP I 173 " pdb="ZN ZN S 301 " model vdw 1.889 2.230 nonbonded pdb=" OD2 ASP G 173 " pdb="ZN ZN Q 301 " model vdw 1.894 2.230 ... (remaining 285539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 213) selection = (chain 'B' and resid 6 through 213) selection = (chain 'C' and resid 6 through 213) selection = (chain 'D' and resid 6 through 213) selection = (chain 'E' and resid 6 through 213) selection = (chain 'F' and resid 6 through 213) selection = (chain 'G' and resid 6 through 213) selection = (chain 'H' and resid 6 through 213) selection = chain 'I' selection = (chain 'J' and resid 6 through 213) selection = (chain 'K' and resid 6 through 213) selection = (chain 'L' and resid 6 through 213) selection = (chain 'M' and resid 6 through 213) selection = (chain 'N' and resid 6 through 213) selection = (chain 'O' and resid 6 through 213) selection = (chain 'P' and resid 6 through 213) selection = (chain 'Q' and resid 6 through 213) selection = (chain 'R' and resid 6 through 213) selection = (chain 'S' and resid 6 through 213) selection = chain 'T' selection = (chain 'U' and resid 6 through 213) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.550 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 0.312 34811 Z= 0.361 Angle : 0.803 10.193 47040 Z= 0.443 Chirality : 0.042 0.258 5985 Planarity : 0.005 0.059 5901 Dihedral : 18.340 89.585 13251 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 0.56 % Allowed : 34.60 % Favored : 64.84 % 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: 3.69 (0.12), residues: 4326 helix: 2.83 (0.08), residues: 3801 sheet: None (None), residues: 0 loop : -0.82 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 131 TYR 0.014 0.001 TYR F 212 PHE 0.044 0.003 PHE K 149 HIS 0.009 0.001 HIS M 47 Details of bonding type rmsd covalent geometry : bond 0.00378 (34734) covalent geometry : angle 0.80344 (47040) hydrogen bonds : bond 0.08039 ( 3238) hydrogen bonds : angle 4.32277 ( 9714) metal coordination : bond 0.19404 ( 77) *********************** 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 755 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 734 time to evaluate : 1.499 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8289 (ttp80) REVERT: B 131 ARG cc_start: 0.9290 (ttm-80) cc_final: 0.9052 (ttm110) REVERT: B 199 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8547 (tm-30) REVERT: C 88 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7970 (mt-10) REVERT: C 133 LEU cc_start: 0.9286 (mt) cc_final: 0.9074 (mt) REVERT: D 88 GLU cc_start: 0.8941 (tt0) cc_final: 0.8671 (mt-10) REVERT: D 91 LEU cc_start: 0.9580 (mt) cc_final: 0.9336 (tt) REVERT: D 137 GLU cc_start: 0.8857 (mp0) cc_final: 0.8367 (mp0) REVERT: E 78 ARG cc_start: 0.7721 (tmm-80) cc_final: 0.7501 (tmm-80) REVERT: E 131 ARG cc_start: 0.9266 (ttm-80) cc_final: 0.8936 (ttm110) REVERT: F 88 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8181 (mt-10) REVERT: F 172 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8678 (ttm110) REVERT: G 78 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7775 (tmm-80) REVERT: G 131 ARG cc_start: 0.9295 (ttm110) cc_final: 0.8845 (ttm110) REVERT: H 78 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6740 (tmm-80) REVERT: I 88 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8074 (mt-10) REVERT: K 30 ASN cc_start: 0.9271 (p0) cc_final: 0.8898 (p0) REVERT: K 92 ARG cc_start: 0.9160 (mmp80) cc_final: 0.8950 (mmp80) REVERT: L 30 ASN cc_start: 0.9502 (p0) cc_final: 0.9253 (p0) REVERT: L 88 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8375 (mt-10) REVERT: L 199 GLU cc_start: 0.8797 (tm-30) cc_final: 0.7827 (tm-30) REVERT: M 180 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8842 (mt0) REVERT: M 206 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8671 (tp30) REVERT: N 199 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8223 (tm-30) REVERT: O 30 ASN cc_start: 0.9446 (p0) cc_final: 0.9151 (p0) REVERT: O 88 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8073 (mt-10) REVERT: O 95 GLU cc_start: 0.9040 (tp30) cc_final: 0.8803 (tp30) REVERT: P 172 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8526 (ttm110) REVERT: Q 78 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7547 (ttp80) REVERT: Q 88 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8008 (tm-30) REVERT: Q 113 ASN cc_start: 0.9364 (m-40) cc_final: 0.9156 (m110) REVERT: R 30 ASN cc_start: 0.9057 (p0) cc_final: 0.8817 (p0) REVERT: R 78 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7661 (ttp80) REVERT: S 190 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8657 (mm110) REVERT: T 78 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7769 (ttp80) REVERT: U 37 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9183 (mmmm) REVERT: U 78 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7806 (tmt170) REVERT: U 113 ASN cc_start: 0.9280 (m-40) cc_final: 0.9064 (m-40) outliers start: 21 outliers final: 2 residues processed: 747 average time/residue: 0.2653 time to fit residues: 295.0450 Evaluate side-chains 647 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 642 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain U residue 78 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 190 GLN C 6 ASN E 6 ASN E 190 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN G 6 ASN G 180 GLN G 190 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN I 6 ASN L 6 ASN M 190 GLN N 190 GLN P 6 ASN P 190 GLN Q 190 GLN U 6 ASN U 108 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049796 restraints weight = 98411.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051583 restraints weight = 61460.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052906 restraints weight = 43170.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053914 restraints weight = 32580.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054659 restraints weight = 25930.211| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34811 Z= 0.176 Angle : 0.636 9.677 47040 Z= 0.333 Chirality : 0.039 0.310 5985 Planarity : 0.005 0.090 5901 Dihedral : 4.457 56.720 4572 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.40 % Allowed : 28.60 % Favored : 66.01 % 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: 4.01 (0.12), residues: 4326 helix: 3.07 (0.07), residues: 3822 sheet: None (None), residues: 0 loop : -1.13 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 78 TYR 0.019 0.002 TYR I 212 PHE 0.023 0.002 PHE K 149 HIS 0.011 0.002 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00385 (34734) covalent geometry : angle 0.63550 (47040) hydrogen bonds : bond 0.04686 ( 3238) hydrogen bonds : angle 3.79300 ( 9714) metal coordination : bond 0.00376 ( 77) *********************** 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 880 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 676 time to evaluate : 1.304 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: 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: 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 30 ASN cc_start: 0.9174 (p0) cc_final: 0.8965 (p0) REVERT: A 84 GLU cc_start: 0.8264 (tp30) cc_final: 0.8055 (tp30) REVERT: A 88 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 78 ARG cc_start: 0.8700 (ttm-80) cc_final: 0.8269 (ttp80) REVERT: B 88 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 172 ARG cc_start: 0.9299 (tpp80) cc_final: 0.9084 (tpp80) REVERT: C 84 GLU cc_start: 0.8295 (tp30) cc_final: 0.7704 (tp30) REVERT: C 88 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7940 (mt-10) REVERT: C 109 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: D 30 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8635 (p0) REVERT: D 88 GLU cc_start: 0.8968 (tt0) cc_final: 0.8707 (mt-10) REVERT: D 91 LEU cc_start: 0.9609 (mt) cc_final: 0.9328 (tt) REVERT: D 140 ARG cc_start: 0.9346 (mmm-85) cc_final: 0.9143 (mmm-85) REVERT: E 88 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 95 GLU cc_start: 0.9244 (tp30) cc_final: 0.8646 (tp30) REVERT: E 190 GLN cc_start: 0.8452 (mt0) cc_final: 0.8147 (mt0) REVERT: F 78 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7833 (ttp80) REVERT: F 84 GLU cc_start: 0.8340 (tp30) cc_final: 0.7880 (tp30) REVERT: F 88 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8169 (mt-10) REVERT: G 12 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9239 (mm-30) REVERT: G 78 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7789 (tmm-80) REVERT: G 84 GLU cc_start: 0.8395 (tp30) cc_final: 0.8142 (tp30) REVERT: G 88 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7869 (mt-10) REVERT: G 95 GLU cc_start: 0.9274 (tp30) cc_final: 0.8975 (tp30) REVERT: G 131 ARG cc_start: 0.9284 (ttm110) cc_final: 0.8795 (ttm110) REVERT: H 199 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8476 (tm-30) REVERT: I 88 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7857 (mt-10) REVERT: I 95 GLU cc_start: 0.9313 (tp30) cc_final: 0.9051 (tp30) REVERT: I 190 GLN cc_start: 0.9224 (mt0) cc_final: 0.8723 (mm-40) REVERT: I 199 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8532 (tm-30) REVERT: J 30 ASN cc_start: 0.9184 (p0) cc_final: 0.8856 (p0) REVERT: J 78 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7574 (tmm-80) REVERT: J 206 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8626 (tp30) REVERT: K 30 ASN cc_start: 0.9168 (p0) cc_final: 0.8847 (p0) REVERT: K 88 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8147 (mt-10) REVERT: K 212 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6425 (t80) REVERT: L 78 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7900 (ttp80) REVERT: L 84 GLU cc_start: 0.8469 (tp30) cc_final: 0.8088 (tp30) REVERT: L 88 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8401 (mt-10) REVERT: L 199 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8235 (tm-30) REVERT: M 78 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7907 (ttp80) REVERT: O 12 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9196 (mm-30) REVERT: O 30 ASN cc_start: 0.9356 (p0) cc_final: 0.9036 (p0) REVERT: O 95 GLU cc_start: 0.9183 (tp30) cc_final: 0.8909 (tm-30) REVERT: O 113 ASN cc_start: 0.9368 (m-40) cc_final: 0.9100 (m110) REVERT: O 198 LEU cc_start: 0.9436 (mp) cc_final: 0.9218 (mm) REVERT: Q 113 ASN cc_start: 0.9360 (m-40) cc_final: 0.9157 (m110) REVERT: Q 190 GLN cc_start: 0.8421 (mt0) cc_final: 0.8181 (mt0) REVERT: R 30 ASN cc_start: 0.9029 (p0) cc_final: 0.8741 (p0) REVERT: R 95 GLU cc_start: 0.9067 (tp30) cc_final: 0.8854 (tp30) REVERT: S 37 LYS cc_start: 0.9557 (mtpp) cc_final: 0.9354 (mmmm) REVERT: S 190 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8556 (mm110) REVERT: T 98 THR cc_start: 0.9405 (p) cc_final: 0.9155 (p) REVERT: T 137 GLU cc_start: 0.8675 (mp0) cc_final: 0.8376 (mp0) REVERT: T 199 GLU cc_start: 0.8501 (tp30) cc_final: 0.8102 (tp30) REVERT: U 37 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9189 (mmmm) REVERT: U 84 GLU cc_start: 0.8481 (tp30) cc_final: 0.8168 (tp30) REVERT: U 88 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7845 (mt-10) REVERT: U 95 GLU cc_start: 0.9085 (tp30) cc_final: 0.8808 (tp30) REVERT: U 113 ASN cc_start: 0.9263 (m-40) cc_final: 0.8979 (m110) REVERT: U 149 PHE cc_start: 0.9404 (m-80) cc_final: 0.9190 (m-80) outliers start: 204 outliers final: 72 residues processed: 846 average time/residue: 0.2464 time to fit residues: 316.6338 Evaluate side-chains 694 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 617 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 195 SER Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain P residue 78 ARG Chi-restraints excluded: chain P residue 79 ASP Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 122 ILE Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 200 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 195 SER Chi-restraints excluded: chain U residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 140 optimal weight: 30.0000 chunk 305 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN G 180 GLN G 190 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN K 190 GLN M 190 GLN P 190 GLN Q 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048991 restraints weight = 98443.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.050716 restraints weight = 61992.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052022 restraints weight = 44016.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052938 restraints weight = 33560.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053673 restraints weight = 27143.937| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34811 Z= 0.183 Angle : 0.613 8.248 47040 Z= 0.324 Chirality : 0.039 0.321 5985 Planarity : 0.004 0.054 5901 Dihedral : 4.271 53.656 4563 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.24 % Allowed : 27.65 % Favored : 67.12 % 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: 4.05 (0.12), residues: 4326 helix: 3.13 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 140 TYR 0.021 0.002 TYR I 212 PHE 0.022 0.002 PHE K 149 HIS 0.006 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00405 (34734) covalent geometry : angle 0.61295 (47040) hydrogen bonds : bond 0.04615 ( 3238) hydrogen bonds : angle 3.74410 ( 9714) metal coordination : bond 0.00428 ( 77) *********************** 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 842 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 644 time to evaluate : 1.380 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8348 (tp30) cc_final: 0.8042 (tp30) REVERT: A 88 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 131 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8962 (ttm110) REVERT: B 78 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8260 (ttp80) REVERT: B 88 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 119 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9406 (tt) REVERT: C 84 GLU cc_start: 0.8445 (tp30) cc_final: 0.7753 (tp30) REVERT: C 88 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 118 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9219 (mm) REVERT: D 30 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8668 (p0) REVERT: D 88 GLU cc_start: 0.8978 (tt0) cc_final: 0.8694 (mt-10) REVERT: D 91 LEU cc_start: 0.9622 (mt) cc_final: 0.9333 (tt) REVERT: D 206 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8760 (tp30) REVERT: E 78 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7744 (ttp80) REVERT: E 88 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8105 (mt-10) REVERT: E 98 THR cc_start: 0.9475 (p) cc_final: 0.9114 (p) REVERT: E 199 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8548 (tm-30) REVERT: F 78 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7790 (ttp80) REVERT: F 84 GLU cc_start: 0.8458 (tp30) cc_final: 0.8033 (tp30) REVERT: F 88 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8220 (mt-10) REVERT: F 99 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8481 (mm-30) REVERT: G 12 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.9255 (mm-30) REVERT: G 82 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7595 (tm-30) REVERT: G 84 GLU cc_start: 0.8484 (tp30) cc_final: 0.8007 (tp30) REVERT: G 88 GLU cc_start: 0.8527 (mt-10) cc_final: 0.7968 (mt-10) REVERT: G 95 GLU cc_start: 0.9257 (tp30) cc_final: 0.8857 (tp30) REVERT: G 131 ARG cc_start: 0.9320 (ttm110) cc_final: 0.8947 (ttm-80) REVERT: H 199 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8264 (tm-30) REVERT: I 30 ASN cc_start: 0.9349 (p0) cc_final: 0.9114 (p0) REVERT: I 88 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8100 (mt-10) REVERT: I 95 GLU cc_start: 0.9245 (tp30) cc_final: 0.8212 (tp30) REVERT: I 98 THR cc_start: 0.9451 (p) cc_final: 0.8946 (p) REVERT: I 182 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9306 (mm) REVERT: I 190 GLN cc_start: 0.9238 (mt0) cc_final: 0.8603 (mm-40) REVERT: I 199 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8444 (tm-30) REVERT: J 30 ASN cc_start: 0.9090 (p0) cc_final: 0.8770 (p0) REVERT: J 78 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7681 (tmm-80) REVERT: J 149 PHE cc_start: 0.9406 (m-80) cc_final: 0.9122 (m-80) REVERT: J 206 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8604 (tp30) REVERT: K 30 ASN cc_start: 0.9163 (p0) cc_final: 0.8831 (p0) REVERT: K 88 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8070 (mt-10) REVERT: L 78 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7839 (ttp80) REVERT: L 84 GLU cc_start: 0.8609 (tp30) cc_final: 0.8105 (tp30) REVERT: L 88 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8354 (mt-10) REVERT: L 199 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8050 (tm-30) REVERT: L 203 ASP cc_start: 0.8145 (t70) cc_final: 0.7799 (t70) REVERT: M 78 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7814 (ttp80) REVERT: M 88 GLU cc_start: 0.8589 (tt0) cc_final: 0.8236 (tt0) REVERT: N 190 GLN cc_start: 0.9125 (mt0) cc_final: 0.8911 (mt0) REVERT: O 12 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9212 (mm-30) REVERT: O 30 ASN cc_start: 0.9242 (p0) cc_final: 0.8903 (p0) REVERT: O 84 GLU cc_start: 0.8677 (tp30) cc_final: 0.7670 (tp30) REVERT: O 95 GLU cc_start: 0.9212 (tp30) cc_final: 0.8865 (tm-30) REVERT: O 99 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8777 (mm-30) REVERT: O 113 ASN cc_start: 0.9388 (m-40) cc_final: 0.9114 (m110) REVERT: Q 88 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7807 (tm-30) REVERT: Q 113 ASN cc_start: 0.9385 (m-40) cc_final: 0.9173 (m110) REVERT: Q 190 GLN cc_start: 0.8394 (mt0) cc_final: 0.8101 (mt0) REVERT: R 12 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9167 (mm-30) REVERT: R 30 ASN cc_start: 0.9046 (p0) cc_final: 0.8745 (p0) REVERT: R 78 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7515 (ttp80) REVERT: R 95 GLU cc_start: 0.9101 (tp30) cc_final: 0.8853 (tp30) REVERT: R 199 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8439 (tm-30) REVERT: S 37 LYS cc_start: 0.9606 (mtpp) cc_final: 0.9354 (mmmm) REVERT: S 113 ASN cc_start: 0.9344 (m-40) cc_final: 0.9051 (m110) REVERT: S 190 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8591 (tp40) REVERT: T 78 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7674 (ttp80) REVERT: T 98 THR cc_start: 0.9440 (p) cc_final: 0.9222 (p) REVERT: T 117 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8572 (tm-30) REVERT: U 37 LYS cc_start: 0.9601 (mmmm) cc_final: 0.9202 (mmmm) REVERT: U 84 GLU cc_start: 0.8582 (tp30) cc_final: 0.8014 (tp30) REVERT: U 88 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7817 (mt-10) REVERT: U 113 ASN cc_start: 0.9265 (m-40) cc_final: 0.8974 (m110) outliers start: 198 outliers final: 100 residues processed: 806 average time/residue: 0.2630 time to fit residues: 321.5260 Evaluate side-chains 726 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 618 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain P residue 79 ASP Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain T residue 200 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 195 SER Chi-restraints excluded: chain U residue 201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 218 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 343 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 413 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 180 GLN C 30 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN G 180 GLN G 190 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN P 190 GLN T 6 ASN U 30 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.049265 restraints weight = 98645.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.050967 restraints weight = 62997.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052447 restraints weight = 45553.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053346 restraints weight = 34357.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.054038 restraints weight = 28147.685| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34811 Z= 0.148 Angle : 0.597 9.174 47040 Z= 0.313 Chirality : 0.039 0.328 5985 Planarity : 0.004 0.039 5901 Dihedral : 4.217 50.929 4563 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.47 % Allowed : 28.36 % Favored : 67.17 % 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: 3.18 (0.07), residues: 3843 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 140 TYR 0.019 0.002 TYR M 212 PHE 0.021 0.002 PHE F 97 HIS 0.008 0.001 HIS N 207 Details of bonding type rmsd covalent geometry : bond 0.00320 (34734) covalent geometry : angle 0.59719 (47040) hydrogen bonds : bond 0.04442 ( 3238) hydrogen bonds : angle 3.61611 ( 9714) metal coordination : bond 0.00266 ( 77) *********************** 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 852 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 683 time to evaluate : 1.393 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: 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 84 GLU cc_start: 0.8390 (tp30) cc_final: 0.7896 (tp30) REVERT: A 88 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 131 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8973 (ttm110) REVERT: A 137 GLU cc_start: 0.9014 (mp0) cc_final: 0.8719 (mp0) REVERT: B 78 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.8171 (ttp80) REVERT: B 88 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8071 (tm-30) REVERT: B 119 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9419 (tt) REVERT: B 149 PHE cc_start: 0.9369 (m-10) cc_final: 0.8879 (m-80) REVERT: C 84 GLU cc_start: 0.8515 (tp30) cc_final: 0.7622 (tp30) REVERT: C 88 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7914 (mt-10) REVERT: C 118 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9185 (mm) REVERT: D 30 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8598 (p0) REVERT: D 91 LEU cc_start: 0.9604 (mt) cc_final: 0.9261 (tt) REVERT: D 206 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8767 (tp30) REVERT: E 78 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7775 (ttp80) REVERT: E 88 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8121 (mt-10) REVERT: E 98 THR cc_start: 0.9400 (p) cc_final: 0.9155 (p) REVERT: E 99 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8547 (mm-30) REVERT: E 172 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8768 (tpp80) REVERT: E 190 GLN cc_start: 0.8364 (mt0) cc_final: 0.8127 (mt0) REVERT: E 199 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8559 (tm-30) REVERT: F 78 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7810 (ttp80) REVERT: F 84 GLU cc_start: 0.8485 (tp30) cc_final: 0.8003 (tp30) REVERT: F 88 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8099 (mt-10) REVERT: F 99 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8283 (tp30) REVERT: G 84 GLU cc_start: 0.8529 (tp30) cc_final: 0.7904 (tp30) REVERT: G 88 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7871 (mt-10) REVERT: G 95 GLU cc_start: 0.9246 (tp30) cc_final: 0.8843 (tp30) REVERT: G 131 ARG cc_start: 0.9324 (ttm110) cc_final: 0.8989 (ttm-80) REVERT: H 78 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7156 (tmm-80) REVERT: H 113 ASN cc_start: 0.9400 (m-40) cc_final: 0.9167 (m-40) REVERT: H 137 GLU cc_start: 0.8978 (mp0) cc_final: 0.8746 (mp0) REVERT: H 199 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8221 (tm-30) REVERT: I 30 ASN cc_start: 0.9297 (p0) cc_final: 0.9097 (p0) REVERT: I 199 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8662 (tm-30) REVERT: J 30 ASN cc_start: 0.9060 (p0) cc_final: 0.8735 (p0) REVERT: J 78 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7649 (tmm-80) REVERT: J 149 PHE cc_start: 0.9396 (m-80) cc_final: 0.9103 (m-80) REVERT: J 169 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9005 (t) REVERT: K 30 ASN cc_start: 0.9059 (p0) cc_final: 0.8730 (p0) REVERT: K 78 ARG cc_start: 0.7825 (tmm-80) cc_final: 0.7510 (tmm-80) REVERT: K 88 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8133 (mt-10) REVERT: K 113 ASN cc_start: 0.9431 (m-40) cc_final: 0.9229 (m110) REVERT: K 212 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6791 (t80) REVERT: L 78 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7789 (ttp80) REVERT: L 84 GLU cc_start: 0.8560 (tp30) cc_final: 0.8115 (tp30) REVERT: L 88 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8238 (mt-10) REVERT: L 199 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7980 (tm-30) REVERT: M 78 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7744 (ttp80) REVERT: N 84 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6943 (tm-30) REVERT: N 95 GLU cc_start: 0.9217 (tp30) cc_final: 0.8848 (tp30) REVERT: N 98 THR cc_start: 0.9346 (m) cc_final: 0.9106 (p) REVERT: O 30 ASN cc_start: 0.9090 (p0) cc_final: 0.8686 (p0) REVERT: O 78 ARG cc_start: 0.8221 (tpp80) cc_final: 0.8017 (ttp-110) REVERT: O 84 GLU cc_start: 0.8604 (tp30) cc_final: 0.8042 (tp30) REVERT: O 88 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7658 (mt-10) REVERT: O 95 GLU cc_start: 0.9240 (tp30) cc_final: 0.8878 (tm-30) REVERT: O 98 THR cc_start: 0.9394 (p) cc_final: 0.9122 (p) REVERT: O 99 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8717 (mm-30) REVERT: O 113 ASN cc_start: 0.9388 (m-40) cc_final: 0.9111 (m110) REVERT: O 198 LEU cc_start: 0.9411 (mp) cc_final: 0.9175 (mm) REVERT: P 79 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: P 198 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9418 (mt) REVERT: Q 78 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7471 (ttp80) REVERT: Q 88 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7807 (tm-30) REVERT: Q 113 ASN cc_start: 0.9391 (m-40) cc_final: 0.9180 (m110) REVERT: Q 190 GLN cc_start: 0.8364 (mt0) cc_final: 0.8129 (mt0) REVERT: R 30 ASN cc_start: 0.9052 (p0) cc_final: 0.8744 (p0) REVERT: R 78 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7461 (ttp80) REVERT: R 95 GLU cc_start: 0.9132 (tp30) cc_final: 0.8759 (tp30) REVERT: R 137 GLU cc_start: 0.8946 (mp0) cc_final: 0.8670 (mp0) REVERT: R 199 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8240 (tm-30) REVERT: S 37 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9319 (mmmm) REVERT: S 113 ASN cc_start: 0.9349 (m-40) cc_final: 0.9057 (m-40) REVERT: S 190 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8624 (tp40) REVERT: T 78 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7775 (ttp80) REVERT: T 82 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7654 (tm-30) REVERT: T 98 THR cc_start: 0.9423 (p) cc_final: 0.9221 (p) REVERT: T 117 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8602 (tm-30) REVERT: T 206 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8922 (tp30) REVERT: U 37 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9260 (mmmm) REVERT: U 84 GLU cc_start: 0.8635 (tp30) cc_final: 0.8085 (tp30) REVERT: U 88 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7714 (mt-10) REVERT: U 113 ASN cc_start: 0.9277 (m-40) cc_final: 0.8951 (m110) REVERT: U 149 PHE cc_start: 0.9413 (m-80) cc_final: 0.9206 (m-80) outliers start: 169 outliers final: 87 residues processed: 812 average time/residue: 0.2651 time to fit residues: 327.2463 Evaluate side-chains 718 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 622 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain P residue 79 ASP Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 198 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 137 GLU Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 200 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 201 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 252 optimal weight: 9.9990 chunk 404 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 chunk 325 optimal weight: 0.3980 chunk 175 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 412 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 281 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN G 180 GLN G 190 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN P 190 GLN U 30 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048985 restraints weight = 98370.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050703 restraints weight = 63300.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052089 restraints weight = 45697.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053018 restraints weight = 34983.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053675 restraints weight = 28537.033| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34811 Z= 0.152 Angle : 0.597 9.754 47040 Z= 0.314 Chirality : 0.039 0.336 5985 Planarity : 0.004 0.039 5901 Dihedral : 4.179 49.383 4563 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.58 % Allowed : 28.33 % Favored : 67.09 % 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: 4.20 (0.12), residues: 4326 helix: 3.21 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -1.69 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 172 TYR 0.022 0.002 TYR F 212 PHE 0.021 0.002 PHE F 97 HIS 0.005 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00330 (34734) covalent geometry : angle 0.59713 (47040) hydrogen bonds : bond 0.04354 ( 3238) hydrogen bonds : angle 3.59254 ( 9714) metal coordination : bond 0.00281 ( 77) *********************** 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 844 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 671 time to evaluate : 1.469 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8439 (tp30) cc_final: 0.7698 (tp30) REVERT: A 88 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 131 ARG cc_start: 0.9204 (ttm110) cc_final: 0.8994 (ttm110) REVERT: A 137 GLU cc_start: 0.8995 (mp0) cc_final: 0.8694 (mp0) REVERT: B 78 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.7983 (ttp80) REVERT: B 88 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 119 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9416 (tt) REVERT: B 149 PHE cc_start: 0.9392 (m-10) cc_final: 0.8879 (m-80) REVERT: C 84 GLU cc_start: 0.8556 (tp30) cc_final: 0.7853 (tp30) REVERT: C 88 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 95 GLU cc_start: 0.9145 (tp30) cc_final: 0.8809 (tp30) REVERT: C 118 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9163 (mm) REVERT: D 30 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8603 (p0) REVERT: D 206 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8768 (tp30) REVERT: E 78 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7815 (ttp80) REVERT: E 88 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 98 THR cc_start: 0.9399 (p) cc_final: 0.9164 (p) REVERT: E 199 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8568 (tm-30) REVERT: F 78 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7837 (ttp80) REVERT: F 84 GLU cc_start: 0.8590 (tp30) cc_final: 0.7985 (tp30) REVERT: F 88 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8035 (mt-10) REVERT: F 99 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8322 (tp30) REVERT: G 12 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9196 (mm-30) REVERT: G 84 GLU cc_start: 0.8572 (tp30) cc_final: 0.8152 (tp30) REVERT: G 88 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8004 (mt-10) REVERT: G 95 GLU cc_start: 0.9242 (tp30) cc_final: 0.8867 (tp30) REVERT: G 131 ARG cc_start: 0.9337 (ttm110) cc_final: 0.9005 (ttm-80) REVERT: G 172 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8749 (tpp80) REVERT: H 30 ASN cc_start: 0.9351 (p0) cc_final: 0.9086 (p0) REVERT: H 78 ARG cc_start: 0.7712 (ttp80) cc_final: 0.6963 (tmm-80) REVERT: H 113 ASN cc_start: 0.9401 (m-40) cc_final: 0.9172 (m-40) REVERT: H 199 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8214 (tm-30) REVERT: I 30 ASN cc_start: 0.9299 (p0) cc_final: 0.9057 (p0) REVERT: I 88 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8156 (mt-10) REVERT: I 99 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8577 (mm-30) REVERT: I 113 ASN cc_start: 0.9280 (m-40) cc_final: 0.9051 (m-40) REVERT: I 199 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8446 (tm-30) REVERT: J 30 ASN cc_start: 0.9031 (p0) cc_final: 0.8816 (p0) REVERT: J 78 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7618 (tmm-80) REVERT: J 149 PHE cc_start: 0.9419 (m-10) cc_final: 0.9119 (m-80) REVERT: K 30 ASN cc_start: 0.9015 (p0) cc_final: 0.8686 (p0) REVERT: K 78 ARG cc_start: 0.7759 (tmm-80) cc_final: 0.7541 (tmm-80) REVERT: K 88 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8201 (mt-10) REVERT: K 212 TYR cc_start: 0.7495 (m-80) cc_final: 0.6895 (t80) REVERT: L 78 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7631 (ttp80) REVERT: L 84 GLU cc_start: 0.8667 (tp30) cc_final: 0.8087 (tp30) REVERT: L 88 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8339 (mt-10) REVERT: L 199 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7936 (tm-30) REVERT: M 78 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7740 (ttp80) REVERT: N 84 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6935 (tm-30) REVERT: N 95 GLU cc_start: 0.9279 (tp30) cc_final: 0.8914 (tp30) REVERT: N 98 THR cc_start: 0.9335 (m) cc_final: 0.9092 (p) REVERT: N 140 ARG cc_start: 0.9270 (mmm-85) cc_final: 0.9068 (mmm-85) REVERT: O 12 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9218 (mm-30) REVERT: O 30 ASN cc_start: 0.9045 (p0) cc_final: 0.8639 (p0) REVERT: O 84 GLU cc_start: 0.8613 (tp30) cc_final: 0.7977 (tp30) REVERT: O 88 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7515 (mt-10) REVERT: O 95 GLU cc_start: 0.9243 (tp30) cc_final: 0.8877 (tm-30) REVERT: O 98 THR cc_start: 0.9399 (p) cc_final: 0.9161 (p) REVERT: O 113 ASN cc_start: 0.9397 (m-40) cc_final: 0.9112 (m110) REVERT: O 137 GLU cc_start: 0.8865 (mp0) cc_final: 0.8512 (mp0) REVERT: O 190 GLN cc_start: 0.8982 (mt0) cc_final: 0.8246 (mm-40) REVERT: P 30 ASN cc_start: 0.9042 (p0) cc_final: 0.8738 (p0) REVERT: P 78 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7296 (ttp-110) REVERT: P 79 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: P 198 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9440 (mt) REVERT: Q 78 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7791 (tmm-80) REVERT: Q 113 ASN cc_start: 0.9396 (m-40) cc_final: 0.9176 (m110) REVERT: Q 190 GLN cc_start: 0.8353 (mt0) cc_final: 0.8070 (mt0) REVERT: R 12 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9213 (mm-30) REVERT: R 30 ASN cc_start: 0.9062 (p0) cc_final: 0.8768 (p0) REVERT: R 78 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7461 (ttp80) REVERT: R 95 GLU cc_start: 0.9125 (tp30) cc_final: 0.8724 (tp30) REVERT: R 137 GLU cc_start: 0.8949 (mp0) cc_final: 0.8661 (mp0) REVERT: R 199 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8455 (tm-30) REVERT: S 37 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9316 (mmmm) REVERT: S 88 GLU cc_start: 0.8145 (pt0) cc_final: 0.7940 (pt0) REVERT: S 113 ASN cc_start: 0.9354 (m-40) cc_final: 0.9054 (m-40) REVERT: S 190 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8622 (tp40) REVERT: S 199 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8569 (tm-30) REVERT: T 78 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7573 (ttp80) REVERT: T 117 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8609 (tm-30) REVERT: T 206 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8849 (tp30) REVERT: U 37 LYS cc_start: 0.9598 (mmmm) cc_final: 0.9262 (mmmm) REVERT: U 84 GLU cc_start: 0.8679 (tp30) cc_final: 0.8041 (tp30) REVERT: U 88 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7796 (mt-10) REVERT: U 113 ASN cc_start: 0.9219 (m-40) cc_final: 0.8867 (m110) outliers start: 173 outliers final: 93 residues processed: 808 average time/residue: 0.2595 time to fit residues: 321.6023 Evaluate side-chains 735 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 632 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 79 ASP Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 198 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 137 GLU Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 294 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 366 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 180 GLN E 30 ASN E 207 HIS F 180 GLN G 180 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN I 30 ASN K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN N 190 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049751 restraints weight = 99101.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051449 restraints weight = 62733.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052832 restraints weight = 44732.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053776 restraints weight = 33908.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054520 restraints weight = 27397.823| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 34811 Z= 0.140 Angle : 0.612 11.297 47040 Z= 0.318 Chirality : 0.039 0.246 5985 Planarity : 0.004 0.038 5901 Dihedral : 4.112 50.205 4561 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.50 % Allowed : 29.10 % Favored : 66.40 % 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: 4.20 (0.12), residues: 4326 helix: 3.22 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 140 TYR 0.023 0.002 TYR G 212 PHE 0.030 0.002 PHE O 149 HIS 0.005 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00292 (34734) covalent geometry : angle 0.61247 (47040) hydrogen bonds : bond 0.04218 ( 3238) hydrogen bonds : angle 3.50552 ( 9714) metal coordination : bond 0.01771 ( 77) *********************** 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 893 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 723 time to evaluate : 1.531 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.8390 (tp30) cc_final: 0.8024 (tp30) REVERT: A 88 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 137 GLU cc_start: 0.9005 (mp0) cc_final: 0.8700 (mp0) REVERT: B 78 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7989 (ttp80) REVERT: B 88 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 119 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9416 (tt) REVERT: B 149 PHE cc_start: 0.9377 (m-10) cc_final: 0.8857 (m-80) REVERT: C 84 GLU cc_start: 0.8399 (tp30) cc_final: 0.7678 (tp30) REVERT: C 88 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8132 (mt-10) REVERT: C 118 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9167 (mm) REVERT: C 150 THR cc_start: 0.9390 (m) cc_final: 0.9114 (p) REVERT: D 30 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8531 (p0) REVERT: D 84 GLU cc_start: 0.8483 (tp30) cc_final: 0.7761 (tp30) REVERT: D 112 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8258 (mp0) REVERT: D 113 ASN cc_start: 0.9476 (m-40) cc_final: 0.9196 (m-40) REVERT: D 137 GLU cc_start: 0.9063 (mp0) cc_final: 0.8776 (mp0) REVERT: D 206 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8724 (tp30) REVERT: E 88 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8256 (mt-10) REVERT: E 199 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8577 (tm-30) REVERT: F 78 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7796 (ttp80) REVERT: F 84 GLU cc_start: 0.8454 (tp30) cc_final: 0.7832 (tp30) REVERT: F 88 GLU cc_start: 0.8652 (mt-10) cc_final: 0.7937 (mt-10) REVERT: F 99 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8342 (tp30) REVERT: G 12 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9194 (mm-30) REVERT: G 84 GLU cc_start: 0.8465 (tp30) cc_final: 0.8136 (tp30) REVERT: G 88 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7922 (mt-10) REVERT: G 95 GLU cc_start: 0.9259 (tp30) cc_final: 0.8869 (tp30) REVERT: G 131 ARG cc_start: 0.9329 (ttm110) cc_final: 0.8800 (ttm110) REVERT: H 78 ARG cc_start: 0.7681 (ttp80) cc_final: 0.6896 (tmm-80) REVERT: H 113 ASN cc_start: 0.9399 (m-40) cc_final: 0.9170 (m-40) REVERT: H 137 GLU cc_start: 0.8971 (mp0) cc_final: 0.8708 (mp0) REVERT: H 199 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8178 (tm-30) REVERT: I 30 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8974 (p0) REVERT: I 88 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8047 (mt-10) REVERT: I 113 ASN cc_start: 0.9271 (m-40) cc_final: 0.9036 (m-40) REVERT: I 199 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8665 (tm-30) REVERT: I 203 ASP cc_start: 0.7698 (t70) cc_final: 0.7462 (t70) REVERT: J 30 ASN cc_start: 0.8980 (p0) cc_final: 0.8650 (p0) REVERT: J 78 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7719 (tmm-80) REVERT: J 95 GLU cc_start: 0.9311 (tp30) cc_final: 0.8988 (tp30) REVERT: J 149 PHE cc_start: 0.9408 (m-10) cc_final: 0.9092 (m-80) REVERT: K 30 ASN cc_start: 0.8977 (p0) cc_final: 0.8621 (p0) REVERT: K 88 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8361 (mt-10) REVERT: K 137 GLU cc_start: 0.8929 (mp0) cc_final: 0.8684 (mp0) REVERT: K 206 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8696 (tp30) REVERT: K 212 TYR cc_start: 0.7497 (m-80) cc_final: 0.6932 (t80) REVERT: L 30 ASN cc_start: 0.8850 (p0) cc_final: 0.8548 (p0) REVERT: L 84 GLU cc_start: 0.8588 (tp30) cc_final: 0.8084 (tp30) REVERT: L 88 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8307 (mt-10) REVERT: L 199 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8025 (tp30) REVERT: L 202 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8802 (tm-30) REVERT: M 78 ARG cc_start: 0.8007 (ttp80) cc_final: 0.7751 (ttp80) REVERT: N 95 GLU cc_start: 0.9287 (tp30) cc_final: 0.8910 (tp30) REVERT: N 98 THR cc_start: 0.9308 (m) cc_final: 0.9089 (p) REVERT: N 137 GLU cc_start: 0.9071 (mp0) cc_final: 0.8763 (mp0) REVERT: O 30 ASN cc_start: 0.8951 (p0) cc_final: 0.8556 (p0) REVERT: O 95 GLU cc_start: 0.9253 (tp30) cc_final: 0.8877 (tm-30) REVERT: O 98 THR cc_start: 0.9379 (p) cc_final: 0.9094 (p) REVERT: O 113 ASN cc_start: 0.9398 (m-40) cc_final: 0.9102 (m110) REVERT: O 137 GLU cc_start: 0.8876 (mp0) cc_final: 0.8567 (mp0) REVERT: O 190 GLN cc_start: 0.8982 (mt0) cc_final: 0.8211 (mm-40) REVERT: P 30 ASN cc_start: 0.8917 (p0) cc_final: 0.8598 (p0) REVERT: Q 37 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9328 (mmmm) REVERT: Q 78 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7843 (tmm-80) REVERT: Q 190 GLN cc_start: 0.8379 (mt0) cc_final: 0.8081 (mt0) REVERT: R 12 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.9246 (mm-30) REVERT: R 30 ASN cc_start: 0.8994 (p0) cc_final: 0.8706 (p0) REVERT: R 78 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7411 (ttp80) REVERT: R 95 GLU cc_start: 0.9156 (tp30) cc_final: 0.8850 (tp30) REVERT: R 137 GLU cc_start: 0.8953 (mp0) cc_final: 0.8663 (mp0) REVERT: R 199 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8424 (tm-30) REVERT: S 30 ASN cc_start: 0.9187 (p0) cc_final: 0.8918 (p0) REVERT: S 37 LYS cc_start: 0.9563 (mtpp) cc_final: 0.9324 (mmmm) REVERT: S 113 ASN cc_start: 0.9353 (m-40) cc_final: 0.9069 (m-40) REVERT: S 190 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8639 (tp40) REVERT: S 199 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8457 (tm-30) REVERT: T 78 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7548 (ttp80) REVERT: T 82 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7577 (tm-30) REVERT: T 92 ARG cc_start: 0.9123 (mmp80) cc_final: 0.8719 (mmt90) REVERT: T 117 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8583 (tm-30) REVERT: T 206 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8844 (tp30) REVERT: U 37 LYS cc_start: 0.9592 (mmmm) cc_final: 0.9243 (mmmm) REVERT: U 84 GLU cc_start: 0.8597 (tp30) cc_final: 0.7865 (tp30) REVERT: U 88 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7768 (mt-10) REVERT: U 113 ASN cc_start: 0.9235 (m-40) cc_final: 0.8901 (m110) REVERT: U 149 PHE cc_start: 0.9358 (m-80) cc_final: 0.9119 (m-80) REVERT: U 190 GLN cc_start: 0.9059 (mt0) cc_final: 0.8506 (mt0) outliers start: 170 outliers final: 89 residues processed: 854 average time/residue: 0.2593 time to fit residues: 337.6351 Evaluate side-chains 760 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 663 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 170 ILE Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 305 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 411 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 387 optimal weight: 8.9990 chunk 414 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 ASN F 180 GLN G 180 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049226 restraints weight = 100971.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050921 restraints weight = 66227.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052211 restraints weight = 48431.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053176 restraints weight = 38029.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053931 restraints weight = 31123.374| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34811 Z= 0.175 Angle : 0.641 13.781 47040 Z= 0.334 Chirality : 0.041 0.353 5985 Planarity : 0.004 0.051 5901 Dihedral : 4.140 50.852 4561 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.23 % Allowed : 30.21 % Favored : 65.56 % 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: 3.21 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 172 TYR 0.022 0.002 TYR G 212 PHE 0.024 0.002 PHE O 149 HIS 0.005 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00387 (34734) covalent geometry : angle 0.64144 (47040) hydrogen bonds : bond 0.04313 ( 3238) hydrogen bonds : angle 3.61754 ( 9714) metal coordination : bond 0.00331 ( 77) *********************** 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 814 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 654 time to evaluate : 1.767 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: 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: symmetry clash REVERT: A 84 GLU cc_start: 0.8580 (tp30) cc_final: 0.7964 (tp30) REVERT: A 88 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 199 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8465 (tm-30) REVERT: B 30 ASN cc_start: 0.9420 (p0) cc_final: 0.9151 (p0) REVERT: B 88 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 119 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9425 (tt) REVERT: B 149 PHE cc_start: 0.9412 (m-10) cc_final: 0.8941 (m-80) REVERT: C 84 GLU cc_start: 0.8530 (tp30) cc_final: 0.7710 (tp30) REVERT: C 88 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8165 (mt-10) REVERT: C 118 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9182 (mm) REVERT: C 150 THR cc_start: 0.9417 (m) cc_final: 0.9141 (p) REVERT: D 30 ASN cc_start: 0.9199 (OUTLIER) cc_final: 0.8586 (p0) REVERT: D 78 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8124 (ttp80) REVERT: D 112 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8259 (mp0) REVERT: D 137 GLU cc_start: 0.9101 (mp0) cc_final: 0.8812 (mp0) REVERT: D 206 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8729 (tp30) REVERT: E 78 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7777 (ttp80) REVERT: E 88 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8234 (mt-10) REVERT: E 177 PHE cc_start: 0.9438 (t80) cc_final: 0.9181 (t80) REVERT: E 199 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8588 (tm-30) REVERT: F 78 ARG cc_start: 0.8222 (ttm-80) cc_final: 0.7854 (ttp80) REVERT: F 84 GLU cc_start: 0.8535 (tp30) cc_final: 0.8152 (tp30) REVERT: F 88 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8054 (mt-10) REVERT: G 12 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9193 (mm-30) REVERT: G 78 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7532 (ttp80) REVERT: G 84 GLU cc_start: 0.8545 (tp30) cc_final: 0.8319 (tp30) REVERT: G 88 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8176 (mt-10) REVERT: G 95 GLU cc_start: 0.9232 (tp30) cc_final: 0.8875 (tp30) REVERT: G 131 ARG cc_start: 0.9372 (ttm110) cc_final: 0.8980 (ttm-80) REVERT: H 78 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7064 (ttp80) REVERT: H 113 ASN cc_start: 0.9409 (m-40) cc_final: 0.9189 (m-40) REVERT: H 199 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8578 (tm-30) REVERT: I 88 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8060 (mt-10) REVERT: I 113 ASN cc_start: 0.9289 (m-40) cc_final: 0.9044 (m110) REVERT: I 199 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8672 (tm-30) REVERT: J 30 ASN cc_start: 0.9005 (p0) cc_final: 0.8773 (p0) REVERT: J 78 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7630 (tmm-80) REVERT: J 149 PHE cc_start: 0.9447 (m-10) cc_final: 0.9122 (m-80) REVERT: K 30 ASN cc_start: 0.8989 (p0) cc_final: 0.8586 (p0) REVERT: K 137 GLU cc_start: 0.8926 (mp0) cc_final: 0.8683 (mp0) REVERT: K 206 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8721 (tp30) REVERT: K 212 TYR cc_start: 0.7549 (m-80) cc_final: 0.7025 (t80) REVERT: L 78 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7654 (ttp80) REVERT: L 84 GLU cc_start: 0.8648 (tp30) cc_final: 0.8036 (tp30) REVERT: L 88 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8508 (mt-10) REVERT: L 199 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8015 (tp30) REVERT: L 202 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8760 (tm-30) REVERT: M 78 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7761 (ttp80) REVERT: N 82 GLU cc_start: 0.7259 (tm-30) cc_final: 0.7003 (tm-30) REVERT: N 84 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7128 (tm-30) REVERT: N 95 GLU cc_start: 0.9283 (tp30) cc_final: 0.8769 (tp30) REVERT: O 30 ASN cc_start: 0.8927 (p0) cc_final: 0.8502 (p0) REVERT: O 95 GLU cc_start: 0.9243 (tp30) cc_final: 0.8841 (tm-30) REVERT: O 98 THR cc_start: 0.9429 (p) cc_final: 0.9166 (p) REVERT: O 113 ASN cc_start: 0.9402 (m-40) cc_final: 0.9075 (m110) REVERT: O 137 GLU cc_start: 0.8888 (mp0) cc_final: 0.8580 (mp0) REVERT: O 190 GLN cc_start: 0.9026 (mt0) cc_final: 0.8238 (mm-40) REVERT: P 30 ASN cc_start: 0.8912 (p0) cc_final: 0.8588 (p0) REVERT: Q 37 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9346 (mmmm) REVERT: Q 78 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7948 (tmm-80) REVERT: Q 190 GLN cc_start: 0.8407 (mt0) cc_final: 0.8094 (mt0) REVERT: Q 199 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8593 (tm-30) REVERT: R 12 GLU cc_start: 0.9460 (OUTLIER) cc_final: 0.9232 (mm-30) REVERT: R 30 ASN cc_start: 0.9009 (p0) cc_final: 0.8708 (p0) REVERT: R 95 GLU cc_start: 0.9191 (tp30) cc_final: 0.8855 (tp30) REVERT: R 137 GLU cc_start: 0.8999 (mp0) cc_final: 0.8688 (mp0) REVERT: R 199 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8466 (tm-30) REVERT: S 37 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9338 (mmmm) REVERT: S 88 GLU cc_start: 0.8113 (pt0) cc_final: 0.7870 (pt0) REVERT: S 113 ASN cc_start: 0.9374 (m-40) cc_final: 0.9134 (m110) REVERT: S 190 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8708 (tp40) REVERT: S 199 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8449 (tm-30) REVERT: T 78 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7547 (ttp80) REVERT: T 92 ARG cc_start: 0.9126 (mmp80) cc_final: 0.8706 (mmt90) REVERT: T 117 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8591 (tm-30) REVERT: T 206 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8854 (tp30) REVERT: U 30 ASN cc_start: 0.9292 (p0) cc_final: 0.8999 (p0) REVERT: U 37 LYS cc_start: 0.9607 (mmmm) cc_final: 0.9258 (mmmm) REVERT: U 84 GLU cc_start: 0.8579 (tp30) cc_final: 0.7993 (tp30) REVERT: U 88 GLU cc_start: 0.8533 (mt-10) cc_final: 0.7894 (mt-10) REVERT: U 113 ASN cc_start: 0.9252 (m-40) cc_final: 0.8915 (m110) REVERT: U 149 PHE cc_start: 0.9396 (m-80) cc_final: 0.9155 (m-80) outliers start: 160 outliers final: 111 residues processed: 775 average time/residue: 0.2669 time to fit residues: 314.2113 Evaluate side-chains 750 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 632 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 134 THR Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 194 LEU Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 57 GLU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 137 GLU Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 386 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 366 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 415 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 GLN G 180 GLN G 190 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN I 30 ASN K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 ASN O 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.049954 restraints weight = 97154.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.051815 restraints weight = 62946.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053069 restraints weight = 44800.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053992 restraints weight = 34757.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054736 restraints weight = 28436.289| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34811 Z= 0.140 Angle : 0.656 14.232 47040 Z= 0.336 Chirality : 0.040 0.386 5985 Planarity : 0.004 0.041 5901 Dihedral : 4.124 51.405 4561 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.31 % Allowed : 31.11 % Favored : 65.58 % 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: 4.21 (0.12), residues: 4326 helix: 3.21 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 140 TYR 0.021 0.002 TYR G 212 PHE 0.032 0.002 PHE T 97 HIS 0.004 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00301 (34734) covalent geometry : angle 0.65592 (47040) hydrogen bonds : bond 0.04161 ( 3238) hydrogen bonds : angle 3.48725 ( 9714) metal coordination : bond 0.00231 ( 77) *********************** 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 852 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 727 time to evaluate : 1.382 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: 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: symmetry clash REVERT: A 84 GLU cc_start: 0.8539 (tp30) cc_final: 0.8062 (tp30) REVERT: A 88 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 30 ASN cc_start: 0.9406 (p0) cc_final: 0.9109 (p0) REVERT: B 78 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7756 (ttp80) REVERT: B 88 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 119 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9419 (tt) REVERT: B 149 PHE cc_start: 0.9388 (m-10) cc_final: 0.8983 (m-80) REVERT: B 190 GLN cc_start: 0.9108 (mt0) cc_final: 0.8461 (mm-40) REVERT: C 84 GLU cc_start: 0.8511 (tp30) cc_final: 0.7563 (tp30) REVERT: C 88 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 118 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9121 (mm) REVERT: D 30 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8503 (p0) REVERT: D 112 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8292 (mp0) REVERT: D 113 ASN cc_start: 0.9496 (m-40) cc_final: 0.9238 (m110) REVERT: D 137 GLU cc_start: 0.9083 (mp0) cc_final: 0.8793 (mp0) REVERT: D 206 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8696 (tp30) REVERT: E 78 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7747 (ttp80) REVERT: E 88 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8271 (mt-10) REVERT: E 113 ASN cc_start: 0.9341 (m-40) cc_final: 0.9126 (m-40) REVERT: E 199 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8585 (tm-30) REVERT: F 78 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7808 (ttp80) REVERT: F 84 GLU cc_start: 0.8571 (tp30) cc_final: 0.8193 (tp30) REVERT: F 88 GLU cc_start: 0.8626 (mt-10) cc_final: 0.7924 (mt-10) REVERT: G 12 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9204 (mm-30) REVERT: G 84 GLU cc_start: 0.8532 (tp30) cc_final: 0.8159 (tp30) REVERT: G 88 GLU cc_start: 0.8663 (mt-10) cc_final: 0.7961 (mt-10) REVERT: G 95 GLU cc_start: 0.9223 (tp30) cc_final: 0.8856 (tp30) REVERT: G 131 ARG cc_start: 0.9369 (ttm110) cc_final: 0.8816 (ttm-80) REVERT: H 23 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8536 (pt0) REVERT: H 30 ASN cc_start: 0.9401 (p0) cc_final: 0.9112 (p0) REVERT: H 78 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7070 (ttp80) REVERT: H 113 ASN cc_start: 0.9394 (m-40) cc_final: 0.9186 (m-40) REVERT: H 137 GLU cc_start: 0.8947 (mp0) cc_final: 0.8715 (mp0) REVERT: H 199 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8192 (tm-30) REVERT: I 40 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8698 (tm-30) REVERT: I 88 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8117 (mt-10) REVERT: I 113 ASN cc_start: 0.9260 (m-40) cc_final: 0.9012 (m110) REVERT: I 199 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8602 (tm-30) REVERT: J 30 ASN cc_start: 0.8966 (p0) cc_final: 0.8721 (p0) REVERT: J 78 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7730 (tmm-80) REVERT: J 149 PHE cc_start: 0.9387 (m-10) cc_final: 0.9066 (m-80) REVERT: J 199 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8542 (tm-30) REVERT: K 30 ASN cc_start: 0.8903 (p0) cc_final: 0.8530 (p0) REVERT: K 88 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8054 (mt-10) REVERT: K 137 GLU cc_start: 0.8893 (mp0) cc_final: 0.8654 (mp0) REVERT: K 206 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8711 (tp30) REVERT: K 212 TYR cc_start: 0.7496 (m-80) cc_final: 0.7026 (t80) REVERT: L 30 ASN cc_start: 0.8785 (p0) cc_final: 0.8546 (p0) REVERT: L 84 GLU cc_start: 0.8624 (tp30) cc_final: 0.8088 (tp30) REVERT: L 88 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8469 (mt-10) REVERT: L 199 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7933 (tp30) REVERT: L 202 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8736 (tm-30) REVERT: M 78 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7752 (ttp80) REVERT: N 30 ASN cc_start: 0.9207 (p0) cc_final: 0.8949 (p0) REVERT: N 137 GLU cc_start: 0.9046 (mp0) cc_final: 0.8768 (mp0) REVERT: N 199 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8422 (tm-30) REVERT: O 30 ASN cc_start: 0.8838 (p0) cc_final: 0.8441 (p0) REVERT: O 95 GLU cc_start: 0.9232 (tp30) cc_final: 0.8838 (tm-30) REVERT: O 98 THR cc_start: 0.9379 (p) cc_final: 0.9095 (p) REVERT: O 113 ASN cc_start: 0.9399 (m-40) cc_final: 0.9140 (m110) REVERT: O 137 GLU cc_start: 0.8862 (mp0) cc_final: 0.8555 (mp0) REVERT: O 139 THR cc_start: 0.9733 (m) cc_final: 0.9505 (p) REVERT: O 190 GLN cc_start: 0.9011 (mt0) cc_final: 0.8238 (mm-40) REVERT: P 30 ASN cc_start: 0.8777 (p0) cc_final: 0.8497 (p0) REVERT: P 48 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8393 (tp-100) REVERT: P 212 TYR cc_start: 0.7061 (m-80) cc_final: 0.6727 (t80) REVERT: Q 30 ASN cc_start: 0.9343 (p0) cc_final: 0.9042 (p0) REVERT: Q 37 LYS cc_start: 0.9613 (mmmm) cc_final: 0.9325 (mmmm) REVERT: Q 78 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7962 (tmm-80) REVERT: Q 190 GLN cc_start: 0.8361 (mt0) cc_final: 0.8066 (mt0) REVERT: Q 199 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8582 (tm-30) REVERT: R 12 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9237 (mm-30) REVERT: R 30 ASN cc_start: 0.8916 (p0) cc_final: 0.8635 (p0) REVERT: R 40 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8841 (tm-30) REVERT: R 78 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7445 (ttp80) REVERT: R 95 GLU cc_start: 0.9174 (tp30) cc_final: 0.8829 (tp30) REVERT: R 137 GLU cc_start: 0.8974 (mp0) cc_final: 0.8673 (mp0) REVERT: R 199 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8470 (tm-30) REVERT: S 30 ASN cc_start: 0.9191 (p0) cc_final: 0.8949 (p0) REVERT: S 37 LYS cc_start: 0.9564 (mtpp) cc_final: 0.9317 (mmmm) REVERT: S 113 ASN cc_start: 0.9360 (m-40) cc_final: 0.9099 (m110) REVERT: S 190 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8692 (tp40) REVERT: S 199 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8218 (tm-30) REVERT: T 78 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7553 (ttp80) REVERT: T 82 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7619 (tm-30) REVERT: T 92 ARG cc_start: 0.9108 (mmp80) cc_final: 0.8698 (mmt90) REVERT: T 117 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8568 (tm-30) REVERT: T 206 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8837 (tp30) REVERT: U 30 ASN cc_start: 0.9240 (p0) cc_final: 0.8991 (p0) REVERT: U 37 LYS cc_start: 0.9581 (mmmm) cc_final: 0.9235 (mmmm) REVERT: U 84 GLU cc_start: 0.8590 (tp30) cc_final: 0.7950 (tp30) REVERT: U 88 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7847 (mt-10) REVERT: U 113 ASN cc_start: 0.9241 (m-40) cc_final: 0.8904 (m110) REVERT: U 149 PHE cc_start: 0.9350 (m-80) cc_final: 0.9117 (m-80) REVERT: U 190 GLN cc_start: 0.9095 (mt0) cc_final: 0.8527 (mt0) outliers start: 125 outliers final: 90 residues processed: 815 average time/residue: 0.2601 time to fit residues: 322.3881 Evaluate side-chains 772 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 675 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 201 ILE Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 355 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN F 180 GLN G 180 GLN G 190 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN I 30 ASN J 190 GLN K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.061700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049704 restraints weight = 98535.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051381 restraints weight = 63817.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.052754 restraints weight = 46537.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053677 restraints weight = 35791.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054451 restraints weight = 29274.632| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34811 Z= 0.168 Angle : 0.667 14.118 47040 Z= 0.346 Chirality : 0.041 0.235 5985 Planarity : 0.004 0.056 5901 Dihedral : 4.177 51.525 4561 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.70 % Allowed : 31.14 % Favored : 65.16 % 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: 4.21 (0.12), residues: 4326 helix: 3.20 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 172 TYR 0.018 0.002 TYR G 212 PHE 0.031 0.002 PHE T 97 HIS 0.005 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00375 (34734) covalent geometry : angle 0.66652 (47040) hydrogen bonds : bond 0.04233 ( 3238) hydrogen bonds : angle 3.59207 ( 9714) metal coordination : bond 0.00337 ( 77) *********************** 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 809 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 669 time to evaluate : 1.416 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7431 (tmm-80) cc_final: 0.6428 (tmm-80) REVERT: A 84 GLU cc_start: 0.8606 (tp30) cc_final: 0.8073 (tp30) REVERT: A 88 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 199 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 30 ASN cc_start: 0.9397 (p0) cc_final: 0.9100 (p0) REVERT: B 88 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 119 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9408 (tt) REVERT: B 149 PHE cc_start: 0.9423 (m-10) cc_final: 0.8981 (m-80) REVERT: B 190 GLN cc_start: 0.9206 (mt0) cc_final: 0.8604 (mm-40) REVERT: B 206 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9076 (tp30) REVERT: C 30 ASN cc_start: 0.9293 (p0) cc_final: 0.8884 (p0) REVERT: C 84 GLU cc_start: 0.8522 (tp30) cc_final: 0.7632 (tp30) REVERT: C 88 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8161 (mt-10) REVERT: C 118 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9143 (mm) REVERT: D 30 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8559 (p0) REVERT: D 113 ASN cc_start: 0.9494 (m-40) cc_final: 0.9239 (m110) REVERT: D 137 GLU cc_start: 0.9144 (mp0) cc_final: 0.8833 (mp0) REVERT: D 206 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8698 (tp30) REVERT: E 78 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7739 (ttp80) REVERT: E 88 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8281 (mt-10) REVERT: E 113 ASN cc_start: 0.9359 (m-40) cc_final: 0.9139 (m110) REVERT: E 199 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8595 (tm-30) REVERT: F 78 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7846 (ttp80) REVERT: F 84 GLU cc_start: 0.8550 (tp30) cc_final: 0.8119 (tp30) REVERT: F 88 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7957 (mt-10) REVERT: G 12 GLU cc_start: 0.9421 (OUTLIER) cc_final: 0.9207 (mm-30) REVERT: G 84 GLU cc_start: 0.8540 (tp30) cc_final: 0.8190 (tp30) REVERT: G 88 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8006 (mt-10) REVERT: G 95 GLU cc_start: 0.9251 (tp30) cc_final: 0.8879 (tp30) REVERT: G 131 ARG cc_start: 0.9372 (ttm110) cc_final: 0.8877 (ttm-80) REVERT: H 23 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8553 (pt0) REVERT: H 30 ASN cc_start: 0.9395 (p0) cc_final: 0.9139 (p0) REVERT: H 78 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7085 (ttp80) REVERT: H 88 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8042 (mt-10) REVERT: H 95 GLU cc_start: 0.9197 (tp30) cc_final: 0.8887 (tp30) REVERT: H 113 ASN cc_start: 0.9404 (m-40) cc_final: 0.9188 (m110) REVERT: H 137 GLU cc_start: 0.8985 (mp0) cc_final: 0.8734 (mp0) REVERT: H 199 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8226 (tm-30) REVERT: I 40 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8709 (tm-30) REVERT: I 88 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8229 (mt-10) REVERT: I 113 ASN cc_start: 0.9269 (m-40) cc_final: 0.9022 (m110) REVERT: I 199 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8421 (tm-30) REVERT: I 203 ASP cc_start: 0.7735 (t70) cc_final: 0.7524 (t70) REVERT: J 30 ASN cc_start: 0.8955 (p0) cc_final: 0.8699 (p0) REVERT: J 78 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7765 (tmm-80) REVERT: J 149 PHE cc_start: 0.9421 (m-10) cc_final: 0.9070 (m-80) REVERT: J 199 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8498 (tm-30) REVERT: K 30 ASN cc_start: 0.8959 (p0) cc_final: 0.8552 (p0) REVERT: K 88 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8093 (mt-10) REVERT: K 95 GLU cc_start: 0.9127 (tp30) cc_final: 0.8884 (tp30) REVERT: K 137 GLU cc_start: 0.8949 (mp0) cc_final: 0.8696 (mp0) REVERT: K 206 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8728 (tp30) REVERT: K 212 TYR cc_start: 0.7536 (m-80) cc_final: 0.7113 (t80) REVERT: L 30 ASN cc_start: 0.8835 (p0) cc_final: 0.8593 (p0) REVERT: L 78 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7596 (ttp80) REVERT: L 84 GLU cc_start: 0.8637 (tp30) cc_final: 0.7971 (tp30) REVERT: L 88 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8524 (mt-10) REVERT: L 95 GLU cc_start: 0.9226 (tp30) cc_final: 0.8869 (tp30) REVERT: L 199 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7956 (tp30) REVERT: L 202 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8749 (tm-30) REVERT: M 78 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7779 (ttp80) REVERT: N 199 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8448 (tm-30) REVERT: O 30 ASN cc_start: 0.8861 (p0) cc_final: 0.8458 (p0) REVERT: O 95 GLU cc_start: 0.9259 (tp30) cc_final: 0.8868 (tm-30) REVERT: O 98 THR cc_start: 0.9397 (p) cc_final: 0.9125 (p) REVERT: O 113 ASN cc_start: 0.9393 (m-40) cc_final: 0.9066 (m-40) REVERT: O 137 GLU cc_start: 0.8889 (mp0) cc_final: 0.8559 (mp0) REVERT: O 190 GLN cc_start: 0.9024 (mt0) cc_final: 0.8212 (mm-40) REVERT: P 30 ASN cc_start: 0.8722 (p0) cc_final: 0.8419 (p0) REVERT: P 82 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7292 (tm-30) REVERT: P 212 TYR cc_start: 0.7180 (m-80) cc_final: 0.6772 (t80) REVERT: Q 37 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9340 (mmmm) REVERT: Q 78 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7951 (tmm-80) REVERT: Q 190 GLN cc_start: 0.8524 (mt0) cc_final: 0.8161 (mt0) REVERT: Q 199 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8630 (tm-30) REVERT: R 12 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9243 (mm-30) REVERT: R 30 ASN cc_start: 0.8951 (p0) cc_final: 0.8650 (p0) REVERT: R 40 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8855 (tm-30) REVERT: R 95 GLU cc_start: 0.9208 (tp30) cc_final: 0.8898 (tp30) REVERT: R 137 GLU cc_start: 0.9005 (mp0) cc_final: 0.8701 (mp0) REVERT: R 190 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8620 (mt0) REVERT: R 199 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8454 (tm-30) REVERT: S 37 LYS cc_start: 0.9567 (mtpp) cc_final: 0.9329 (mmmm) REVERT: S 78 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7908 (ttp80) REVERT: S 88 GLU cc_start: 0.8465 (pt0) cc_final: 0.8231 (pt0) REVERT: S 113 ASN cc_start: 0.9369 (m-40) cc_final: 0.9072 (m-40) REVERT: S 190 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8686 (tp40) REVERT: S 199 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8234 (tm-30) REVERT: T 78 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7524 (ttp80) REVERT: T 82 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7589 (tm-30) REVERT: T 92 ARG cc_start: 0.9143 (mmp80) cc_final: 0.8732 (mmt90) REVERT: T 117 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8603 (tm-30) REVERT: T 206 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8847 (tp30) REVERT: U 37 LYS cc_start: 0.9601 (mmmm) cc_final: 0.9249 (mmmm) REVERT: U 84 GLU cc_start: 0.8623 (tp30) cc_final: 0.7934 (tp30) REVERT: U 88 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7909 (mt-10) REVERT: U 113 ASN cc_start: 0.9247 (m-40) cc_final: 0.8910 (m110) outliers start: 140 outliers final: 91 residues processed: 777 average time/residue: 0.2670 time to fit residues: 314.2256 Evaluate side-chains 747 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 648 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 118 ILE Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain M residue 7 VAL Chi-restraints excluded: chain M residue 35 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 35 LEU Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain P residue 7 VAL Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 182 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 7 VAL Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain S residue 195 SER Chi-restraints excluded: chain T residue 7 VAL Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 409 optimal weight: 4.9990 chunk 408 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 194 optimal weight: 0.0970 chunk 310 optimal weight: 0.0870 chunk 337 optimal weight: 0.6980 chunk 178 optimal weight: 0.0870 chunk 37 optimal weight: 7.9990 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 190 GLN F 180 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN K 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.051339 restraints weight = 97304.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053218 restraints weight = 61192.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054457 restraints weight = 42815.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055410 restraints weight = 32909.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056181 restraints weight = 26543.874| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34811 Z= 0.146 Angle : 0.732 17.792 47040 Z= 0.368 Chirality : 0.043 0.510 5985 Planarity : 0.004 0.038 5901 Dihedral : 4.207 51.732 4561 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.43 % Allowed : 32.67 % Favored : 64.89 % 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: 4.05 (0.12), residues: 4326 helix: 3.09 (0.07), residues: 3864 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 140 TYR 0.018 0.002 TYR G 212 PHE 0.031 0.002 PHE T 97 HIS 0.004 0.001 HIS G 207 Details of bonding type rmsd covalent geometry : bond 0.00308 (34734) covalent geometry : angle 0.73162 (47040) hydrogen bonds : bond 0.04071 ( 3238) hydrogen bonds : angle 3.48155 ( 9714) metal coordination : bond 0.00186 ( 77) ********************** 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 893 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 801 time to evaluate : 1.390 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: 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: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7353 (tmm-80) cc_final: 0.6309 (tmm-80) REVERT: A 84 GLU cc_start: 0.8471 (tp30) cc_final: 0.7843 (tp30) REVERT: A 88 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 199 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8394 (tm-30) REVERT: B 30 ASN cc_start: 0.9336 (p0) cc_final: 0.9059 (p0) REVERT: B 78 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7674 (ttp80) REVERT: B 79 ASP cc_start: 0.7869 (m-30) cc_final: 0.7560 (m-30) REVERT: B 85 PHE cc_start: 0.9203 (t80) cc_final: 0.8960 (t80) REVERT: B 88 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 149 PHE cc_start: 0.9360 (m-10) cc_final: 0.8990 (m-80) REVERT: B 190 GLN cc_start: 0.9128 (mt0) cc_final: 0.8472 (mm-40) REVERT: B 199 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8580 (tm-30) REVERT: B 206 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9081 (tp30) REVERT: C 30 ASN cc_start: 0.9214 (p0) cc_final: 0.8857 (p0) REVERT: C 84 GLU cc_start: 0.8484 (tp30) cc_final: 0.7567 (tp30) REVERT: C 88 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 30 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8408 (p0) REVERT: D 113 ASN cc_start: 0.9395 (m-40) cc_final: 0.9067 (m-40) REVERT: D 137 GLU cc_start: 0.9132 (mp0) cc_final: 0.8844 (mp0) REVERT: D 206 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8665 (tp30) REVERT: E 78 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7700 (ttp80) REVERT: E 88 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8314 (mt-10) REVERT: E 113 ASN cc_start: 0.9348 (m-40) cc_final: 0.9125 (m-40) REVERT: E 199 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8552 (tm-30) REVERT: F 78 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7772 (ttp80) REVERT: F 84 GLU cc_start: 0.8395 (tp30) cc_final: 0.7748 (tp30) REVERT: F 88 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7795 (mt-10) REVERT: G 84 GLU cc_start: 0.8494 (tp30) cc_final: 0.7972 (tp30) REVERT: G 88 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8033 (mt-10) REVERT: G 95 GLU cc_start: 0.9252 (tp30) cc_final: 0.8891 (tp30) REVERT: G 131 ARG cc_start: 0.9367 (ttm110) cc_final: 0.8847 (ttm-80) REVERT: G 190 GLN cc_start: 0.9038 (mt0) cc_final: 0.8313 (mm-40) REVERT: H 30 ASN cc_start: 0.9325 (p0) cc_final: 0.9066 (p0) REVERT: H 40 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8540 (tm-30) REVERT: H 78 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6950 (ttp80) REVERT: H 88 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8146 (mt-10) REVERT: H 131 ARG cc_start: 0.9285 (ttm110) cc_final: 0.8929 (ttm110) REVERT: H 137 GLU cc_start: 0.8968 (mp0) cc_final: 0.8711 (mp0) REVERT: H 199 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8154 (tm-30) REVERT: H 212 TYR cc_start: 0.7337 (m-80) cc_final: 0.7094 (m-80) REVERT: I 40 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8653 (tm-30) REVERT: I 88 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8313 (mt-10) REVERT: I 113 ASN cc_start: 0.9235 (m-40) cc_final: 0.8987 (m110) REVERT: I 199 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8432 (tm-30) REVERT: I 203 ASP cc_start: 0.7839 (t70) cc_final: 0.7605 (t70) REVERT: J 30 ASN cc_start: 0.8926 (p0) cc_final: 0.8588 (p0) REVERT: J 40 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8807 (tm-30) REVERT: J 78 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7593 (tmm-80) REVERT: J 149 PHE cc_start: 0.9369 (m-10) cc_final: 0.9052 (m-80) REVERT: J 182 LEU cc_start: 0.9556 (mt) cc_final: 0.9229 (mm) REVERT: J 190 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8540 (mm110) REVERT: K 30 ASN cc_start: 0.8806 (p0) cc_final: 0.8455 (p0) REVERT: K 88 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7965 (mt-10) REVERT: K 137 GLU cc_start: 0.8932 (mp0) cc_final: 0.8699 (mp0) REVERT: K 206 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8719 (tp30) REVERT: L 30 ASN cc_start: 0.8606 (p0) cc_final: 0.8370 (p0) REVERT: L 78 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7620 (ttp80) REVERT: L 82 GLU cc_start: 0.7512 (tm-30) cc_final: 0.5448 (tm-30) REVERT: L 95 GLU cc_start: 0.9252 (tp30) cc_final: 0.9043 (tp30) REVERT: L 199 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7912 (tp30) REVERT: L 202 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8759 (tm-30) REVERT: M 78 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7632 (ttp80) REVERT: N 30 ASN cc_start: 0.9270 (p0) cc_final: 0.9026 (p0) REVERT: N 137 GLU cc_start: 0.9044 (mp0) cc_final: 0.8768 (mp0) REVERT: N 199 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8499 (tm-30) REVERT: O 30 ASN cc_start: 0.8682 (p0) cc_final: 0.8322 (p0) REVERT: O 79 ASP cc_start: 0.7830 (m-30) cc_final: 0.7609 (m-30) REVERT: O 95 GLU cc_start: 0.9242 (tp30) cc_final: 0.8911 (tm-30) REVERT: O 113 ASN cc_start: 0.9385 (m-40) cc_final: 0.9091 (m110) REVERT: O 137 GLU cc_start: 0.8881 (mp0) cc_final: 0.8585 (mp0) REVERT: O 139 THR cc_start: 0.9731 (m) cc_final: 0.9493 (p) REVERT: O 190 GLN cc_start: 0.8985 (mt0) cc_final: 0.8195 (mm-40) REVERT: P 30 ASN cc_start: 0.8572 (p0) cc_final: 0.8300 (p0) REVERT: P 48 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8374 (tp-100) REVERT: P 137 GLU cc_start: 0.9078 (mp0) cc_final: 0.8787 (mp0) REVERT: P 190 GLN cc_start: 0.9081 (mt0) cc_final: 0.8732 (mm-40) REVERT: P 212 TYR cc_start: 0.6983 (m-80) cc_final: 0.6623 (t80) REVERT: Q 30 ASN cc_start: 0.9277 (p0) cc_final: 0.8992 (p0) REVERT: Q 37 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9333 (mmmm) REVERT: Q 78 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7890 (tmm-80) REVERT: Q 149 PHE cc_start: 0.9322 (m-80) cc_final: 0.9024 (m-80) REVERT: Q 190 GLN cc_start: 0.8420 (mt0) cc_final: 0.8155 (mt0) REVERT: Q 199 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8536 (tm-30) REVERT: R 12 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9240 (mm-30) REVERT: R 30 ASN cc_start: 0.8844 (p0) cc_final: 0.8572 (p0) REVERT: R 40 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8819 (tm-30) REVERT: R 78 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7520 (ttp80) REVERT: R 95 GLU cc_start: 0.9182 (tp30) cc_final: 0.8852 (tp30) REVERT: R 137 GLU cc_start: 0.8988 (mp0) cc_final: 0.8696 (mp0) REVERT: R 190 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8558 (mt0) REVERT: R 199 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8277 (tm-30) REVERT: S 30 ASN cc_start: 0.9051 (p0) cc_final: 0.8819 (p0) REVERT: S 37 LYS cc_start: 0.9556 (mtpp) cc_final: 0.9317 (mmmm) REVERT: S 88 GLU cc_start: 0.8359 (pt0) cc_final: 0.8124 (pt0) REVERT: S 107 SER cc_start: 0.6423 (p) cc_final: 0.6024 (t) REVERT: S 113 ASN cc_start: 0.9349 (m-40) cc_final: 0.9103 (m110) REVERT: S 190 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8658 (tp40) REVERT: S 199 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8225 (tm-30) REVERT: T 78 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7735 (ttp80) REVERT: T 82 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7580 (tm-30) REVERT: T 92 ARG cc_start: 0.9096 (mmp80) cc_final: 0.8683 (mmt90) REVERT: T 117 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8585 (tm-30) REVERT: T 206 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8825 (tp30) REVERT: U 30 ASN cc_start: 0.9165 (p0) cc_final: 0.8880 (p0) REVERT: U 37 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9285 (mmmm) REVERT: U 71 ASN cc_start: 0.8863 (m110) cc_final: 0.8567 (m110) REVERT: U 84 GLU cc_start: 0.8498 (tp30) cc_final: 0.8074 (tp30) REVERT: U 113 ASN cc_start: 0.9251 (m-40) cc_final: 0.8914 (m110) REVERT: U 149 PHE cc_start: 0.9273 (m-80) cc_final: 0.9064 (m-80) REVERT: U 190 GLN cc_start: 0.9039 (mt0) cc_final: 0.8520 (mt0) outliers start: 92 outliers final: 64 residues processed: 861 average time/residue: 0.2612 time to fit residues: 343.5952 Evaluate side-chains 785 residues out of total 3780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 715 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 118 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 190 GLN Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain M residue 79 ASP Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 79 ASP Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain O residue 142 LEU Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 194 LEU Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 201 ILE Chi-restraints excluded: chain Q residue 78 ARG Chi-restraints excluded: chain Q residue 195 SER Chi-restraints excluded: chain Q residue 201 ILE Chi-restraints excluded: chain R residue 12 GLU Chi-restraints excluded: chain R residue 79 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain S residue 35 LEU Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain S residue 190 GLN Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 143 ILE Chi-restraints excluded: chain T residue 195 SER Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 148 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 416 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 301 optimal weight: 6.9990 chunk 89 optimal weight: 0.0370 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 180 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.062774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.050814 restraints weight = 97803.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052560 restraints weight = 63611.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053917 restraints weight = 45989.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054850 restraints weight = 35418.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.055607 restraints weight = 28885.606| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34811 Z= 0.158 Angle : 0.743 15.928 47040 Z= 0.373 Chirality : 0.044 0.404 5985 Planarity : 0.004 0.043 5901 Dihedral : 4.230 51.314 4561 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.20 % Allowed : 33.65 % Favored : 64.15 % 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: 3.99 (0.12), residues: 4326 helix: 3.05 (0.08), residues: 3864 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 172 TYR 0.023 0.002 TYR F 212 PHE 0.034 0.002 PHE Q 85 HIS 0.005 0.001 HIS F 47 Details of bonding type rmsd covalent geometry : bond 0.00353 (34734) covalent geometry : angle 0.74257 (47040) hydrogen bonds : bond 0.04066 ( 3238) hydrogen bonds : angle 3.60215 ( 9714) metal coordination : bond 0.00296 ( 77) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6108.27 seconds wall clock time: 106 minutes 46.86 seconds (6406.86 seconds total)