Starting phenix.real_space_refine on Sat Feb 7 20:34:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k84_62160/02_2026/9k84_62160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k84_62160/02_2026/9k84_62160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k84_62160/02_2026/9k84_62160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k84_62160/02_2026/9k84_62160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k84_62160/02_2026/9k84_62160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k84_62160/02_2026/9k84_62160.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 42 6.06 5 S 21 5.16 5 C 23898 2.51 5 N 5733 2.21 5 O 6468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 307 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36162 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "D" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "G" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "I" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "J" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "K" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "L" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "M" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "N" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "O" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "P" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "Q" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "R" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "S" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "T" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "U" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1720 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.57, per 1000 atoms: 0.24 Number of scatterers: 36162 At special positions: 0 Unit cell: (128.199, 126.044, 184.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 42 29.99 S 21 16.00 O 6468 8.00 N 5733 7.00 C 23898 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS K 47 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 124 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 207 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS B 75 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 47 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS J 124 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS I 47 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 124 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 207 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS D 75 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 47 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS L 124 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 207 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS A 75 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS M 47 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 124 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 47 " pdb="ZN ZN C 303 " - 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 D 207 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS F 75 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 47 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS N 124 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 207 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS C 75 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS O 47 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 124 " pdb=" ZN E 303 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS G 207 " pdb="ZN ZN E 303 " - pdb=" NE2 HIS E 75 " pdb=" ZN E 304 " pdb="ZN ZN E 304 " - pdb=" NE2 HIS E 47 " pdb="ZN ZN E 304 " - pdb=" NE2 HIS F 124 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 207 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS H 75 " 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 Q 47 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 124 " pdb=" ZN G 302 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS I 207 " pdb="ZN ZN G 302 " - pdb=" NE2 HIS G 75 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS 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 I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS S 47 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 124 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS K 207 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS I 75 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 207 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS L 75 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS J 47 " pdb="ZN ZN J 302 " - pdb=" NE2 HIS T 124 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS U 47 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 124 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS M 207 " pdb="ZN ZN K 302 " - pdb=" NE2 HIS K 75 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS 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 N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 207 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS P 75 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS O 207 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS M 75 " pdb=" ZN O 302 " pdb="ZN ZN O 302 " - pdb=" NE2 HIS O 124 " pdb=" ZN O 303 " pdb="ZN ZN O 303 " - pdb=" NE2 HIS Q 207 " pdb="ZN ZN O 303 " - pdb=" NE2 HIS O 75 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 207 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS R 75 " pdb=" ZN Q 301 " pdb="ZN ZN Q 301 " - pdb=" NE2 HIS Q 124 " pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 207 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS T 75 " pdb=" ZN S 301 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS S 207 " pdb="ZN ZN S 301 " - pdb=" NE2 HIS Q 75 " pdb=" ZN S 302 " pdb="ZN ZN S 302 " - pdb=" NE2 HIS S 124 " pdb=" ZN U 301 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS U 207 " pdb="ZN ZN U 301 " - pdb=" NE2 HIS S 75 " pdb=" ZN U 302 " pdb="ZN ZN U 302 " - pdb=" NE2 HIS U 124 " pdb=" ZN U 303 " pdb="ZN ZN U 303 " - pdb=" NE2 HIS U 75 " 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8568 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 92.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.804A pdb=" N ASN A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 52 Processing helix chain 'A' and resid 57 through 78 removed outlier: 4.117A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 108 through 131 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 159 through 183 removed outlier: 3.583A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 213 removed outlier: 3.808A pdb=" N GLN A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 3.658A pdb=" N ASN B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 57 through 80 removed outlier: 4.112A pdb=" N ILE B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.539A pdb=" N ARG B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 159 through 183 removed outlier: 3.634A pdb=" N ARG B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 213 removed outlier: 3.854A pdb=" N GLN B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 28 removed outlier: 3.745A pdb=" N ASN C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 52 Processing helix chain 'C' and resid 57 through 80 removed outlier: 4.083A pdb=" N ILE C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 105 Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.609A pdb=" N ARG C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 159 through 183 removed outlier: 3.625A pdb=" N ARG C 163 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 167 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 213 removed outlier: 3.790A pdb=" N GLN C 190 " --> pdb=" O PRO C 186 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 191 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 28 removed outlier: 3.783A pdb=" N ASN D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 52 Processing helix chain 'D' and resid 57 through 80 removed outlier: 4.206A pdb=" N ILE D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 105 Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.533A pdb=" N ARG D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 159 through 183 removed outlier: 3.634A pdb=" N ARG D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 213 removed outlier: 3.823A pdb=" N GLN D 190 " --> pdb=" O PRO D 186 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 191 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE D 213 " --> pdb=" O PHE D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 Processing helix chain 'E' and resid 30 through 52 Processing helix chain 'E' and resid 57 through 80 removed outlier: 4.142A pdb=" N ILE E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 Processing helix chain 'E' and resid 108 through 131 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 159 through 183 removed outlier: 3.663A pdb=" N ARG E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 213 removed outlier: 3.852A pdb=" N GLN E 190 " --> pdb=" O PRO E 186 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU E 192 " --> pdb=" O GLU E 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 213 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.553A pdb=" N GLU F 27 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 57 through 80 removed outlier: 4.163A pdb=" N ILE F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 105 Processing helix chain 'F' and resid 108 through 131 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 159 through 183 removed outlier: 3.660A pdb=" N ARG F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 213 removed outlier: 3.849A pdb=" N GLN F 190 " --> pdb=" O PRO F 186 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE F 191 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE F 213 " --> pdb=" O PHE F 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 28 removed outlier: 3.535A pdb=" N GLU G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 52 Processing helix chain 'G' and resid 57 through 80 removed outlier: 4.090A pdb=" N ILE G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 105 Processing helix chain 'G' and resid 108 through 131 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 159 through 183 removed outlier: 3.677A pdb=" N ARG G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE G 167 " --> pdb=" O ARG G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 213 removed outlier: 3.824A pdb=" N GLN G 190 " --> pdb=" O PRO G 186 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE G 191 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 27 removed outlier: 3.552A pdb=" N GLU H 27 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 52 Processing helix chain 'H' and resid 57 through 78 removed outlier: 4.137A pdb=" N ILE H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 105 Processing helix chain 'H' and resid 108 through 131 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 159 through 183 removed outlier: 3.692A pdb=" N ARG H 163 " --> pdb=" O PRO H 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE H 167 " --> pdb=" O ARG H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 213 removed outlier: 3.829A pdb=" N GLN H 190 " --> pdb=" O PRO H 186 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 27 Processing helix chain 'I' and resid 30 through 52 Processing helix chain 'I' and resid 57 through 80 removed outlier: 4.165A pdb=" N ILE I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 108 through 131 removed outlier: 3.529A pdb=" N ARG I 112 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 159 through 183 removed outlier: 3.602A pdb=" N ARG I 163 " --> pdb=" O PRO I 159 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE I 167 " --> pdb=" O ARG I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 213 removed outlier: 3.881A pdb=" N GLN I 190 " --> pdb=" O PRO I 186 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE I 191 " --> pdb=" O VAL I 187 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 27 Processing helix chain 'J' and resid 30 through 52 Processing helix chain 'J' and resid 57 through 80 removed outlier: 4.003A pdb=" N ILE J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 105 Processing helix chain 'J' and resid 108 through 131 removed outlier: 3.568A pdb=" N ARG J 112 " --> pdb=" O THR J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 159 through 183 removed outlier: 3.631A pdb=" N ARG J 163 " --> pdb=" O PRO J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 213 removed outlier: 3.793A pdb=" N GLN J 190 " --> pdb=" O PRO J 186 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE J 191 " --> pdb=" O VAL J 187 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE J 213 " --> pdb=" O PHE J 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 28 removed outlier: 3.844A pdb=" N ASN K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 52 Processing helix chain 'K' and resid 57 through 80 removed outlier: 4.169A pdb=" N ILE K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 Processing helix chain 'K' and resid 108 through 131 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 159 through 183 removed outlier: 3.666A pdb=" N ARG K 163 " --> pdb=" O PRO K 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE K 167 " --> pdb=" O ARG K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 213 removed outlier: 3.854A pdb=" N GLN K 190 " --> pdb=" O PRO K 186 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 191 " --> pdb=" O VAL K 187 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU K 192 " --> pdb=" O GLU K 188 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE K 213 " --> pdb=" O PHE K 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 27 Processing helix chain 'L' and resid 30 through 52 Processing helix chain 'L' and resid 57 through 80 removed outlier: 4.173A pdb=" N ILE L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 105 Processing helix chain 'L' and resid 108 through 131 removed outlier: 3.570A pdb=" N ARG L 112 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 159 through 183 removed outlier: 3.731A pdb=" N ARG L 163 " --> pdb=" O PRO L 159 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE L 167 " --> pdb=" O ARG L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 213 removed outlier: 3.855A pdb=" N GLN L 190 " --> pdb=" O PRO L 186 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE L 191 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE L 213 " --> pdb=" O PHE L 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 27 Processing helix chain 'M' and resid 30 through 52 Processing helix chain 'M' and resid 57 through 80 removed outlier: 4.130A pdb=" N ILE M 61 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 105 Processing helix chain 'M' and resid 108 through 131 removed outlier: 3.500A pdb=" N ARG M 112 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 159 through 183 removed outlier: 3.588A pdb=" N ARG M 163 " --> pdb=" O PRO M 159 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE M 167 " --> pdb=" O ARG M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 213 removed outlier: 3.899A pdb=" N GLN M 190 " --> pdb=" O PRO M 186 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE M 191 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE M 213 " --> pdb=" O PHE M 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 28 removed outlier: 3.505A pdb=" N GLU N 27 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN N 28 " --> pdb=" O GLU N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 52 Processing helix chain 'N' and resid 57 through 80 removed outlier: 4.130A pdb=" N ILE N 61 " --> pdb=" O GLU N 57 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 105 Processing helix chain 'N' and resid 108 through 131 removed outlier: 3.548A pdb=" N ARG N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 159 through 183 removed outlier: 3.609A pdb=" N ARG N 163 " --> pdb=" O PRO N 159 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE N 167 " --> pdb=" O ARG N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 213 removed outlier: 3.801A pdb=" N GLN N 190 " --> pdb=" O PRO N 186 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE N 191 " --> pdb=" O VAL N 187 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE N 213 " --> pdb=" O PHE N 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 27 removed outlier: 3.581A pdb=" N GLU O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 52 Processing helix chain 'O' and resid 57 through 80 removed outlier: 4.122A pdb=" N ILE O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 105 Processing helix chain 'O' and resid 108 through 131 removed outlier: 3.594A pdb=" N ARG O 112 " --> pdb=" O THR O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 159 through 183 removed outlier: 3.705A pdb=" N ARG O 163 " --> pdb=" O PRO O 159 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE O 167 " --> pdb=" O ARG O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 213 removed outlier: 3.832A pdb=" N GLN O 190 " --> pdb=" O PRO O 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE O 191 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE O 213 " --> pdb=" O PHE O 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 28 removed outlier: 3.719A pdb=" N ASN P 28 " --> pdb=" O GLU P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 52 Processing helix chain 'P' and resid 57 through 80 removed outlier: 4.089A pdb=" N ILE P 61 " --> pdb=" O GLU P 57 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 105 Processing helix chain 'P' and resid 108 through 131 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 159 through 183 removed outlier: 3.651A pdb=" N ARG P 163 " --> pdb=" O PRO P 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE P 167 " --> pdb=" O ARG P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 213 removed outlier: 3.822A pdb=" N GLN P 190 " --> pdb=" O PRO P 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE P 191 " --> pdb=" O VAL P 187 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 28 removed outlier: 3.744A pdb=" N ASN Q 28 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 52 Processing helix chain 'Q' and resid 57 through 78 removed outlier: 4.146A pdb=" N ILE Q 61 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 105 Processing helix chain 'Q' and resid 108 through 131 removed outlier: 3.541A pdb=" N ARG Q 112 " --> pdb=" O THR Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 159 through 183 removed outlier: 3.749A pdb=" N ARG Q 163 " --> pdb=" O PRO Q 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE Q 167 " --> pdb=" O ARG Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 213 removed outlier: 3.841A pdb=" N GLN Q 190 " --> pdb=" O PRO Q 186 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE Q 191 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU Q 192 " --> pdb=" O GLU Q 188 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE Q 213 " --> pdb=" O PHE Q 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 28 removed outlier: 3.798A pdb=" N ASN R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 52 removed outlier: 3.510A pdb=" N LEU R 51 " --> pdb=" O HIS R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 80 removed outlier: 4.215A pdb=" N ILE R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 105 removed outlier: 3.551A pdb=" N GLY R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 131 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 159 through 183 removed outlier: 3.632A pdb=" N ARG R 163 " --> pdb=" O PRO R 159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE R 167 " --> pdb=" O ARG R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 213 removed outlier: 3.796A pdb=" N GLN R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE R 191 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE R 213 " --> pdb=" O PHE R 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 28 removed outlier: 3.550A pdb=" N GLU S 27 " --> pdb=" O LYS S 23 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN S 28 " --> pdb=" O GLU S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 52 Processing helix chain 'S' and resid 57 through 80 removed outlier: 4.204A pdb=" N ILE S 61 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 105 Processing helix chain 'S' and resid 108 through 131 removed outlier: 3.585A pdb=" N ARG S 112 " --> pdb=" O THR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 159 through 183 removed outlier: 3.634A pdb=" N ARG S 163 " --> pdb=" O PRO S 159 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE S 167 " --> pdb=" O ARG S 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 186 through 213 removed outlier: 3.904A pdb=" N GLN S 190 " --> pdb=" O PRO S 186 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE S 191 " --> pdb=" O VAL S 187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU S 192 " --> pdb=" O GLU S 188 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE S 213 " --> pdb=" O PHE S 209 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 28 removed outlier: 3.795A pdb=" N ASN T 28 " --> pdb=" O GLU T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 52 Processing helix chain 'T' and resid 57 through 78 removed outlier: 4.150A pdb=" N ILE T 61 " --> pdb=" O GLU T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 105 Processing helix chain 'T' and resid 108 through 131 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 159 through 183 removed outlier: 3.683A pdb=" N ARG T 163 " --> pdb=" O PRO T 159 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE T 167 " --> pdb=" O ARG T 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 213 removed outlier: 3.786A pdb=" N GLN T 190 " --> pdb=" O PRO T 186 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE T 191 " --> pdb=" O VAL T 187 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE T 213 " --> pdb=" O PHE T 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 28 removed outlier: 3.815A pdb=" N ASN U 28 " --> pdb=" O GLU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 52 Processing helix chain 'U' and resid 57 through 80 removed outlier: 4.210A pdb=" N ILE U 61 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY U 80 " --> pdb=" O ALA U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 105 Processing helix chain 'U' and resid 108 through 131 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 159 through 183 removed outlier: 3.600A pdb=" N ARG U 163 " --> pdb=" O PRO U 159 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE U 167 " --> pdb=" O ARG U 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 186 through 213 removed outlier: 3.836A pdb=" N GLN U 190 " --> pdb=" O PRO U 186 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE U 191 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE U 213 " --> pdb=" O PHE U 209 " (cutoff:3.500A) 3173 hydrogen bonds defined for protein. 9519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.32 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: 1.23 - 1.34: 11494 1.34 - 1.46: 3464 1.46 - 1.57: 21750 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 36750 Sorted by residual: bond pdb=" CE LYS L 20 " pdb=" NZ LYS L 20 " ideal model delta sigma weight residual 1.489 1.448 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CG GLU M 144 " pdb=" CD GLU M 144 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.79e+00 bond pdb=" CB GLU H 71 " pdb=" CG GLU H 71 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CE LYS F 20 " pdb=" NZ LYS F 20 " ideal model delta sigma weight residual 1.489 1.450 0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CE LYS Q 20 " pdb=" NZ LYS Q 20 " ideal model delta sigma weight residual 1.489 1.450 0.039 3.00e-02 1.11e+03 1.68e+00 ... (remaining 36745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 48850 2.06 - 4.12: 756 4.12 - 6.18: 92 6.18 - 8.24: 26 8.24 - 10.30: 4 Bond angle restraints: 49728 Sorted by residual: angle pdb=" CA LYS G 20 " pdb=" CB LYS G 20 " pdb=" CG LYS G 20 " ideal model delta sigma weight residual 114.10 124.40 -10.30 2.00e+00 2.50e-01 2.65e+01 angle pdb=" CA LYS M 20 " pdb=" CB LYS M 20 " pdb=" CG LYS M 20 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLN J 54 " pdb=" CB GLN J 54 " pdb=" CG GLN J 54 " ideal model delta sigma weight residual 114.10 122.61 -8.51 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CA LYS S 20 " pdb=" CB LYS S 20 " pdb=" CG LYS S 20 " ideal model delta sigma weight residual 114.10 122.43 -8.33 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CA LYS Q 20 " pdb=" CB LYS Q 20 " pdb=" CG LYS Q 20 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 ... (remaining 49723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19272 17.95 - 35.90: 2644 35.90 - 53.85: 641 53.85 - 71.80: 107 71.80 - 89.75: 79 Dihedral angle restraints: 22743 sinusoidal: 9744 harmonic: 12999 Sorted by residual: dihedral pdb=" CA LEU G 184 " pdb=" C LEU G 184 " pdb=" N TYR G 185 " pdb=" CA TYR G 185 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP T 173 " pdb=" CB ASP T 173 " pdb=" CG ASP T 173 " pdb=" OD1 ASP T 173 " ideal model delta sinusoidal sigma weight residual -30.00 -91.37 61.37 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" CA ASP I 173 " pdb=" CB ASP I 173 " pdb=" CG ASP I 173 " pdb=" OD1 ASP I 173 " ideal model delta sinusoidal sigma weight residual -30.00 -89.45 59.45 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 22740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5046 0.048 - 0.096: 864 0.096 - 0.144: 123 0.144 - 0.192: 3 0.192 - 0.239: 12 Chirality restraints: 6048 Sorted by residual: chirality pdb=" CB ILE O 127 " pdb=" CA ILE O 127 " pdb=" CG1 ILE O 127 " pdb=" CG2 ILE O 127 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CG LEU R 12 " pdb=" CB LEU R 12 " pdb=" CD1 LEU R 12 " pdb=" CD2 LEU R 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS R 20 " pdb=" N LYS R 20 " pdb=" C LYS R 20 " pdb=" CB LYS R 20 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6045 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 44 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" CD GLU D 44 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU D 44 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 44 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG S 64 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C ARG S 64 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG S 64 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL S 65 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG K 64 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ARG K 64 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG K 64 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL K 65 " 0.011 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 417 2.62 - 3.19: 34578 3.19 - 3.76: 60155 3.76 - 4.33: 72433 4.33 - 4.90: 126204 Nonbonded interactions: 293787 Sorted by model distance: nonbonded pdb=" OD1 ASP E 79 " pdb="ZN ZN E 303 " model vdw 2.052 2.230 nonbonded pdb=" OD1 ASP R 79 " pdb="ZN ZN P 301 " model vdw 2.054 2.230 nonbonded pdb=" OD1 ASP S 79 " pdb="ZN ZN U 301 " model vdw 2.054 2.230 nonbonded pdb=" OD1 ASP M 79 " pdb="ZN ZN O 301 " model vdw 2.060 2.230 nonbonded pdb=" OD1 ASP I 79 " pdb="ZN ZN I 302 " model vdw 2.060 2.230 ... (remaining 293782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 213) selection = (chain 'B' and resid 6 through 213) selection = (chain 'C' and resid 6 through 213) selection = (chain 'D' and resid 6 through 213) selection = (chain 'E' and resid 6 through 213) selection = (chain 'F' and resid 6 through 213) selection = (chain 'G' and resid 6 through 213) selection = (chain 'H' and resid 6 through 213) selection = (chain 'I' and resid 6 through 213) selection = (chain 'J' and resid 6 through 213) selection = (chain 'K' and resid 6 through 213) selection = (chain 'L' and resid 6 through 213) selection = (chain 'M' and resid 6 through 213) selection = (chain 'N' and resid 6 through 213) selection = (chain 'O' and resid 6 through 213) selection = (chain 'P' and resid 6 through 213) selection = (chain 'Q' and resid 6 through 213) selection = (chain 'R' and resid 6 through 213) selection = (chain 'S' and resid 6 through 213) selection = chain 'T' selection = (chain 'U' and resid 6 through 213) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.480 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.008 0.522 36828 Z= 0.278 Angle : 0.630 10.297 49728 Z= 0.351 Chirality : 0.037 0.239 6048 Planarity : 0.005 0.039 6216 Dihedral : 17.774 89.751 14175 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.17 % Allowed : 23.93 % Favored : 75.89 % 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: 3.68 (0.12), residues: 4326 helix: 2.83 (0.08), residues: 3801 sheet: None (None), residues: 0 loop : -0.88 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG S 64 TYR 0.023 0.002 TYR C 116 PHE 0.022 0.001 PHE M 94 HIS 0.003 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00366 (36750) covalent geometry : angle 0.62957 (49728) hydrogen bonds : bond 0.10032 ( 3173) hydrogen bonds : angle 4.25697 ( 9519) metal coordination : bond 0.14758 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 614 time to evaluate : 1.774 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: E 116 TYR cc_start: 0.9110 (m-80) cc_final: 0.8771 (m-80) REVERT: H 168 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8417 (mm-30) REVERT: K 92 GLU cc_start: 0.8050 (mp0) cc_final: 0.7767 (mp0) REVERT: K 137 GLU cc_start: 0.9240 (mp0) cc_final: 0.8837 (mp0) REVERT: L 188 GLU cc_start: 0.8336 (mp0) cc_final: 0.8124 (mp0) REVERT: T 144 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8187 (mp0) REVERT: T 188 GLU cc_start: 0.3469 (tt0) cc_final: 0.3251 (tt0) outliers start: 7 outliers final: 1 residues processed: 618 average time/residue: 0.2740 time to fit residues: 260.9016 Evaluate side-chains 568 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 567 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 212 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.4980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.2980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN E 54 GLN F 6 ASN G 6 ASN H 6 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075759 restraints weight = 69324.824| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.90 r_work: 0.3020 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36828 Z= 0.145 Angle : 0.510 5.829 49728 Z= 0.268 Chirality : 0.035 0.191 6048 Planarity : 0.004 0.046 6216 Dihedral : 4.027 48.325 4664 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.48 % Allowed : 21.40 % Favored : 76.12 % 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: 3.06 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 37 TYR 0.018 0.002 TYR C 116 PHE 0.020 0.001 PHE M 94 HIS 0.005 0.001 HIS U 75 Details of bonding type rmsd covalent geometry : bond 0.00335 (36750) covalent geometry : angle 0.51030 (49728) hydrogen bonds : bond 0.05329 ( 3173) hydrogen bonds : angle 3.59632 ( 9519) metal coordination : bond 0.00438 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 628 time to evaluate : 1.545 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: symmetry clash REVERT: A 12 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9107 (mm) REVERT: A 44 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 103 THR cc_start: 0.9258 (t) cc_final: 0.9003 (p) REVERT: B 24 GLU cc_start: 0.9108 (tp30) cc_final: 0.8857 (tp30) REVERT: B 163 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7466 (mtp180) REVERT: B 199 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8606 (mm-30) REVERT: C 103 THR cc_start: 0.9300 (t) cc_final: 0.8993 (p) REVERT: C 199 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8742 (mm-30) REVERT: E 116 TYR cc_start: 0.9108 (m-80) cc_final: 0.8836 (m-80) REVERT: G 103 THR cc_start: 0.9234 (t) cc_final: 0.8994 (p) REVERT: H 149 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8851 (mp) REVERT: K 137 GLU cc_start: 0.9167 (mp0) cc_final: 0.8851 (mp0) REVERT: K 149 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8799 (mp) REVERT: K 199 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: L 199 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8730 (mm-30) REVERT: M 199 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: O 175 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8824 (mp) REVERT: P 24 GLU cc_start: 0.9114 (tp30) cc_final: 0.8753 (tp30) REVERT: P 144 GLU cc_start: 0.8741 (mp0) cc_final: 0.8538 (mp0) REVERT: P 199 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: R 8 LEU cc_start: 0.8741 (tp) cc_final: 0.8460 (tp) REVERT: R 12 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8933 (mm) REVERT: R 199 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8622 (mm-30) REVERT: T 139 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8637 (mm) REVERT: T 188 GLU cc_start: 0.3608 (tt0) cc_final: 0.3307 (tt0) REVERT: U 195 GLU cc_start: 0.8485 (tp30) cc_final: 0.8080 (tp30) outliers start: 100 outliers final: 37 residues processed: 697 average time/residue: 0.2571 time to fit residues: 276.6832 Evaluate side-chains 621 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 571 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 199 GLU Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 199 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 384 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 239 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN C 176 ASN E 176 ASN F 6 ASN G 6 ASN G 176 ASN H 6 ASN H 86 ASN I 54 GLN J 86 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 6 ASN S 54 GLN T 6 ASN T 86 ASN U 54 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.075238 restraints weight = 68887.213| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.10 r_work: 0.2943 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36828 Z= 0.144 Angle : 0.500 7.341 49728 Z= 0.262 Chirality : 0.035 0.227 6048 Planarity : 0.004 0.038 6216 Dihedral : 4.021 49.844 4664 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.95 % Allowed : 21.43 % Favored : 75.62 % 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: 4.04 (0.12), residues: 4326 helix: 3.14 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.58 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 64 TYR 0.018 0.002 TYR C 116 PHE 0.017 0.001 PHE M 94 HIS 0.002 0.001 HIS K 207 Details of bonding type rmsd covalent geometry : bond 0.00333 (36750) covalent geometry : angle 0.50004 (49728) hydrogen bonds : bond 0.05156 ( 3173) hydrogen bonds : angle 3.46980 ( 9519) metal coordination : bond 0.00115 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 620 time to evaluate : 1.473 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: A 44 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 103 THR cc_start: 0.9184 (t) cc_final: 0.8880 (p) REVERT: B 163 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7488 (mtm180) REVERT: C 64 ARG cc_start: 0.8810 (mtm110) cc_final: 0.8479 (mtm180) REVERT: C 103 THR cc_start: 0.9291 (t) cc_final: 0.8960 (p) REVERT: C 199 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8759 (mm-30) REVERT: D 199 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: F 116 TYR cc_start: 0.9394 (m-10) cc_final: 0.9046 (m-10) REVERT: G 103 THR cc_start: 0.9191 (t) cc_final: 0.8920 (p) REVERT: H 144 GLU cc_start: 0.8600 (mp0) cc_final: 0.8245 (mp0) REVERT: K 149 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8828 (mp) REVERT: K 195 GLU cc_start: 0.8706 (tp30) cc_final: 0.8451 (tp30) REVERT: K 199 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8644 (mm-30) REVERT: L 40 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8423 (tt0) REVERT: L 199 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8691 (mm-30) REVERT: M 12 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8883 (mm) REVERT: N 199 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8663 (mm-30) REVERT: O 37 ARG cc_start: 0.9133 (mmm-85) cc_final: 0.8817 (mmm-85) REVERT: O 137 GLU cc_start: 0.9139 (mp0) cc_final: 0.8850 (mp0) REVERT: O 175 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8818 (mp) REVERT: Q 59 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7754 (mtm-85) REVERT: R 195 GLU cc_start: 0.8591 (tp30) cc_final: 0.8315 (tp30) REVERT: R 199 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8638 (mm-30) REVERT: S 127 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9247 (mm) REVERT: S 144 GLU cc_start: 0.8866 (mp0) cc_final: 0.8283 (mp0) REVERT: T 139 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8549 (mm) REVERT: U 195 GLU cc_start: 0.8458 (tp30) cc_final: 0.8092 (tp30) outliers start: 119 outliers final: 62 residues processed: 706 average time/residue: 0.2530 time to fit residues: 275.2027 Evaluate side-chains 640 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 567 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 175 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 303 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 316 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 343 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 327 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 176 ASN B 6 ASN B 176 ASN F 6 ASN G 6 ASN H 6 ASN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN I 176 ASN J 176 ASN K 176 ASN L 6 ASN N 176 ASN ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 ASN R 6 ASN R 176 ASN S 6 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 ASN T 86 ASN T 176 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075864 restraints weight = 68423.630| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.11 r_work: 0.2957 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36828 Z= 0.132 Angle : 0.491 6.977 49728 Z= 0.255 Chirality : 0.034 0.191 6048 Planarity : 0.004 0.060 6216 Dihedral : 3.993 51.344 4664 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.35 % Allowed : 21.70 % Favored : 74.95 % 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: 4.09 (0.12), residues: 4326 helix: 3.17 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 64 TYR 0.017 0.002 TYR C 116 PHE 0.015 0.001 PHE M 94 HIS 0.001 0.000 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00298 (36750) covalent geometry : angle 0.49082 (49728) hydrogen bonds : bond 0.04883 ( 3173) hydrogen bonds : angle 3.36067 ( 9519) metal coordination : bond 0.00072 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 616 time to evaluate : 1.412 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: A 44 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 103 THR cc_start: 0.9153 (t) cc_final: 0.8839 (p) REVERT: A 137 GLU cc_start: 0.9277 (mp0) cc_final: 0.9064 (mp0) REVERT: B 163 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7488 (mtm180) REVERT: C 199 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8802 (mm-30) REVERT: D 199 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: F 116 TYR cc_start: 0.9402 (m-10) cc_final: 0.9077 (m-10) REVERT: G 20 LYS cc_start: 0.9215 (mmtm) cc_final: 0.9012 (mmtm) REVERT: G 103 THR cc_start: 0.9158 (t) cc_final: 0.8889 (p) REVERT: H 12 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8980 (mm) REVERT: H 64 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8383 (mtm-85) REVERT: H 144 GLU cc_start: 0.8628 (mp0) cc_final: 0.8366 (mp0) REVERT: K 103 THR cc_start: 0.9093 (t) cc_final: 0.8787 (p) REVERT: K 149 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8819 (mp) REVERT: K 195 GLU cc_start: 0.8662 (tp30) cc_final: 0.8394 (tp30) REVERT: K 199 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8647 (mm-30) REVERT: M 12 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8899 (mm) REVERT: N 199 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: O 37 ARG cc_start: 0.9145 (mmm-85) cc_final: 0.8832 (mmm-85) REVERT: P 199 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8688 (mm-30) REVERT: Q 59 ARG cc_start: 0.7911 (ttm110) cc_final: 0.7568 (mtm-85) REVERT: Q 64 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8476 (mtm-85) REVERT: Q 180 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8867 (mtmm) REVERT: R 71 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8094 (tm-30) REVERT: R 199 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8718 (mm-30) REVERT: S 127 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9231 (mm) REVERT: S 144 GLU cc_start: 0.8861 (mp0) cc_final: 0.8265 (mp0) REVERT: T 64 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8347 (mmm-85) REVERT: T 139 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8547 (mm) REVERT: T 144 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8230 (mp0) REVERT: T 185 TYR cc_start: 0.8666 (m-10) cc_final: 0.8461 (m-10) REVERT: U 195 GLU cc_start: 0.8440 (tp30) cc_final: 0.8022 (tp30) outliers start: 135 outliers final: 76 residues processed: 711 average time/residue: 0.2502 time to fit residues: 274.6161 Evaluate side-chains 647 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 559 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 199 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 127 ILE Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 212 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 156 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 207 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 chunk 374 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 375 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN D 176 ASN F 6 ASN H 6 ASN H 86 ASN H 176 ASN L 6 ASN M 176 ASN O 176 ASN P 54 GLN Q 176 ASN R 6 ASN R 54 GLN S 6 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 ASN U 176 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077231 restraints weight = 68751.718| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.10 r_work: 0.2977 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36828 Z= 0.124 Angle : 0.496 8.164 49728 Z= 0.256 Chirality : 0.034 0.173 6048 Planarity : 0.004 0.037 6216 Dihedral : 3.975 52.549 4664 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.17 % Allowed : 22.05 % Favored : 74.78 % 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: 4.10 (0.12), residues: 4326 helix: 3.18 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 64 TYR 0.017 0.002 TYR S 116 PHE 0.013 0.001 PHE M 94 HIS 0.001 0.000 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00274 (36750) covalent geometry : angle 0.49572 (49728) hydrogen bonds : bond 0.04579 ( 3173) hydrogen bonds : angle 3.29454 ( 9519) metal coordination : bond 0.00047 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 614 time to evaluate : 1.445 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: A 44 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 103 THR cc_start: 0.9140 (t) cc_final: 0.8802 (p) REVERT: B 12 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 163 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7490 (mtm180) REVERT: C 175 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9056 (mp) REVERT: C 199 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8714 (mm-30) REVERT: D 199 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: F 116 TYR cc_start: 0.9400 (m-10) cc_final: 0.9047 (m-10) REVERT: G 40 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8541 (mt-10) REVERT: G 103 THR cc_start: 0.9116 (t) cc_final: 0.8827 (p) REVERT: H 64 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8318 (mtm-85) REVERT: H 150 GLU cc_start: 0.9064 (tp30) cc_final: 0.8842 (tp30) REVERT: K 70 MET cc_start: 0.9021 (tpt) cc_final: 0.8773 (tpt) REVERT: K 103 THR cc_start: 0.9118 (t) cc_final: 0.8760 (p) REVERT: K 149 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8833 (mp) REVERT: K 195 GLU cc_start: 0.8617 (tp30) cc_final: 0.8283 (tp30) REVERT: K 199 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8612 (mm-30) REVERT: L 40 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8467 (mt-10) REVERT: N 44 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8650 (tm-30) REVERT: N 64 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8534 (mtm-85) REVERT: N 199 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8661 (mm-30) REVERT: O 37 ARG cc_start: 0.9122 (mmm-85) cc_final: 0.8824 (mmm-85) REVERT: O 137 GLU cc_start: 0.9161 (mp0) cc_final: 0.8796 (mp0) REVERT: Q 59 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7546 (mtm-85) REVERT: Q 64 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8191 (mtm110) REVERT: Q 180 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8783 (mtmm) REVERT: R 12 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8967 (mm) REVERT: R 71 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8064 (tm-30) REVERT: R 199 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8526 (mm-30) REVERT: S 144 GLU cc_start: 0.8881 (mp0) cc_final: 0.8279 (mp0) REVERT: T 103 THR cc_start: 0.9156 (t) cc_final: 0.8884 (p) REVERT: T 139 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8498 (mm) REVERT: T 150 GLU cc_start: 0.9118 (tp30) cc_final: 0.8907 (tp30) REVERT: T 195 GLU cc_start: 0.8632 (tp30) cc_final: 0.8073 (tp30) REVERT: T 199 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: U 37 ARG cc_start: 0.9137 (mmm-85) cc_final: 0.8859 (mmm-85) REVERT: U 195 GLU cc_start: 0.8408 (tp30) cc_final: 0.7947 (tp30) outliers start: 128 outliers final: 72 residues processed: 700 average time/residue: 0.2571 time to fit residues: 277.9315 Evaluate side-chains 647 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 563 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 84 LEU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain T residue 199 GLU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 149 LEU 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 209 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 393 optimal weight: 9.9990 chunk 359 optimal weight: 0.9980 chunk 352 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 142 optimal weight: 0.0770 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN D 54 GLN G 6 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN R 54 GLN R 162 GLN S 6 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.100842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075205 restraints weight = 68998.224| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.09 r_work: 0.2943 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36828 Z= 0.154 Angle : 0.525 8.643 49728 Z= 0.270 Chirality : 0.035 0.225 6048 Planarity : 0.004 0.039 6216 Dihedral : 3.936 52.546 4664 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.08 % Allowed : 22.30 % Favored : 74.63 % 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: 4.13 (0.12), residues: 4326 helix: 3.20 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 164 TYR 0.019 0.002 TYR D 116 PHE 0.012 0.001 PHE M 94 HIS 0.002 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00371 (36750) covalent geometry : angle 0.52465 (49728) hydrogen bonds : bond 0.04943 ( 3173) hydrogen bonds : angle 3.36608 ( 9519) metal coordination : bond 0.00121 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 588 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 103 THR cc_start: 0.9161 (t) cc_final: 0.8816 (p) REVERT: B 12 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9004 (mm) REVERT: B 163 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7553 (mtm180) REVERT: C 64 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8450 (mtm180) REVERT: C 175 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9154 (mp) REVERT: C 199 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8753 (mm-30) REVERT: D 199 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8505 (mm-30) REVERT: F 64 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8365 (mmm-85) REVERT: F 116 TYR cc_start: 0.9404 (m-10) cc_final: 0.9028 (m-10) REVERT: F 199 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8694 (mm-30) REVERT: G 40 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8520 (mt-10) REVERT: G 103 THR cc_start: 0.9126 (t) cc_final: 0.8877 (p) REVERT: J 163 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7614 (mtp180) REVERT: K 40 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8353 (mt-10) REVERT: K 103 THR cc_start: 0.9150 (t) cc_final: 0.8791 (p) REVERT: K 149 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8817 (mp) REVERT: K 195 GLU cc_start: 0.8643 (tp30) cc_final: 0.8355 (tp30) REVERT: K 199 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8648 (mm-30) REVERT: L 40 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8513 (mt-10) REVERT: L 64 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8275 (mmm-85) REVERT: N 20 LYS cc_start: 0.9109 (mmtm) cc_final: 0.8907 (mmtm) REVERT: N 199 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8740 (mm-30) REVERT: O 44 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8699 (tm-30) REVERT: P 54 GLN cc_start: 0.7561 (tm130) cc_final: 0.7036 (tm-30) REVERT: Q 64 ARG cc_start: 0.8711 (mtm-85) cc_final: 0.8457 (mtm-85) REVERT: Q 180 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8963 (mtmm) REVERT: R 71 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8123 (tm-30) REVERT: R 168 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8700 (mm-30) REVERT: R 199 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8561 (mm-30) REVERT: S 144 GLU cc_start: 0.8904 (mp0) cc_final: 0.8307 (mp0) REVERT: T 103 THR cc_start: 0.9202 (t) cc_final: 0.8924 (p) REVERT: T 139 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8574 (mm) REVERT: T 144 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8227 (mp0) REVERT: T 195 GLU cc_start: 0.8692 (tp30) cc_final: 0.8168 (tp30) REVERT: T 199 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8604 (mm-30) REVERT: U 37 ARG cc_start: 0.9135 (mmm-85) cc_final: 0.8853 (mmm-85) REVERT: U 195 GLU cc_start: 0.8532 (tp30) cc_final: 0.8080 (tp30) outliers start: 124 outliers final: 82 residues processed: 675 average time/residue: 0.2597 time to fit residues: 268.6653 Evaluate side-chains 642 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 549 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 199 GLU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain T residue 199 GLU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 187 VAL 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 49 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 309 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 142 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN G 6 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 86 ASN K 162 GLN R 54 GLN S 6 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.074423 restraints weight = 69082.099| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.09 r_work: 0.2928 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36828 Z= 0.161 Angle : 0.538 8.010 49728 Z= 0.277 Chirality : 0.036 0.213 6048 Planarity : 0.004 0.039 6216 Dihedral : 3.954 52.594 4664 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.95 % Allowed : 22.82 % Favored : 74.23 % 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: 4.15 (0.12), residues: 4326 helix: 3.22 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.61 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 37 TYR 0.020 0.002 TYR D 116 PHE 0.012 0.001 PHE M 94 HIS 0.002 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00388 (36750) covalent geometry : angle 0.53762 (49728) hydrogen bonds : bond 0.05121 ( 3173) hydrogen bonds : angle 3.39343 ( 9519) metal coordination : bond 0.00136 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 570 time to evaluate : 1.470 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: A 44 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 103 THR cc_start: 0.9176 (t) cc_final: 0.8831 (p) REVERT: B 12 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8997 (mm) REVERT: B 163 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7598 (mtp180) REVERT: C 175 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9225 (mp) REVERT: C 199 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8739 (mm-30) REVERT: D 136 GLU cc_start: 0.8327 (mp0) cc_final: 0.7974 (mm-30) REVERT: D 199 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8504 (mm-30) REVERT: F 116 TYR cc_start: 0.9416 (m-10) cc_final: 0.9061 (m-10) REVERT: F 199 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8718 (mm-30) REVERT: G 103 THR cc_start: 0.9138 (t) cc_final: 0.8895 (p) REVERT: H 64 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: J 163 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7682 (mtp180) REVERT: K 103 THR cc_start: 0.9138 (t) cc_final: 0.8774 (p) REVERT: K 149 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8854 (mp) REVERT: K 195 GLU cc_start: 0.8671 (tp30) cc_final: 0.8398 (tp30) REVERT: K 199 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8645 (mm-30) REVERT: L 40 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8569 (mt-10) REVERT: M 64 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8529 (mmm-85) REVERT: O 37 ARG cc_start: 0.9152 (mmm-85) cc_final: 0.8935 (mmm-85) REVERT: O 44 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8711 (tm-30) REVERT: Q 64 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8455 (mtm-85) REVERT: Q 180 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.9035 (mtmm) REVERT: R 71 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8184 (tm-30) REVERT: R 168 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8698 (mm-30) REVERT: R 199 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8567 (mm-30) REVERT: S 144 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: T 103 THR cc_start: 0.9244 (t) cc_final: 0.8982 (p) REVERT: T 139 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8559 (mm) REVERT: T 164 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8764 (ttp80) REVERT: T 195 GLU cc_start: 0.8750 (tp30) cc_final: 0.8257 (tp30) REVERT: T 199 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8609 (mm-30) REVERT: U 37 ARG cc_start: 0.9127 (mmm-85) cc_final: 0.8840 (mmm-85) REVERT: U 195 GLU cc_start: 0.8554 (tp30) cc_final: 0.8071 (tp30) outliers start: 119 outliers final: 84 residues processed: 654 average time/residue: 0.2645 time to fit residues: 264.9222 Evaluate side-chains 637 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 542 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 139 LEU Chi-restraints excluded: chain T residue 148 LEU Chi-restraints excluded: chain T residue 199 GLU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 149 LEU 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 399 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 131 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 86 ASN M 54 GLN ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN R 54 GLN S 6 ASN ** S 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076445 restraints weight = 68829.789| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.11 r_work: 0.2966 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36828 Z= 0.129 Angle : 0.539 9.826 49728 Z= 0.277 Chirality : 0.035 0.257 6048 Planarity : 0.004 0.037 6216 Dihedral : 3.973 53.585 4664 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.75 % Allowed : 23.21 % Favored : 74.03 % 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: 4.10 (0.12), residues: 4326 helix: 3.19 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.67 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 37 TYR 0.017 0.002 TYR B 116 PHE 0.012 0.001 PHE M 94 HIS 0.001 0.000 HIS L 47 Details of bonding type rmsd covalent geometry : bond 0.00291 (36750) covalent geometry : angle 0.53864 (49728) hydrogen bonds : bond 0.04651 ( 3173) hydrogen bonds : angle 3.31385 ( 9519) metal coordination : bond 0.00055 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 595 time to evaluate : 1.547 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: A 44 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8636 (tm-30) REVERT: A 103 THR cc_start: 0.9123 (t) cc_final: 0.8776 (p) REVERT: B 12 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 163 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7594 (mtp180) REVERT: C 175 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9185 (mp) REVERT: C 199 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8801 (mm-30) REVERT: D 116 TYR cc_start: 0.9293 (m-10) cc_final: 0.9093 (m-80) REVERT: D 195 GLU cc_start: 0.8639 (tp30) cc_final: 0.8228 (tp30) REVERT: D 199 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: E 64 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8429 (mmm-85) REVERT: F 64 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8365 (mmm-85) REVERT: F 116 TYR cc_start: 0.9424 (m-10) cc_final: 0.9086 (m-10) REVERT: F 199 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8656 (mm-30) REVERT: G 103 THR cc_start: 0.9090 (t) cc_final: 0.8844 (p) REVERT: G 150 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8724 (tm-30) REVERT: H 150 GLU cc_start: 0.9089 (tp30) cc_final: 0.8859 (tp30) REVERT: J 54 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: K 70 MET cc_start: 0.9035 (tpt) cc_final: 0.8774 (tpt) REVERT: K 92 GLU cc_start: 0.8165 (mp0) cc_final: 0.7913 (mp0) REVERT: K 103 THR cc_start: 0.9119 (t) cc_final: 0.8746 (p) REVERT: K 195 GLU cc_start: 0.8612 (tp30) cc_final: 0.8279 (tp30) REVERT: K 199 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8634 (mm-30) REVERT: L 40 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8426 (mt-10) REVERT: L 64 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8341 (mmm-85) REVERT: M 12 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8942 (mm) REVERT: M 20 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8880 (mmtm) REVERT: N 64 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.8391 (mtm-85) REVERT: O 44 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8687 (tm-30) REVERT: O 137 GLU cc_start: 0.9176 (mp0) cc_final: 0.8708 (mp0) REVERT: Q 180 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8888 (mtmm) REVERT: R 71 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8172 (tm-30) REVERT: R 168 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8733 (mm-30) REVERT: R 199 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: S 144 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: T 103 THR cc_start: 0.9185 (t) cc_final: 0.8926 (p) REVERT: T 144 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8257 (mp0) REVERT: T 195 GLU cc_start: 0.8688 (tp30) cc_final: 0.8107 (tp30) REVERT: T 199 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8497 (mm-30) REVERT: U 37 ARG cc_start: 0.9121 (mmm-85) cc_final: 0.8848 (mmm-85) REVERT: U 195 GLU cc_start: 0.8415 (tp30) cc_final: 0.7887 (tp30) outliers start: 111 outliers final: 82 residues processed: 671 average time/residue: 0.2631 time to fit residues: 270.3676 Evaluate side-chains 653 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 560 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 54 GLN Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 199 GLU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 175 LEU Chi-restraints excluded: chain U residue 187 VAL 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 330 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 359 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 86 ASN ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN R 54 GLN T 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076901 restraints weight = 69271.719| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.04 r_work: 0.2983 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36828 Z= 0.131 Angle : 0.562 11.126 49728 Z= 0.288 Chirality : 0.036 0.278 6048 Planarity : 0.004 0.037 6216 Dihedral : 3.957 54.062 4664 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.53 % Allowed : 23.76 % Favored : 73.71 % 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: 4.12 (0.12), residues: 4326 helix: 3.24 (0.08), residues: 3801 sheet: None (None), residues: 0 loop : -1.73 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 64 TYR 0.019 0.002 TYR S 116 PHE 0.011 0.001 PHE M 94 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00301 (36750) covalent geometry : angle 0.56201 (49728) hydrogen bonds : bond 0.04495 ( 3173) hydrogen bonds : angle 3.31138 ( 9519) metal coordination : bond 0.00070 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 591 time to evaluate : 1.489 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: A 44 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8597 (tm-30) REVERT: B 12 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9046 (mm) REVERT: B 163 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7594 (mtp180) REVERT: C 175 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9191 (mp) REVERT: D 195 GLU cc_start: 0.8610 (tp30) cc_final: 0.8183 (tp30) REVERT: D 199 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8545 (mm-30) REVERT: E 64 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: E 116 TYR cc_start: 0.9166 (m-80) cc_final: 0.8870 (m-80) REVERT: F 20 LYS cc_start: 0.9217 (mmtm) cc_final: 0.9014 (mmtm) REVERT: F 64 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8331 (mmm-85) REVERT: F 116 TYR cc_start: 0.9425 (m-10) cc_final: 0.9092 (m-10) REVERT: F 199 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8665 (mm-30) REVERT: G 64 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8336 (mmm-85) REVERT: G 103 THR cc_start: 0.9094 (t) cc_final: 0.8858 (p) REVERT: G 150 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8701 (tm-30) REVERT: H 12 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9033 (mm) REVERT: H 150 GLU cc_start: 0.9112 (tp30) cc_final: 0.8880 (tp30) REVERT: I 40 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8550 (mt-10) REVERT: J 24 GLU cc_start: 0.9024 (tp30) cc_final: 0.8774 (tp30) REVERT: J 54 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: J 150 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8588 (tm-30) REVERT: K 70 MET cc_start: 0.9009 (tpt) cc_final: 0.8775 (tpt) REVERT: K 103 THR cc_start: 0.9106 (t) cc_final: 0.8731 (p) REVERT: K 199 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8715 (mm-30) REVERT: L 40 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8398 (mt-10) REVERT: L 64 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.8349 (mmm-85) REVERT: M 12 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8995 (mm) REVERT: O 44 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8661 (tm-30) REVERT: O 137 GLU cc_start: 0.9171 (mp0) cc_final: 0.8683 (mp0) REVERT: Q 37 ARG cc_start: 0.9068 (mmm-85) cc_final: 0.8781 (mmm-85) REVERT: Q 150 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8465 (tm-30) REVERT: Q 180 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8781 (mtmm) REVERT: R 71 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8179 (tm-30) REVERT: R 168 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8708 (mm-30) REVERT: R 199 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: S 144 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: T 103 THR cc_start: 0.9180 (t) cc_final: 0.8915 (p) REVERT: T 144 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8225 (mp0) REVERT: T 150 GLU cc_start: 0.9025 (tp30) cc_final: 0.8824 (tt0) REVERT: T 195 GLU cc_start: 0.8654 (tp30) cc_final: 0.8175 (tp30) REVERT: T 199 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: U 37 ARG cc_start: 0.9110 (mmm-85) cc_final: 0.8846 (mmm-85) REVERT: U 195 GLU cc_start: 0.8414 (tp30) cc_final: 0.7894 (tp30) outliers start: 102 outliers final: 85 residues processed: 660 average time/residue: 0.2643 time to fit residues: 266.5635 Evaluate side-chains 653 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 557 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 54 GLN Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 199 GLU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 175 LEU 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 188 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 371 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 294 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 176 ASN G 6 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 86 ASN ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 ASN R 54 GLN T 6 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076342 restraints weight = 69022.995| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.09 r_work: 0.2966 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36828 Z= 0.141 Angle : 0.583 13.867 49728 Z= 0.299 Chirality : 0.036 0.357 6048 Planarity : 0.004 0.042 6216 Dihedral : 3.948 54.146 4664 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.48 % Allowed : 23.93 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.12), residues: 4326 helix: 3.18 (0.08), residues: 3822 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 164 TYR 0.017 0.002 TYR D 116 PHE 0.010 0.001 PHE M 94 HIS 0.001 0.000 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (36750) covalent geometry : angle 0.58287 (49728) hydrogen bonds : bond 0.04612 ( 3173) hydrogen bonds : angle 3.38306 ( 9519) metal coordination : bond 0.00094 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8652 Ramachandran restraints generated. 4326 Oldfield, 0 Emsley, 4326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 566 time to evaluate : 1.618 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: A 44 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 103 THR cc_start: 0.9144 (t) cc_final: 0.8808 (p) REVERT: B 12 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9038 (mm) REVERT: B 163 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7618 (mtm180) REVERT: C 175 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9195 (mp) REVERT: D 136 GLU cc_start: 0.8309 (mp0) cc_final: 0.7960 (mm-30) REVERT: D 195 GLU cc_start: 0.8628 (tp30) cc_final: 0.8225 (tp30) REVERT: D 199 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8561 (mm-30) REVERT: E 116 TYR cc_start: 0.9172 (m-80) cc_final: 0.8874 (m-80) REVERT: F 64 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8352 (mmm-85) REVERT: F 116 TYR cc_start: 0.9437 (m-10) cc_final: 0.9101 (m-10) REVERT: F 199 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8697 (mm-30) REVERT: G 64 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: G 103 THR cc_start: 0.9107 (t) cc_final: 0.8872 (p) REVERT: G 150 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8726 (tm-30) REVERT: H 12 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9013 (mm) REVERT: H 40 GLU cc_start: 0.8834 (tp30) cc_final: 0.8368 (tp30) REVERT: H 150 GLU cc_start: 0.9129 (tp30) cc_final: 0.8904 (tp30) REVERT: I 40 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8707 (tm-30) REVERT: I 144 GLU cc_start: 0.8362 (mp0) cc_final: 0.8142 (mp0) REVERT: J 54 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: K 70 MET cc_start: 0.9029 (tpt) cc_final: 0.8769 (tpt) REVERT: K 92 GLU cc_start: 0.8124 (mp0) cc_final: 0.7891 (mp0) REVERT: K 103 THR cc_start: 0.9116 (t) cc_final: 0.8740 (p) REVERT: L 40 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8413 (mt-10) REVERT: M 12 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8967 (mm) REVERT: N 116 TYR cc_start: 0.9292 (m-80) cc_final: 0.9024 (m-80) REVERT: O 44 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8678 (tm-30) REVERT: O 64 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8407 (mmm-85) REVERT: O 137 GLU cc_start: 0.9177 (mp0) cc_final: 0.8696 (mp0) REVERT: P 64 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8235 (mmm-85) REVERT: Q 37 ARG cc_start: 0.9096 (mmm-85) cc_final: 0.8816 (mmm-85) REVERT: Q 180 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8802 (mtmm) REVERT: R 71 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8177 (tm-30) REVERT: R 168 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8728 (mm-30) REVERT: R 199 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: S 144 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: T 103 THR cc_start: 0.9200 (t) cc_final: 0.8939 (p) REVERT: T 144 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8232 (mp0) REVERT: T 195 GLU cc_start: 0.8670 (tp30) cc_final: 0.8203 (tp30) REVERT: T 199 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8603 (mm-30) REVERT: U 37 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8845 (mmm-85) REVERT: U 195 GLU cc_start: 0.8415 (tp30) cc_final: 0.7905 (tp30) outliers start: 100 outliers final: 82 residues processed: 635 average time/residue: 0.2600 time to fit residues: 252.2815 Evaluate side-chains 645 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 553 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 212 TYR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 212 TYR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 212 TYR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 144 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 54 GLN Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 191 ILE Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 212 TYR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 212 TYR Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 212 TYR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 212 TYR Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 212 TYR Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 133 LEU Chi-restraints excluded: chain Q residue 180 LYS Chi-restraints excluded: chain Q residue 212 TYR Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 199 GLU Chi-restraints excluded: chain R residue 212 TYR Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 212 TYR Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 199 GLU Chi-restraints excluded: chain T residue 212 TYR Chi-restraints excluded: chain U residue 108 THR Chi-restraints excluded: chain U residue 120 THR 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 188 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 361 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 316 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 ASN ** G 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 ASN H 86 ASN P 54 GLN Q 6 ASN R 54 GLN T 6 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075911 restraints weight = 69028.448| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.03 r_work: 0.2963 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36828 Z= 0.143 Angle : 0.588 12.040 49728 Z= 0.301 Chirality : 0.037 0.373 6048 Planarity : 0.004 0.044 6216 Dihedral : 3.950 54.240 4664 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.36 % Allowed : 24.21 % Favored : 73.44 % 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: 4.09 (0.12), residues: 4326 helix: 3.21 (0.08), residues: 3801 sheet: None (None), residues: 0 loop : -1.74 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 64 TYR 0.018 0.002 TYR L 116 PHE 0.011 0.001 PHE M 94 HIS 0.002 0.000 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00339 (36750) covalent geometry : angle 0.58829 (49728) hydrogen bonds : bond 0.04689 ( 3173) hydrogen bonds : angle 3.40996 ( 9519) metal coordination : bond 0.00102 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7725.14 seconds wall clock time: 133 minutes 40.32 seconds (8020.32 seconds total)