Starting phenix.real_space_refine on Sat Feb 7 07:47:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k80_62156/02_2026/9k80_62156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k80_62156/02_2026/9k80_62156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k80_62156/02_2026/9k80_62156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k80_62156/02_2026/9k80_62156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k80_62156/02_2026/9k80_62156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k80_62156/02_2026/9k80_62156.map" } resolution = 2.62 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= 0.014 sd= 0.197 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 26 6.06 5 S 128 5.16 5 C 20240 2.51 5 N 5136 2.21 5 O 5808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31338 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "B" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "C" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "D" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "E" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "F" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "G" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "I" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "J" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "K" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "L" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "M" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "N" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "O" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} Chain: "P" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1957 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 242} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.38, per 1000 atoms: 0.24 Number of scatterers: 31338 At special positions: 0 Unit cell: (118.503, 112.039, 232.697, 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 26 29.99 S 128 16.00 O 5808 8.00 N 5136 7.00 C 20240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS C 21 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 56 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS K 231 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 21 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 56 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 231 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 56 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS E 21 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS M 231 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS B 21 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 231 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" NE2 HIS D 23 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS G 21 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 56 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS O 231 " pdb="ZN ZN E 302 " - pdb=" NE2 HIS E 23 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS D 21 " pdb=" ZN F 302 " pdb="ZN ZN F 302 " - pdb=" NE2 HIS E 231 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS I 21 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 56 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 23 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS F 21 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 56 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 231 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS K 21 " pdb="ZN ZN I 302 " - pdb=" NE2 HIS I 56 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS H 21 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS M 21 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 56 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS J 21 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS L 56 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS O 21 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 56 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS L 21 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 56 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS F 231 " pdb=" ZN P 302 " pdb="ZN ZN P 302 " - pdb=" NE2 HIS N 21 " pdb="ZN ZN P 302 " - pdb=" NE2 HIS P 56 " 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 0 sheets defined 93.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 5 through 30 removed outlier: 4.115A pdb=" N GLU A 10 " --> pdb=" O MET A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 64 removed outlier: 3.663A pdb=" N ARG A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.816A pdb=" N GLU A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 127 through 152 Processing helix chain 'A' and resid 154 through 186 removed outlier: 3.783A pdb=" N VAL A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 212 removed outlier: 3.684A pdb=" N VAL A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 247 Processing helix chain 'B' and resid 5 through 30 removed outlier: 4.106A pdb=" N GLU B 10 " --> pdb=" O MET B 6 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 64 removed outlier: 3.636A pdb=" N ARG B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 91 removed outlier: 3.929A pdb=" N GLU B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 127 through 152 Processing helix chain 'B' and resid 154 through 186 removed outlier: 3.561A pdb=" N ILE B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 212 removed outlier: 3.655A pdb=" N VAL B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 Processing helix chain 'C' and resid 5 through 30 removed outlier: 3.874A pdb=" N GLU C 10 " --> pdb=" O MET C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 64 removed outlier: 3.613A pdb=" N ARG C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 90 removed outlier: 3.911A pdb=" N GLU C 71 " --> pdb=" O PRO C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 127 through 152 Processing helix chain 'C' and resid 154 through 186 removed outlier: 3.540A pdb=" N GLN C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 212 removed outlier: 3.676A pdb=" N VAL C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 247 Processing helix chain 'D' and resid 5 through 30 removed outlier: 3.952A pdb=" N GLU D 10 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 64 removed outlier: 3.581A pdb=" N ARG D 49 " --> pdb=" O GLY D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 91 removed outlier: 4.275A pdb=" N VAL D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 127 through 152 Processing helix chain 'D' and resid 154 through 186 removed outlier: 3.531A pdb=" N ILE D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 212 removed outlier: 3.621A pdb=" N VAL D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 247 Processing helix chain 'E' and resid 7 through 30 removed outlier: 3.543A pdb=" N MET E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 64 removed outlier: 3.650A pdb=" N ARG E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 91 removed outlier: 3.807A pdb=" N GLU E 71 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 91 " --> pdb=" O LEU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 125 Proline residue: E 117 - end of helix Processing helix chain 'E' and resid 127 through 152 Processing helix chain 'E' and resid 154 through 186 removed outlier: 3.796A pdb=" N VAL E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 212 removed outlier: 3.684A pdb=" N VAL E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 247 Processing helix chain 'F' and resid 5 through 30 removed outlier: 4.276A pdb=" N GLU F 10 " --> pdb=" O MET F 6 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 64 removed outlier: 3.622A pdb=" N ARG F 49 " --> pdb=" O GLY F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 90 removed outlier: 4.277A pdb=" N VAL F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 125 Proline residue: F 117 - end of helix Processing helix chain 'F' and resid 127 through 152 Processing helix chain 'F' and resid 154 through 186 removed outlier: 3.768A pdb=" N VAL F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 212 removed outlier: 3.660A pdb=" N VAL F 192 " --> pdb=" O ILE F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 247 Processing helix chain 'G' and resid 5 through 30 removed outlier: 4.020A pdb=" N GLU G 10 " --> pdb=" O MET G 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 64 removed outlier: 3.604A pdb=" N ARG G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 91 removed outlier: 4.296A pdb=" N VAL G 70 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 91 " --> pdb=" O LEU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 Proline residue: G 117 - end of helix Processing helix chain 'G' and resid 127 through 152 Processing helix chain 'G' and resid 154 through 186 removed outlier: 3.504A pdb=" N GLN G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL G 171 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 212 removed outlier: 3.694A pdb=" N VAL G 192 " --> pdb=" O ILE G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 247 Processing helix chain 'H' and resid 5 through 30 removed outlier: 4.032A pdb=" N GLU H 10 " --> pdb=" O MET H 6 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 64 removed outlier: 3.593A pdb=" N ARG H 49 " --> pdb=" O GLY H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 91 removed outlier: 3.883A pdb=" N GLU H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 Proline residue: H 117 - end of helix Processing helix chain 'H' and resid 127 through 152 Processing helix chain 'H' and resid 154 through 186 removed outlier: 3.742A pdb=" N VAL H 171 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 212 removed outlier: 3.647A pdb=" N VAL H 192 " --> pdb=" O ILE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 247 Processing helix chain 'I' and resid 7 through 30 removed outlier: 3.665A pdb=" N MET I 11 " --> pdb=" O ALA I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 64 removed outlier: 3.641A pdb=" N ARG I 49 " --> pdb=" O GLY I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 91 removed outlier: 4.211A pdb=" N VAL I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 125 Proline residue: I 117 - end of helix Processing helix chain 'I' and resid 127 through 152 Processing helix chain 'I' and resid 154 through 186 removed outlier: 3.779A pdb=" N VAL I 171 " --> pdb=" O ALA I 167 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 212 removed outlier: 3.697A pdb=" N VAL I 192 " --> pdb=" O ILE I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 247 Processing helix chain 'J' and resid 7 through 30 removed outlier: 3.591A pdb=" N MET J 11 " --> pdb=" O ALA J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 64 removed outlier: 3.579A pdb=" N ARG J 49 " --> pdb=" O GLY J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 91 removed outlier: 3.871A pdb=" N GLU J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 125 Proline residue: J 117 - end of helix Processing helix chain 'J' and resid 127 through 152 Processing helix chain 'J' and resid 154 through 186 removed outlier: 3.541A pdb=" N ILE J 158 " --> pdb=" O SER J 154 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL J 171 " --> pdb=" O ALA J 167 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 212 removed outlier: 3.649A pdb=" N VAL J 192 " --> pdb=" O ILE J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 247 Processing helix chain 'K' and resid 5 through 30 removed outlier: 3.751A pdb=" N GLU K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU K 10 " --> pdb=" O MET K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 64 removed outlier: 3.595A pdb=" N ARG K 49 " --> pdb=" O GLY K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 91 removed outlier: 4.194A pdb=" N VAL K 70 " --> pdb=" O ILE K 66 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 125 Proline residue: K 117 - end of helix Processing helix chain 'K' and resid 127 through 152 Processing helix chain 'K' and resid 156 through 186 removed outlier: 3.794A pdb=" N VAL K 171 " --> pdb=" O ALA K 167 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 212 removed outlier: 3.686A pdb=" N VAL K 192 " --> pdb=" O ILE K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 247 Processing helix chain 'L' and resid 7 through 30 removed outlier: 3.592A pdb=" N MET L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 64 removed outlier: 3.627A pdb=" N ARG L 49 " --> pdb=" O GLY L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 90 removed outlier: 3.818A pdb=" N GLU L 71 " --> pdb=" O PRO L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 125 removed outlier: 3.697A pdb=" N ARG L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) Proline residue: L 117 - end of helix Processing helix chain 'L' and resid 127 through 152 Processing helix chain 'L' and resid 154 through 186 removed outlier: 3.507A pdb=" N ILE L 158 " --> pdb=" O SER L 154 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL L 171 " --> pdb=" O ALA L 167 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE L 182 " --> pdb=" O ASP L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 212 removed outlier: 3.683A pdb=" N VAL L 192 " --> pdb=" O ILE L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 247 Processing helix chain 'M' and resid 5 through 30 removed outlier: 3.510A pdb=" N GLU M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU M 10 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET M 11 " --> pdb=" O ALA M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 64 removed outlier: 3.589A pdb=" N ARG M 49 " --> pdb=" O GLY M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 90 removed outlier: 3.858A pdb=" N GLU M 71 " --> pdb=" O PRO M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 125 removed outlier: 3.626A pdb=" N ARG M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) Proline residue: M 117 - end of helix Processing helix chain 'M' and resid 127 through 152 Processing helix chain 'M' and resid 154 through 186 removed outlier: 3.745A pdb=" N VAL M 171 " --> pdb=" O ALA M 167 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE M 182 " --> pdb=" O ASP M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 212 removed outlier: 3.721A pdb=" N VAL M 192 " --> pdb=" O ILE M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 247 Processing helix chain 'N' and resid 7 through 30 removed outlier: 3.577A pdb=" N MET N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 64 removed outlier: 3.607A pdb=" N ARG N 49 " --> pdb=" O GLY N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 91 removed outlier: 3.732A pdb=" N GLU N 71 " --> pdb=" O PRO N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 125 Proline residue: N 117 - end of helix Processing helix chain 'N' and resid 127 through 152 Processing helix chain 'N' and resid 154 through 186 removed outlier: 3.756A pdb=" N VAL N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE N 182 " --> pdb=" O ASP N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 212 removed outlier: 3.711A pdb=" N VAL N 192 " --> pdb=" O ILE N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 247 Processing helix chain 'O' and resid 5 through 30 removed outlier: 3.893A pdb=" N GLU O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 64 removed outlier: 3.585A pdb=" N ARG O 49 " --> pdb=" O GLY O 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET O 64 " --> pdb=" O ARG O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 90 removed outlier: 4.248A pdb=" N VAL O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU O 71 " --> pdb=" O PRO O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 125 Proline residue: O 117 - end of helix Processing helix chain 'O' and resid 127 through 152 Processing helix chain 'O' and resid 154 through 186 removed outlier: 3.749A pdb=" N VAL O 171 " --> pdb=" O ALA O 167 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE O 182 " --> pdb=" O ASP O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 212 removed outlier: 3.695A pdb=" N VAL O 192 " --> pdb=" O ILE O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 247 Processing helix chain 'P' and resid 7 through 30 Processing helix chain 'P' and resid 32 through 64 removed outlier: 3.659A pdb=" N ARG P 49 " --> pdb=" O GLY P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 90 removed outlier: 4.251A pdb=" N VAL P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU P 71 " --> pdb=" O PRO P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 125 Proline residue: P 117 - end of helix removed outlier: 3.789A pdb=" N MET P 125 " --> pdb=" O LEU P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 152 Processing helix chain 'P' and resid 154 through 186 removed outlier: 3.509A pdb=" N ILE P 158 " --> pdb=" O SER P 154 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN P 159 " --> pdb=" O ASP P 155 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL P 171 " --> pdb=" O ALA P 167 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE P 182 " --> pdb=" O ASP P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 212 removed outlier: 3.719A pdb=" N VAL P 192 " --> pdb=" O ILE P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 247 3041 hydrogen bonds defined for protein. 9123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5568 1.31 - 1.44: 7077 1.44 - 1.56: 18875 1.56 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 31776 Sorted by residual: bond pdb=" CA HIS H 56 " pdb=" C HIS H 56 " ideal model delta sigma weight residual 1.524 1.468 0.055 1.29e-02 6.01e+03 1.83e+01 bond pdb=" CA HIS J 56 " pdb=" C HIS J 56 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.29e-02 6.01e+03 1.65e+01 bond pdb=" C HIS H 56 " pdb=" O HIS H 56 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.19e-02 7.06e+03 1.57e+01 bond pdb=" CA HIS E 56 " pdb=" C HIS E 56 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" CA HIS L 56 " pdb=" C HIS L 56 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.29e-02 6.01e+03 1.28e+01 ... (remaining 31771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 41785 1.58 - 3.15: 561 3.15 - 4.73: 148 4.73 - 6.30: 12 6.30 - 7.88: 6 Bond angle restraints: 42512 Sorted by residual: angle pdb=" CA GLU N 233 " pdb=" CB GLU N 233 " pdb=" CG GLU N 233 " ideal model delta sigma weight residual 114.10 121.98 -7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA GLU P 233 " pdb=" CB GLU P 233 " pdb=" CG GLU P 233 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" N ASP M 180 " pdb=" CA ASP M 180 " pdb=" C ASP M 180 " ideal model delta sigma weight residual 111.82 115.28 -3.46 1.16e+00 7.43e-01 8.89e+00 angle pdb=" O LEU H 55 " pdb=" C LEU H 55 " pdb=" N HIS H 56 " ideal model delta sigma weight residual 122.22 118.84 3.38 1.17e+00 7.31e-01 8.36e+00 angle pdb=" O LEU G 55 " pdb=" C LEU G 55 " pdb=" N HIS G 56 " ideal model delta sigma weight residual 122.12 119.22 2.90 1.06e+00 8.90e-01 7.46e+00 ... (remaining 42507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 16577 18.16 - 36.32: 2073 36.32 - 54.48: 744 54.48 - 72.64: 195 72.64 - 90.80: 59 Dihedral angle restraints: 19648 sinusoidal: 8192 harmonic: 11456 Sorted by residual: dihedral pdb=" CA ASP O 17 " pdb=" CB ASP O 17 " pdb=" CG ASP O 17 " pdb=" OD1 ASP O 17 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP P 17 " pdb=" CB ASP P 17 " pdb=" CG ASP P 17 " pdb=" OD1 ASP P 17 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP J 17 " pdb=" CB ASP J 17 " pdb=" CG ASP J 17 " pdb=" OD1 ASP J 17 " ideal model delta sinusoidal sigma weight residual -30.00 -88.16 58.16 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 19645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3786 0.035 - 0.071: 700 0.071 - 0.106: 210 0.106 - 0.142: 23 0.142 - 0.177: 1 Chirality restraints: 4720 Sorted by residual: chirality pdb=" CA TYR M 79 " pdb=" N TYR M 79 " pdb=" C TYR M 79 " pdb=" CB TYR M 79 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA ASP O 163 " pdb=" N ASP O 163 " pdb=" C ASP O 163 " pdb=" CB ASP O 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA TYR K 79 " pdb=" N TYR K 79 " pdb=" C TYR K 79 " pdb=" CB TYR K 79 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 4717 not shown) Planarity restraints: 5456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 230 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C LEU E 230 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU E 230 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS E 231 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP O 180 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" CG ASP O 180 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP O 180 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP O 180 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 79 " 0.015 2.00e-02 2.50e+03 1.18e-02 2.81e+00 pdb=" CG TYR B 79 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 79 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 79 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 79 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 79 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 79 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 79 " 0.000 2.00e-02 2.50e+03 ... (remaining 5453 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 251 2.60 - 3.17: 25492 3.17 - 3.75: 51053 3.75 - 4.32: 65375 4.32 - 4.90: 114689 Nonbonded interactions: 256860 Sorted by model distance: nonbonded pdb=" OD1 ASP G 52 " pdb="ZN ZN G 301 " model vdw 2.019 2.230 nonbonded pdb=" OD1 ASP M 52 " pdb="ZN ZN M 301 " model vdw 2.040 2.230 nonbonded pdb=" OD1 ASP I 52 " pdb="ZN ZN I 302 " model vdw 2.050 2.230 nonbonded pdb=" OD1 ASP E 52 " pdb="ZN ZN E 301 " model vdw 2.054 2.230 nonbonded pdb=" OD1 ASP A 52 " pdb="ZN ZN A 302 " model vdw 2.056 2.230 ... (remaining 256855 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 1 through 249) selection = (chain 'B' and resid 1 through 249) selection = (chain 'C' and resid 1 through 249) selection = (chain 'D' and resid 1 through 249) selection = (chain 'E' and resid 1 through 249) selection = (chain 'F' and resid 1 through 249) selection = (chain 'G' and resid 1 through 249) selection = (chain 'H' and resid 1 through 249) selection = (chain 'I' and resid 1 through 249) selection = (chain 'J' and resid 1 through 249) selection = (chain 'K' and resid 1 through 249) selection = (chain 'L' and resid 1 through 249) selection = (chain 'M' and resid 1 through 249) selection = (chain 'N' and resid 1 through 249) selection = chain 'O' selection = (chain 'P' and resid 1 through 249) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.013 0.671 31814 Z= 0.463 Angle : 0.478 7.876 42512 Z= 0.266 Chirality : 0.032 0.177 4720 Planarity : 0.003 0.038 5456 Dihedral : 19.139 90.805 12256 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.98 % Allowed : 27.20 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.62 (0.12), residues: 3952 helix: 3.25 (0.08), residues: 3664 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 114 TYR 0.029 0.002 TYR B 79 PHE 0.019 0.002 PHE B 77 HIS 0.005 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00312 (31776) covalent geometry : angle 0.47835 (42512) hydrogen bonds : bond 0.11207 ( 3041) hydrogen bonds : angle 3.63140 ( 9123) metal coordination : bond 0.37134 ( 38) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 642 time to evaluate : 0.971 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: A 38 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7835 (ttmm) REVERT: A 41 GLU cc_start: 0.7641 (pt0) cc_final: 0.7179 (pp20) REVERT: A 187 ASP cc_start: 0.7880 (t0) cc_final: 0.7463 (t0) REVERT: A 240 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7918 (ttmm) REVERT: B 6 MET cc_start: 0.8104 (ttm) cc_final: 0.7900 (tpt) REVERT: B 96 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 187 ASP cc_start: 0.8029 (t0) cc_final: 0.7692 (t70) REVERT: C 170 ASP cc_start: 0.8773 (t70) cc_final: 0.8351 (t70) REVERT: D 109 ASP cc_start: 0.8083 (t70) cc_final: 0.7744 (t0) REVERT: D 120 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7426 (mp0) REVERT: E 71 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7666 (mm-30) REVERT: E 113 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7702 (mm-30) REVERT: E 120 GLU cc_start: 0.8321 (tt0) cc_final: 0.8097 (tm-30) REVERT: E 170 ASP cc_start: 0.8613 (t70) cc_final: 0.8185 (t70) REVERT: F 24 GLN cc_start: 0.8441 (mt0) cc_final: 0.8148 (mt0) REVERT: F 170 ASP cc_start: 0.8503 (t70) cc_final: 0.8054 (t70) REVERT: F 174 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7389 (mm-30) REVERT: F 180 ASP cc_start: 0.8416 (t70) cc_final: 0.8009 (t0) REVERT: F 187 ASP cc_start: 0.7784 (t0) cc_final: 0.7300 (t0) REVERT: G 17 ASP cc_start: 0.7740 (t70) cc_final: 0.7438 (t70) REVERT: G 24 GLN cc_start: 0.7728 (mt0) cc_final: 0.7504 (mt0) REVERT: G 64 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6317 (mpp) REVERT: G 174 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7698 (mm-30) REVERT: H 187 ASP cc_start: 0.7773 (t0) cc_final: 0.7413 (t0) REVERT: I 6 MET cc_start: 0.7236 (tmt) cc_final: 0.6839 (pp-130) REVERT: I 10 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7049 (mp0) REVERT: I 11 MET cc_start: 0.8433 (mtt) cc_final: 0.8161 (mtt) REVERT: I 53 TYR cc_start: 0.8012 (t80) cc_final: 0.7693 (t80) REVERT: I 71 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7276 (mm-30) REVERT: I 109 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: I 120 GLU cc_start: 0.8018 (tt0) cc_final: 0.7718 (tm-30) REVERT: J 6 MET cc_start: 0.7988 (tmm) cc_final: 0.7577 (tpt) REVERT: J 86 GLU cc_start: 0.7643 (mp0) cc_final: 0.7386 (mp0) REVERT: J 132 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7417 (mt-10) REVERT: J 174 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7021 (mm-30) REVERT: J 187 ASP cc_start: 0.7664 (t70) cc_final: 0.7411 (t70) REVERT: J 240 LYS cc_start: 0.7245 (ttmt) cc_final: 0.6867 (ttmm) REVERT: K 6 MET cc_start: 0.8097 (tpt) cc_final: 0.7538 (tpt) REVERT: K 10 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6562 (mm-30) REVERT: K 17 ASP cc_start: 0.7218 (t70) cc_final: 0.6903 (t70) REVERT: K 62 LYS cc_start: 0.7476 (tppt) cc_final: 0.7182 (ttpt) REVERT: K 72 MET cc_start: 0.7496 (mtm) cc_final: 0.7274 (mtm) REVERT: K 120 GLU cc_start: 0.7904 (tt0) cc_final: 0.7585 (mp0) REVERT: K 197 GLU cc_start: 0.7153 (tt0) cc_final: 0.6951 (tt0) REVERT: L 49 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7665 (ttp80) REVERT: L 62 LYS cc_start: 0.7678 (tptm) cc_final: 0.7142 (ttpt) REVERT: L 94 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7213 (tm-30) REVERT: L 120 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6969 (mm-30) REVERT: L 180 ASP cc_start: 0.7554 (t70) cc_final: 0.7352 (t0) REVERT: L 204 LYS cc_start: 0.7784 (tptp) cc_final: 0.7289 (mtmt) REVERT: M 6 MET cc_start: 0.7968 (tpt) cc_final: 0.7086 (pp-130) REVERT: M 10 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6225 (tp30) REVERT: M 38 LYS cc_start: 0.6585 (ptpt) cc_final: 0.6095 (pttp) REVERT: M 48 MET cc_start: 0.7676 (mmm) cc_final: 0.7470 (mmp) REVERT: M 71 GLU cc_start: 0.7004 (mp0) cc_final: 0.6582 (mm-30) REVERT: M 109 ASP cc_start: 0.7289 (t0) cc_final: 0.7017 (t0) REVERT: M 178 ASP cc_start: 0.7984 (t0) cc_final: 0.7767 (t0) REVERT: M 180 ASP cc_start: 0.8288 (t0) cc_final: 0.7891 (t0) REVERT: N 41 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: N 109 ASP cc_start: 0.7549 (t0) cc_final: 0.6915 (m-30) REVERT: N 170 ASP cc_start: 0.8257 (t0) cc_final: 0.7916 (t70) REVERT: N 187 ASP cc_start: 0.7676 (t0) cc_final: 0.7162 (t70) REVERT: N 204 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6599 (mtmt) REVERT: N 243 PHE cc_start: 0.6480 (m-10) cc_final: 0.6188 (t80) REVERT: O 10 GLU cc_start: 0.6735 (mt-10) cc_final: 0.5975 (tp30) REVERT: O 28 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6751 (mt-10) REVERT: O 34 GLU cc_start: 0.6567 (mp0) cc_final: 0.6188 (pm20) REVERT: O 62 LYS cc_start: 0.6928 (mmmm) cc_final: 0.6667 (tppt) REVERT: O 109 ASP cc_start: 0.6896 (t0) cc_final: 0.6416 (t0) REVERT: O 110 TYR cc_start: 0.7113 (t80) cc_final: 0.6827 (t80) REVERT: O 113 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6957 (mm-30) REVERT: O 114 ARG cc_start: 0.7392 (mpt180) cc_final: 0.7176 (mpt180) REVERT: O 147 GLU cc_start: 0.7007 (tt0) cc_final: 0.6700 (tt0) REVERT: O 170 ASP cc_start: 0.8038 (t70) cc_final: 0.7534 (t70) REVERT: O 174 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6933 (mm-30) REVERT: P 16 ARG cc_start: 0.7784 (mtt-85) cc_final: 0.6946 (mtt-85) REVERT: P 62 LYS cc_start: 0.7237 (tptt) cc_final: 0.6940 (tppt) REVERT: P 95 GLU cc_start: 0.7661 (tp30) cc_final: 0.7411 (tp30) REVERT: P 98 ARG cc_start: 0.7311 (mtm-85) cc_final: 0.6749 (mtm-85) REVERT: P 109 ASP cc_start: 0.7545 (t0) cc_final: 0.6801 (m-30) REVERT: P 113 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6754 (mm-30) REVERT: P 204 LYS cc_start: 0.6989 (tppp) cc_final: 0.6316 (mtmm) REVERT: P 208 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6398 (mm-30) REVERT: P 242 TYR cc_start: 0.6995 (t80) cc_final: 0.6631 (t80) REVERT: P 246 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.6374 (ttp-170) outliers start: 62 outliers final: 35 residues processed: 693 average time/residue: 0.7881 time to fit residues: 631.2696 Evaluate side-chains 585 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 547 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 139 LYS Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 41 GLU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 139 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN E 24 GLN H 24 GLN I 24 GLN M 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102411 restraints weight = 32968.052| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.81 r_work: 0.3137 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31814 Z= 0.138 Angle : 0.444 7.686 42512 Z= 0.236 Chirality : 0.031 0.130 4720 Planarity : 0.003 0.028 5456 Dihedral : 5.629 79.885 4371 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.38 % Allowed : 23.47 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.89 (0.12), residues: 3952 helix: 3.38 (0.08), residues: 3696 sheet: None (None), residues: 0 loop : -0.12 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 124 TYR 0.027 0.002 TYR B 79 PHE 0.018 0.002 PHE D 77 HIS 0.005 0.001 HIS H 21 Details of bonding type rmsd covalent geometry : bond 0.00288 (31776) covalent geometry : angle 0.44377 (42512) hydrogen bonds : bond 0.05625 ( 3041) hydrogen bonds : angle 3.07614 ( 9123) metal coordination : bond 0.00662 ( 38) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 583 time to evaluate : 1.337 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: A 6 MET cc_start: 0.7716 (tpt) cc_final: 0.7395 (mmm) REVERT: A 38 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7941 (ttmm) REVERT: A 41 GLU cc_start: 0.7918 (pt0) cc_final: 0.7451 (pp20) REVERT: A 187 ASP cc_start: 0.8072 (t0) cc_final: 0.7621 (t0) REVERT: B 6 MET cc_start: 0.8281 (ttm) cc_final: 0.7835 (tpt) REVERT: B 86 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7805 (mm-30) REVERT: B 96 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7733 (mt-10) REVERT: B 187 ASP cc_start: 0.8250 (t0) cc_final: 0.7886 (t70) REVERT: C 86 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: C 170 ASP cc_start: 0.8782 (t70) cc_final: 0.8317 (t70) REVERT: D 86 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: D 109 ASP cc_start: 0.8126 (t70) cc_final: 0.7809 (t0) REVERT: D 120 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7487 (mp0) REVERT: D 154 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8131 (p) REVERT: D 245 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6366 (mtt90) REVERT: E 6 MET cc_start: 0.7584 (ppp) cc_final: 0.7226 (tpt) REVERT: E 71 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7790 (mm-30) REVERT: E 86 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: E 120 GLU cc_start: 0.8466 (tt0) cc_final: 0.8241 (tm-30) REVERT: E 170 ASP cc_start: 0.8773 (t70) cc_final: 0.8449 (t70) REVERT: F 24 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: F 86 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: F 139 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7422 (ttpt) REVERT: F 170 ASP cc_start: 0.8648 (t70) cc_final: 0.8217 (t70) REVERT: F 174 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7552 (mm-30) REVERT: F 180 ASP cc_start: 0.8602 (t0) cc_final: 0.8242 (t0) REVERT: F 187 ASP cc_start: 0.8084 (t0) cc_final: 0.7621 (t0) REVERT: G 17 ASP cc_start: 0.8335 (t70) cc_final: 0.8078 (t70) REVERT: G 24 GLN cc_start: 0.8191 (mt0) cc_final: 0.7915 (mt0) REVERT: G 64 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6639 (mtt) REVERT: G 240 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8105 (ttmm) REVERT: H 53 TYR cc_start: 0.8759 (t80) cc_final: 0.8272 (t80) REVERT: H 109 ASP cc_start: 0.8220 (t0) cc_final: 0.7651 (m-30) REVERT: H 139 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7789 (ttmm) REVERT: H 170 ASP cc_start: 0.8825 (t70) cc_final: 0.8455 (t70) REVERT: H 187 ASP cc_start: 0.8089 (t0) cc_final: 0.7708 (t0) REVERT: H 245 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7485 (mpt90) REVERT: I 11 MET cc_start: 0.9003 (mtt) cc_final: 0.8725 (mtt) REVERT: I 41 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: I 71 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7829 (mm-30) REVERT: I 110 TYR cc_start: 0.8579 (t80) cc_final: 0.8355 (t80) REVERT: I 120 GLU cc_start: 0.8422 (tt0) cc_final: 0.8126 (tm-30) REVERT: J 6 MET cc_start: 0.8489 (tmm) cc_final: 0.7811 (tmt) REVERT: J 132 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7830 (mt-10) REVERT: J 174 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7659 (mm-30) REVERT: J 187 ASP cc_start: 0.8034 (t70) cc_final: 0.7740 (t70) REVERT: J 240 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8012 (ttmm) REVERT: K 10 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7018 (tp30) REVERT: K 17 ASP cc_start: 0.8380 (t70) cc_final: 0.8138 (t70) REVERT: K 62 LYS cc_start: 0.8022 (tppt) cc_final: 0.7698 (tppt) REVERT: K 142 MET cc_start: 0.8920 (mmp) cc_final: 0.8513 (mmp) REVERT: K 170 ASP cc_start: 0.8563 (t70) cc_final: 0.8343 (t70) REVERT: K 180 ASP cc_start: 0.8277 (t0) cc_final: 0.7933 (t0) REVERT: L 6 MET cc_start: 0.8256 (tpt) cc_final: 0.7569 (ppp) REVERT: L 49 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7800 (mtp180) REVERT: L 62 LYS cc_start: 0.7886 (tptm) cc_final: 0.7279 (ttpt) REVERT: L 86 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7664 (mp0) REVERT: L 94 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7025 (tm-30) REVERT: L 113 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7731 (mm-30) REVERT: L 120 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7441 (mm-30) REVERT: L 180 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8172 (t0) REVERT: L 204 LYS cc_start: 0.8354 (tptp) cc_final: 0.7850 (mtmt) REVERT: M 6 MET cc_start: 0.8353 (tpt) cc_final: 0.6979 (pp-130) REVERT: M 10 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7660 (mp0) REVERT: M 27 ASP cc_start: 0.7577 (m-30) cc_final: 0.7368 (m-30) REVERT: M 38 LYS cc_start: 0.8222 (ptpt) cc_final: 0.7625 (pttp) REVERT: M 48 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8847 (mmp) REVERT: M 71 GLU cc_start: 0.8028 (mp0) cc_final: 0.7662 (mm-30) REVERT: M 109 ASP cc_start: 0.8132 (t0) cc_final: 0.7914 (t0) REVERT: M 170 ASP cc_start: 0.8555 (t70) cc_final: 0.8203 (t70) REVERT: M 220 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (ttpt) REVERT: M 240 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (ttmm) REVERT: N 6 MET cc_start: 0.8457 (tmt) cc_final: 0.7863 (ppp) REVERT: N 38 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7968 (ttmm) REVERT: N 94 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7278 (tp30) REVERT: N 96 GLU cc_start: 0.7717 (mp0) cc_final: 0.7469 (mp0) REVERT: N 109 ASP cc_start: 0.7946 (t0) cc_final: 0.7267 (m-30) REVERT: N 156 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7652 (mp0) REVERT: N 187 ASP cc_start: 0.8331 (t0) cc_final: 0.7931 (t70) REVERT: N 204 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7711 (mtmt) REVERT: O 10 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7579 (tp30) REVERT: O 28 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7564 (mt-10) REVERT: O 38 LYS cc_start: 0.8172 (pttm) cc_final: 0.7868 (pttp) REVERT: O 62 LYS cc_start: 0.7802 (mmmm) cc_final: 0.7527 (tppt) REVERT: O 93 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.7723 (p) REVERT: O 109 ASP cc_start: 0.8064 (t0) cc_final: 0.7592 (t0) REVERT: O 110 TYR cc_start: 0.8287 (t80) cc_final: 0.8082 (t80) REVERT: O 113 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7910 (mm-30) REVERT: O 147 GLU cc_start: 0.7842 (tt0) cc_final: 0.7513 (tt0) REVERT: O 157 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: O 170 ASP cc_start: 0.8723 (t70) cc_final: 0.8278 (t70) REVERT: O 174 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7741 (mm-30) REVERT: P 10 GLU cc_start: 0.7809 (mp0) cc_final: 0.7466 (mp0) REVERT: P 62 LYS cc_start: 0.7796 (tptt) cc_final: 0.7489 (tppt) REVERT: P 109 ASP cc_start: 0.8177 (t0) cc_final: 0.7505 (m-30) REVERT: P 113 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7525 (mm-30) REVERT: P 204 LYS cc_start: 0.7955 (tppp) cc_final: 0.7486 (mtmm) REVERT: P 246 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7222 (ttp-170) outliers start: 106 outliers final: 23 residues processed: 656 average time/residue: 0.7257 time to fit residues: 553.3888 Evaluate side-chains 577 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 532 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain H residue 139 LYS Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 180 ASP Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain M residue 240 LYS Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 157 GLU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 116 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 55 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 307 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN D 131 GLN I 24 GLN M 24 GLN N 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098772 restraints weight = 33272.242| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.80 r_work: 0.3092 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31814 Z= 0.179 Angle : 0.487 9.204 42512 Z= 0.257 Chirality : 0.033 0.144 4720 Planarity : 0.003 0.030 5456 Dihedral : 4.335 57.385 4304 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.64 % Allowed : 22.58 % Favored : 73.79 % 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: 4.81 (0.12), residues: 3952 helix: 3.35 (0.08), residues: 3696 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 49 TYR 0.034 0.002 TYR B 79 PHE 0.019 0.002 PHE F 77 HIS 0.005 0.001 HIS P 21 Details of bonding type rmsd covalent geometry : bond 0.00416 (31776) covalent geometry : angle 0.48681 (42512) hydrogen bonds : bond 0.06480 ( 3041) hydrogen bonds : angle 3.12634 ( 9123) metal coordination : bond 0.00316 ( 38) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 565 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.7525 (tpt) cc_final: 0.6980 (mmm) REVERT: A 10 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7451 (mp0) REVERT: A 38 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7984 (ttmm) REVERT: A 41 GLU cc_start: 0.7985 (pt0) cc_final: 0.7493 (pp20) REVERT: A 126 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8024 (mptp) REVERT: A 187 ASP cc_start: 0.8106 (t0) cc_final: 0.7663 (t0) REVERT: A 247 LEU cc_start: 0.8026 (mt) cc_final: 0.7779 (mt) REVERT: B 86 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 96 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 24 GLN cc_start: 0.8258 (mt0) cc_final: 0.8054 (mt0) REVERT: C 86 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: C 170 ASP cc_start: 0.8755 (t70) cc_final: 0.8321 (t70) REVERT: D 86 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: D 109 ASP cc_start: 0.8143 (t70) cc_final: 0.7798 (t0) REVERT: D 120 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7524 (mp0) REVERT: D 154 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8027 (p) REVERT: E 71 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7752 (mm-30) REVERT: E 86 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: E 170 ASP cc_start: 0.8784 (t70) cc_final: 0.8425 (t70) REVERT: E 178 ASP cc_start: 0.8339 (t0) cc_final: 0.8133 (t70) REVERT: F 24 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: F 86 GLU cc_start: 0.7510 (mp0) cc_final: 0.7267 (mp0) REVERT: F 170 ASP cc_start: 0.8698 (t70) cc_final: 0.8459 (t70) REVERT: F 180 ASP cc_start: 0.8648 (t70) cc_final: 0.8225 (t0) REVERT: F 187 ASP cc_start: 0.8160 (t0) cc_final: 0.7686 (t0) REVERT: G 17 ASP cc_start: 0.8392 (t70) cc_final: 0.8129 (t70) REVERT: G 64 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6793 (mtt) REVERT: G 96 GLU cc_start: 0.7783 (mp0) cc_final: 0.7570 (mp0) REVERT: G 187 ASP cc_start: 0.8256 (t0) cc_final: 0.7908 (t0) REVERT: H 53 TYR cc_start: 0.8759 (t80) cc_final: 0.8283 (t80) REVERT: H 109 ASP cc_start: 0.8251 (t0) cc_final: 0.7619 (m-30) REVERT: H 170 ASP cc_start: 0.8801 (t70) cc_final: 0.8450 (t70) REVERT: H 187 ASP cc_start: 0.8320 (t0) cc_final: 0.7931 (t0) REVERT: H 245 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7572 (mpt90) REVERT: H 246 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8008 (ttt-90) REVERT: I 71 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7835 (mm-30) REVERT: I 110 TYR cc_start: 0.8753 (t80) cc_final: 0.8421 (t80) REVERT: I 187 ASP cc_start: 0.8189 (t70) cc_final: 0.7841 (t70) REVERT: J 6 MET cc_start: 0.8535 (tmm) cc_final: 0.7572 (tmt) REVERT: J 10 GLU cc_start: 0.7917 (mp0) cc_final: 0.7383 (mp0) REVERT: J 156 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7447 (mp0) REVERT: J 187 ASP cc_start: 0.8092 (t70) cc_final: 0.7753 (t70) REVERT: J 240 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8060 (ttmm) REVERT: K 10 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7663 (mm-30) REVERT: K 17 ASP cc_start: 0.8537 (t70) cc_final: 0.8328 (t70) REVERT: K 62 LYS cc_start: 0.8072 (tppt) cc_final: 0.7755 (tppt) REVERT: K 170 ASP cc_start: 0.8549 (t70) cc_final: 0.8268 (t70) REVERT: K 180 ASP cc_start: 0.8400 (t0) cc_final: 0.8036 (t0) REVERT: K 197 GLU cc_start: 0.7866 (tt0) cc_final: 0.7620 (tm-30) REVERT: L 6 MET cc_start: 0.8340 (tpt) cc_final: 0.7805 (ppp) REVERT: L 10 GLU cc_start: 0.7882 (mp0) cc_final: 0.7009 (tp30) REVERT: L 48 MET cc_start: 0.9030 (mmm) cc_final: 0.8775 (mmp) REVERT: L 49 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7841 (mtp180) REVERT: L 62 LYS cc_start: 0.8095 (tptm) cc_final: 0.7593 (ttpt) REVERT: L 86 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7724 (mp0) REVERT: L 109 ASP cc_start: 0.8169 (t0) cc_final: 0.7517 (m-30) REVERT: L 113 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7888 (mm-30) REVERT: L 114 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.6732 (mpp-170) REVERT: L 120 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7541 (mm-30) REVERT: L 180 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (t0) REVERT: L 204 LYS cc_start: 0.8434 (tptp) cc_final: 0.7883 (mtmt) REVERT: M 6 MET cc_start: 0.8442 (tpt) cc_final: 0.7193 (pp-130) REVERT: M 27 ASP cc_start: 0.7969 (m-30) cc_final: 0.7695 (m-30) REVERT: M 38 LYS cc_start: 0.8249 (ptpt) cc_final: 0.7622 (pttp) REVERT: M 48 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8818 (mmp) REVERT: M 71 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: M 94 GLU cc_start: 0.8185 (tt0) cc_final: 0.7322 (tm-30) REVERT: M 170 ASP cc_start: 0.8501 (t70) cc_final: 0.8150 (t70) REVERT: M 187 ASP cc_start: 0.8189 (t70) cc_final: 0.7947 (t70) REVERT: M 220 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7765 (ttpt) REVERT: M 240 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: N 6 MET cc_start: 0.8407 (tmt) cc_final: 0.7662 (ppp) REVERT: N 10 GLU cc_start: 0.8090 (mp0) cc_final: 0.7716 (mp0) REVERT: N 86 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7705 (mm-30) REVERT: N 94 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: N 96 GLU cc_start: 0.7811 (mp0) cc_final: 0.7609 (mp0) REVERT: N 156 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7689 (mp0) REVERT: N 187 ASP cc_start: 0.8396 (t0) cc_final: 0.8007 (t70) REVERT: N 204 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7752 (mtmt) REVERT: O 10 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7699 (mp0) REVERT: O 27 ASP cc_start: 0.8243 (m-30) cc_final: 0.7915 (m-30) REVERT: O 38 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7951 (pttp) REVERT: O 62 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7625 (tppt) REVERT: O 86 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: O 93 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8223 (p) REVERT: O 109 ASP cc_start: 0.8037 (t0) cc_final: 0.7629 (t0) REVERT: O 113 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7868 (mm-30) REVERT: O 147 GLU cc_start: 0.7987 (tt0) cc_final: 0.7676 (tt0) REVERT: O 170 ASP cc_start: 0.8754 (t70) cc_final: 0.8474 (t70) REVERT: O 180 ASP cc_start: 0.8493 (t70) cc_final: 0.8107 (t0) REVERT: P 10 GLU cc_start: 0.7989 (mp0) cc_final: 0.7480 (mp0) REVERT: P 98 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7260 (mtm-85) REVERT: P 109 ASP cc_start: 0.8321 (t0) cc_final: 0.7584 (m-30) REVERT: P 113 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7766 (mm-30) REVERT: P 156 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7410 (mp0) REVERT: P 204 LYS cc_start: 0.8144 (tppp) cc_final: 0.7828 (mtmm) REVERT: P 246 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7366 (ttp-170) outliers start: 114 outliers final: 35 residues processed: 648 average time/residue: 0.7530 time to fit residues: 568.4555 Evaluate side-chains 596 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 541 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 246 ARG Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LYS Chi-restraints excluded: chain L residue 114 ARG Chi-restraints excluded: chain L residue 180 ASP Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain M residue 240 LYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 93 SER Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 98 ARG Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 128 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 251 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 382 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 320 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN B 131 GLN D 131 GLN E 131 GLN G 24 GLN I 24 GLN M 24 GLN N 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102960 restraints weight = 32811.788| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.81 r_work: 0.3145 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31814 Z= 0.122 Angle : 0.425 8.402 42512 Z= 0.225 Chirality : 0.031 0.181 4720 Planarity : 0.003 0.027 5456 Dihedral : 3.972 59.458 4294 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.74 % Allowed : 23.47 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.09 (0.12), residues: 3952 helix: 3.53 (0.08), residues: 3696 sheet: None (None), residues: 0 loop : -0.35 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 114 TYR 0.026 0.002 TYR B 79 PHE 0.018 0.002 PHE B 77 HIS 0.004 0.001 HIS H 21 Details of bonding type rmsd covalent geometry : bond 0.00237 (31776) covalent geometry : angle 0.42463 (42512) hydrogen bonds : bond 0.05157 ( 3041) hydrogen bonds : angle 2.97476 ( 9123) metal coordination : bond 0.00242 ( 38) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 565 time to evaluate : 1.239 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: A 38 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7890 (ttmm) REVERT: A 41 GLU cc_start: 0.7847 (pt0) cc_final: 0.7348 (pp20) REVERT: A 113 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7658 (mm-30) REVERT: A 187 ASP cc_start: 0.7999 (t0) cc_final: 0.7552 (t0) REVERT: B 86 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 187 ASP cc_start: 0.8212 (t0) cc_final: 0.7848 (t70) REVERT: C 86 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: C 113 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 170 ASP cc_start: 0.8752 (t70) cc_final: 0.8284 (t70) REVERT: D 86 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 109 ASP cc_start: 0.8068 (t70) cc_final: 0.7762 (t0) REVERT: D 120 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7408 (mp0) REVERT: D 154 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7988 (p) REVERT: D 245 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6355 (mtt90) REVERT: E 53 TYR cc_start: 0.8704 (t80) cc_final: 0.8501 (t80) REVERT: E 71 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7620 (mm-30) REVERT: E 86 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: E 170 ASP cc_start: 0.8755 (t70) cc_final: 0.8397 (t70) REVERT: E 178 ASP cc_start: 0.8280 (t0) cc_final: 0.8048 (t70) REVERT: E 240 LYS cc_start: 0.8234 (ttmm) cc_final: 0.7834 (ttpt) REVERT: F 24 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: F 86 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: F 170 ASP cc_start: 0.8656 (t70) cc_final: 0.8208 (t70) REVERT: F 174 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7547 (mm-30) REVERT: F 180 ASP cc_start: 0.8527 (t70) cc_final: 0.8152 (t0) REVERT: F 187 ASP cc_start: 0.8033 (t0) cc_final: 0.7493 (t0) REVERT: G 17 ASP cc_start: 0.8318 (t70) cc_final: 0.8046 (t70) REVERT: G 24 GLN cc_start: 0.8250 (mt0) cc_final: 0.8010 (mt0) REVERT: G 64 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6535 (mtt) REVERT: G 96 GLU cc_start: 0.7812 (mp0) cc_final: 0.7559 (mp0) REVERT: H 109 ASP cc_start: 0.8190 (t0) cc_final: 0.7853 (t0) REVERT: H 113 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7550 (mm-30) REVERT: H 170 ASP cc_start: 0.8762 (t70) cc_final: 0.8384 (t70) REVERT: H 187 ASP cc_start: 0.8164 (t0) cc_final: 0.7786 (t0) REVERT: H 245 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7332 (mpt90) REVERT: I 41 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: I 71 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7686 (mm-30) REVERT: I 109 ASP cc_start: 0.7874 (t0) cc_final: 0.7351 (m-30) REVERT: I 110 TYR cc_start: 0.8495 (t80) cc_final: 0.8180 (t80) REVERT: I 187 ASP cc_start: 0.8220 (t70) cc_final: 0.7867 (t70) REVERT: J 6 MET cc_start: 0.8540 (tmm) cc_final: 0.7926 (tmt) REVERT: J 86 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: J 106 SER cc_start: 0.8387 (m) cc_final: 0.8123 (m) REVERT: J 156 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7382 (mp0) REVERT: J 174 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: J 187 ASP cc_start: 0.8004 (t70) cc_final: 0.7662 (t70) REVERT: J 240 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7937 (ttmm) REVERT: K 10 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7601 (mm-30) REVERT: K 17 ASP cc_start: 0.8443 (t70) cc_final: 0.8223 (t70) REVERT: K 62 LYS cc_start: 0.7986 (tppt) cc_final: 0.7637 (tppt) REVERT: K 170 ASP cc_start: 0.8506 (t70) cc_final: 0.8256 (t70) REVERT: K 180 ASP cc_start: 0.8381 (t0) cc_final: 0.7929 (t0) REVERT: K 197 GLU cc_start: 0.7658 (tt0) cc_final: 0.7403 (tt0) REVERT: K 240 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7680 (ttmm) REVERT: L 6 MET cc_start: 0.8493 (tpt) cc_final: 0.7822 (ppp) REVERT: L 10 GLU cc_start: 0.7733 (mp0) cc_final: 0.6802 (tp30) REVERT: L 49 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7655 (mtp180) REVERT: L 62 LYS cc_start: 0.7811 (tptm) cc_final: 0.7306 (ttpt) REVERT: L 86 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7572 (mp0) REVERT: L 113 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7616 (mm-30) REVERT: L 120 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7442 (mm-30) REVERT: L 180 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8119 (t0) REVERT: L 187 ASP cc_start: 0.8272 (t0) cc_final: 0.7832 (t0) REVERT: L 208 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7359 (mm-30) REVERT: M 6 MET cc_start: 0.8319 (tpt) cc_final: 0.7585 (pp-130) REVERT: M 10 GLU cc_start: 0.7520 (mp0) cc_final: 0.6735 (tp30) REVERT: M 27 ASP cc_start: 0.7871 (m-30) cc_final: 0.7617 (m-30) REVERT: M 48 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8852 (mmp) REVERT: M 71 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: M 96 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7488 (mt-10) REVERT: M 170 ASP cc_start: 0.8515 (t70) cc_final: 0.8168 (t70) REVERT: M 187 ASP cc_start: 0.8122 (t70) cc_final: 0.7840 (t70) REVERT: M 220 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7583 (ttpt) REVERT: N 6 MET cc_start: 0.8428 (tmt) cc_final: 0.7726 (ppp) REVERT: N 96 GLU cc_start: 0.7776 (mp0) cc_final: 0.7575 (mp0) REVERT: N 156 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7542 (mp0) REVERT: N 187 ASP cc_start: 0.8242 (t0) cc_final: 0.7891 (t70) REVERT: N 204 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7646 (mtmt) REVERT: O 10 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7538 (mp0) REVERT: O 27 ASP cc_start: 0.8021 (m-30) cc_final: 0.7697 (m-30) REVERT: O 62 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7494 (tppt) REVERT: O 86 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: O 109 ASP cc_start: 0.7978 (t0) cc_final: 0.7594 (t0) REVERT: O 113 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7798 (mm-30) REVERT: O 147 GLU cc_start: 0.7908 (tt0) cc_final: 0.7593 (tt0) REVERT: O 170 ASP cc_start: 0.8725 (t70) cc_final: 0.8462 (t70) REVERT: O 180 ASP cc_start: 0.8371 (t70) cc_final: 0.7985 (t0) REVERT: P 10 GLU cc_start: 0.7786 (mp0) cc_final: 0.7250 (mp0) REVERT: P 113 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7556 (mm-30) REVERT: P 156 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7276 (mp0) REVERT: P 187 ASP cc_start: 0.8047 (t0) cc_final: 0.7616 (t0) REVERT: P 204 LYS cc_start: 0.8053 (tppp) cc_final: 0.7649 (mtmm) REVERT: P 246 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7264 (ttp-170) outliers start: 86 outliers final: 25 residues processed: 625 average time/residue: 0.7287 time to fit residues: 529.4799 Evaluate side-chains 577 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 534 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 180 ASP Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 340 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN E 24 GLN F 131 GLN I 24 GLN J 131 GLN N 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099998 restraints weight = 32865.694| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.81 r_work: 0.3079 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31814 Z= 0.154 Angle : 0.463 8.567 42512 Z= 0.244 Chirality : 0.032 0.189 4720 Planarity : 0.003 0.028 5456 Dihedral : 3.741 57.061 4289 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.25 % Allowed : 23.66 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.03 (0.12), residues: 3952 helix: 3.49 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 49 TYR 0.032 0.002 TYR B 79 PHE 0.017 0.002 PHE O 77 HIS 0.004 0.001 HIS G 21 Details of bonding type rmsd covalent geometry : bond 0.00345 (31776) covalent geometry : angle 0.46307 (42512) hydrogen bonds : bond 0.05913 ( 3041) hydrogen bonds : angle 3.01404 ( 9123) metal coordination : bond 0.00292 ( 38) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 554 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7943 (ttmm) REVERT: A 41 GLU cc_start: 0.7906 (pt0) cc_final: 0.7398 (pp20) REVERT: A 113 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 187 ASP cc_start: 0.8048 (t0) cc_final: 0.7592 (t0) REVERT: B 38 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8308 (ttmm) REVERT: B 86 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 208 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: C 24 GLN cc_start: 0.8130 (mt0) cc_final: 0.7821 (mt0) REVERT: C 86 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: C 113 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7893 (mm-30) REVERT: C 170 ASP cc_start: 0.8716 (t70) cc_final: 0.8267 (t70) REVERT: D 86 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 109 ASP cc_start: 0.8125 (t70) cc_final: 0.7780 (t0) REVERT: D 120 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7468 (mp0) REVERT: E 71 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7663 (mm-30) REVERT: E 86 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: E 170 ASP cc_start: 0.8767 (t70) cc_final: 0.8381 (t70) REVERT: E 178 ASP cc_start: 0.8342 (t0) cc_final: 0.8117 (t70) REVERT: F 24 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: F 86 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: F 170 ASP cc_start: 0.8665 (t70) cc_final: 0.8391 (t70) REVERT: F 179 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7936 (mp) REVERT: F 180 ASP cc_start: 0.8577 (t70) cc_final: 0.8180 (t0) REVERT: F 187 ASP cc_start: 0.8088 (t0) cc_final: 0.7566 (t0) REVERT: G 17 ASP cc_start: 0.8370 (t70) cc_final: 0.8099 (t70) REVERT: G 24 GLN cc_start: 0.8315 (mt0) cc_final: 0.8057 (mt0) REVERT: G 64 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6801 (mtt) REVERT: G 96 GLU cc_start: 0.7890 (mp0) cc_final: 0.7622 (mp0) REVERT: G 120 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: G 187 ASP cc_start: 0.8305 (t0) cc_final: 0.7886 (t0) REVERT: H 109 ASP cc_start: 0.8223 (t0) cc_final: 0.7856 (t0) REVERT: H 113 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7611 (mm-30) REVERT: H 170 ASP cc_start: 0.8768 (t70) cc_final: 0.8391 (t70) REVERT: H 187 ASP cc_start: 0.8221 (t0) cc_final: 0.7840 (t0) REVERT: H 245 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7424 (mpt90) REVERT: I 25 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7540 (mtmt) REVERT: I 41 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: I 71 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7806 (mm-30) REVERT: I 109 ASP cc_start: 0.8078 (t0) cc_final: 0.7577 (m-30) REVERT: I 110 TYR cc_start: 0.8668 (t80) cc_final: 0.8416 (t80) REVERT: J 6 MET cc_start: 0.8553 (tmm) cc_final: 0.7496 (tmt) REVERT: J 10 GLU cc_start: 0.7859 (mp0) cc_final: 0.7218 (mp0) REVERT: J 106 SER cc_start: 0.8392 (m) cc_final: 0.8107 (m) REVERT: J 156 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7406 (mp0) REVERT: J 187 ASP cc_start: 0.8098 (t70) cc_final: 0.7735 (t70) REVERT: J 240 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7961 (ttmm) REVERT: K 10 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7652 (mm-30) REVERT: K 17 ASP cc_start: 0.8506 (t70) cc_final: 0.8291 (t70) REVERT: K 62 LYS cc_start: 0.7994 (tppt) cc_final: 0.7657 (tppt) REVERT: K 170 ASP cc_start: 0.8545 (t70) cc_final: 0.8276 (t70) REVERT: K 180 ASP cc_start: 0.8427 (t0) cc_final: 0.7967 (t0) REVERT: K 197 GLU cc_start: 0.7778 (tt0) cc_final: 0.7525 (tm-30) REVERT: L 10 GLU cc_start: 0.7792 (mp0) cc_final: 0.6932 (tp30) REVERT: L 49 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7741 (mtp180) REVERT: L 62 LYS cc_start: 0.8033 (tptm) cc_final: 0.7550 (ttpt) REVERT: L 86 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7643 (mp0) REVERT: L 113 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7674 (mm-30) REVERT: L 120 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7470 (mm-30) REVERT: L 156 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7408 (mp0) REVERT: L 180 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8145 (t0) REVERT: L 247 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8110 (mm) REVERT: M 6 MET cc_start: 0.8289 (tpt) cc_final: 0.7632 (pp-130) REVERT: M 10 GLU cc_start: 0.7719 (mp0) cc_final: 0.6941 (tp30) REVERT: M 27 ASP cc_start: 0.7934 (m-30) cc_final: 0.7663 (m-30) REVERT: M 48 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8781 (mmp) REVERT: M 71 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: M 96 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7574 (mt-10) REVERT: M 170 ASP cc_start: 0.8559 (t70) cc_final: 0.8228 (t70) REVERT: M 187 ASP cc_start: 0.8192 (t70) cc_final: 0.7890 (t70) REVERT: M 220 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7674 (ttpt) REVERT: M 240 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7732 (ttmm) REVERT: N 6 MET cc_start: 0.8390 (tmt) cc_final: 0.7431 (ppp) REVERT: N 10 GLU cc_start: 0.8015 (mp0) cc_final: 0.7608 (mp0) REVERT: N 86 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7679 (mm-30) REVERT: N 94 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: N 156 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7602 (mp0) REVERT: N 187 ASP cc_start: 0.8391 (t0) cc_final: 0.8005 (t70) REVERT: N 204 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7658 (mtmt) REVERT: O 10 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7595 (mp0) REVERT: O 27 ASP cc_start: 0.7975 (m-30) cc_final: 0.7646 (m-30) REVERT: O 38 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7856 (pttp) REVERT: O 62 LYS cc_start: 0.7771 (mmmm) cc_final: 0.7496 (tppt) REVERT: O 86 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: O 94 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: O 96 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7604 (mp0) REVERT: O 109 ASP cc_start: 0.8024 (t0) cc_final: 0.7635 (t0) REVERT: O 113 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7781 (mm-30) REVERT: O 147 GLU cc_start: 0.7955 (tt0) cc_final: 0.7636 (tt0) REVERT: O 170 ASP cc_start: 0.8766 (t70) cc_final: 0.8491 (t70) REVERT: O 180 ASP cc_start: 0.8438 (t70) cc_final: 0.8072 (t0) REVERT: P 10 GLU cc_start: 0.7824 (mp0) cc_final: 0.7253 (mp0) REVERT: P 113 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7677 (mm-30) REVERT: P 156 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7324 (mp0) REVERT: P 204 LYS cc_start: 0.8119 (tppp) cc_final: 0.7750 (mtmt) REVERT: P 207 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8446 (tp) REVERT: P 244 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7342 (ttpt) outliers start: 102 outliers final: 32 residues processed: 626 average time/residue: 0.7380 time to fit residues: 538.4216 Evaluate side-chains 591 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 534 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 180 ASP Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain M residue 240 LYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 244 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 238 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 358 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN B 131 GLN I 24 GLN J 131 GLN N 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101042 restraints weight = 32806.349| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.80 r_work: 0.3125 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31814 Z= 0.142 Angle : 0.449 8.838 42512 Z= 0.238 Chirality : 0.032 0.185 4720 Planarity : 0.003 0.026 5456 Dihedral : 3.723 58.282 4289 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 2.93 % Allowed : 23.98 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.05 (0.12), residues: 3952 helix: 3.51 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 114 TYR 0.030 0.002 TYR B 79 PHE 0.017 0.002 PHE H 77 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00306 (31776) covalent geometry : angle 0.44855 (42512) hydrogen bonds : bond 0.05619 ( 3041) hydrogen bonds : angle 2.99328 ( 9123) metal coordination : bond 0.00309 ( 38) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 559 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8008 (ttmm) REVERT: A 41 GLU cc_start: 0.7971 (pt0) cc_final: 0.7482 (pp20) REVERT: A 113 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 187 ASP cc_start: 0.8114 (t0) cc_final: 0.7675 (t0) REVERT: B 38 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8322 (ttmm) REVERT: B 187 ASP cc_start: 0.8228 (t0) cc_final: 0.7858 (t70) REVERT: B 208 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: C 24 GLN cc_start: 0.8191 (mt0) cc_final: 0.7930 (mt0) REVERT: C 86 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: C 113 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 170 ASP cc_start: 0.8774 (t70) cc_final: 0.8314 (t70) REVERT: D 6 MET cc_start: 0.7856 (pmm) cc_final: 0.7655 (ptm) REVERT: D 86 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: D 109 ASP cc_start: 0.8223 (t70) cc_final: 0.7884 (t0) REVERT: D 120 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7526 (mp0) REVERT: D 154 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8059 (p) REVERT: E 71 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7739 (mm-30) REVERT: E 86 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: E 170 ASP cc_start: 0.8768 (t70) cc_final: 0.8382 (t70) REVERT: E 178 ASP cc_start: 0.8416 (t0) cc_final: 0.8197 (t70) REVERT: E 240 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7926 (tttm) REVERT: F 6 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7842 (ppp) REVERT: F 24 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: F 86 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: F 170 ASP cc_start: 0.8631 (t70) cc_final: 0.8116 (t70) REVERT: F 174 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7676 (mm-30) REVERT: F 180 ASP cc_start: 0.8606 (t70) cc_final: 0.8236 (t0) REVERT: F 187 ASP cc_start: 0.8137 (t0) cc_final: 0.7621 (t0) REVERT: G 6 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8214 (tpt) REVERT: G 17 ASP cc_start: 0.8408 (t70) cc_final: 0.8135 (t70) REVERT: G 24 GLN cc_start: 0.8326 (mt0) cc_final: 0.8116 (mt0) REVERT: G 64 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6808 (mtt) REVERT: G 120 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: G 174 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7754 (mm-30) REVERT: G 187 ASP cc_start: 0.8309 (t0) cc_final: 0.7881 (t0) REVERT: H 109 ASP cc_start: 0.8291 (t0) cc_final: 0.7935 (t0) REVERT: H 113 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7627 (mm-30) REVERT: H 170 ASP cc_start: 0.8768 (t70) cc_final: 0.8372 (t70) REVERT: H 187 ASP cc_start: 0.8194 (t0) cc_final: 0.7834 (t0) REVERT: H 245 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7448 (mpt90) REVERT: I 25 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7674 (mtmt) REVERT: I 41 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: I 71 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7849 (mm-30) REVERT: I 109 ASP cc_start: 0.8073 (t0) cc_final: 0.7583 (m-30) REVERT: I 110 TYR cc_start: 0.8701 (t80) cc_final: 0.8445 (t80) REVERT: I 120 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: J 6 MET cc_start: 0.8610 (tmm) cc_final: 0.7330 (tmt) REVERT: J 10 GLU cc_start: 0.7811 (mp0) cc_final: 0.7164 (mp0) REVERT: J 86 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: J 106 SER cc_start: 0.8418 (m) cc_final: 0.8134 (m) REVERT: J 156 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7482 (mp0) REVERT: J 174 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: J 187 ASP cc_start: 0.8127 (t70) cc_final: 0.7752 (t70) REVERT: J 240 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8051 (ttmm) REVERT: K 10 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7654 (mm-30) REVERT: K 17 ASP cc_start: 0.8484 (t70) cc_final: 0.8278 (t70) REVERT: K 62 LYS cc_start: 0.8041 (tppt) cc_final: 0.7719 (tppt) REVERT: K 120 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: K 170 ASP cc_start: 0.8579 (t70) cc_final: 0.8309 (t70) REVERT: K 180 ASP cc_start: 0.8438 (t0) cc_final: 0.7978 (t0) REVERT: K 197 GLU cc_start: 0.7768 (tt0) cc_final: 0.7498 (tm-30) REVERT: L 10 GLU cc_start: 0.7796 (mp0) cc_final: 0.6896 (tp30) REVERT: L 49 ARG cc_start: 0.8173 (ttm-80) cc_final: 0.7791 (mtp180) REVERT: L 62 LYS cc_start: 0.7965 (tptm) cc_final: 0.7470 (ttpt) REVERT: L 86 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7723 (mp0) REVERT: L 109 ASP cc_start: 0.8224 (t0) cc_final: 0.7446 (m-30) REVERT: L 113 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7876 (mm-30) REVERT: L 120 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7531 (mm-30) REVERT: L 156 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7494 (mp0) REVERT: L 180 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8219 (t0) REVERT: M 6 MET cc_start: 0.8279 (tpt) cc_final: 0.7719 (pp-130) REVERT: M 10 GLU cc_start: 0.7812 (mp0) cc_final: 0.6989 (tp30) REVERT: M 27 ASP cc_start: 0.7966 (m-30) cc_final: 0.7674 (m-30) REVERT: M 48 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8876 (mmp) REVERT: M 71 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: M 96 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7613 (mt-10) REVERT: M 147 GLU cc_start: 0.7927 (tt0) cc_final: 0.7604 (tt0) REVERT: M 170 ASP cc_start: 0.8600 (t70) cc_final: 0.8257 (t70) REVERT: M 187 ASP cc_start: 0.8252 (t70) cc_final: 0.7926 (t70) REVERT: M 220 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7697 (ttpt) REVERT: N 6 MET cc_start: 0.8429 (tmt) cc_final: 0.7466 (ppp) REVERT: N 10 GLU cc_start: 0.8050 (mp0) cc_final: 0.7648 (mp0) REVERT: N 94 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: N 156 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7579 (mp0) REVERT: N 187 ASP cc_start: 0.8366 (t0) cc_final: 0.7999 (t70) REVERT: N 204 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7675 (mtmt) REVERT: O 10 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7588 (mp0) REVERT: O 27 ASP cc_start: 0.8009 (m-30) cc_final: 0.7689 (m-30) REVERT: O 38 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7890 (pttp) REVERT: O 62 LYS cc_start: 0.7767 (mmmm) cc_final: 0.7506 (tppt) REVERT: O 86 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: O 94 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7220 (tp30) REVERT: O 109 ASP cc_start: 0.8033 (t0) cc_final: 0.7662 (t0) REVERT: O 113 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7841 (mm-30) REVERT: O 147 GLU cc_start: 0.8001 (tt0) cc_final: 0.7704 (tt0) REVERT: O 170 ASP cc_start: 0.8756 (t70) cc_final: 0.8487 (t70) REVERT: O 180 ASP cc_start: 0.8436 (t70) cc_final: 0.8080 (t0) REVERT: P 10 GLU cc_start: 0.7812 (mp0) cc_final: 0.7345 (mp0) REVERT: P 113 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7680 (mm-30) REVERT: P 156 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7330 (mp0) REVERT: P 204 LYS cc_start: 0.8202 (tppp) cc_final: 0.7817 (mtmm) outliers start: 92 outliers final: 36 residues processed: 623 average time/residue: 0.7169 time to fit residues: 520.0823 Evaluate side-chains 599 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 535 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 LYS Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 180 ASP Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 163 optimal weight: 2.9990 chunk 293 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 292 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN B 131 GLN I 24 GLN J 131 GLN N 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104386 restraints weight = 32835.318| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.78 r_work: 0.3168 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 31814 Z= 0.118 Angle : 0.420 8.302 42512 Z= 0.223 Chirality : 0.030 0.158 4720 Planarity : 0.003 0.027 5456 Dihedral : 3.656 57.797 4289 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 2.81 % Allowed : 24.36 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.20 (0.12), residues: 3952 helix: 3.60 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 114 TYR 0.025 0.002 TYR B 79 PHE 0.018 0.002 PHE H 77 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00232 (31776) covalent geometry : angle 0.41963 (42512) hydrogen bonds : bond 0.04870 ( 3041) hydrogen bonds : angle 2.91293 ( 9123) metal coordination : bond 0.00262 ( 38) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 554 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7943 (ttmm) REVERT: A 41 GLU cc_start: 0.7894 (pt0) cc_final: 0.7417 (pp20) REVERT: A 113 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 187 ASP cc_start: 0.8058 (t0) cc_final: 0.7629 (t0) REVERT: B 62 LYS cc_start: 0.8049 (tttm) cc_final: 0.7560 (ttpt) REVERT: B 143 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7598 (mttp) REVERT: B 187 ASP cc_start: 0.8093 (t0) cc_final: 0.7754 (t70) REVERT: B 208 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: C 86 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: C 113 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7896 (mm-30) REVERT: C 240 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7955 (ttpp) REVERT: D 86 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: D 109 ASP cc_start: 0.8069 (t70) cc_final: 0.7804 (t0) REVERT: D 113 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 245 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6304 (mtt90) REVERT: E 71 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7677 (mm-30) REVERT: E 86 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: E 170 ASP cc_start: 0.8768 (t70) cc_final: 0.8396 (t70) REVERT: E 240 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7812 (tttm) REVERT: F 6 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7852 (ppp) REVERT: F 24 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: F 86 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: F 170 ASP cc_start: 0.8617 (t70) cc_final: 0.8150 (t70) REVERT: F 174 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7615 (mm-30) REVERT: F 180 ASP cc_start: 0.8548 (t70) cc_final: 0.8234 (t0) REVERT: F 187 ASP cc_start: 0.8099 (t0) cc_final: 0.7586 (t0) REVERT: G 6 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8191 (tpt) REVERT: G 17 ASP cc_start: 0.8386 (t70) cc_final: 0.8115 (t70) REVERT: G 120 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: G 174 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7685 (mm-30) REVERT: G 187 ASP cc_start: 0.8262 (t0) cc_final: 0.7856 (t0) REVERT: H 109 ASP cc_start: 0.8098 (t0) cc_final: 0.7789 (t0) REVERT: H 113 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7615 (mm-30) REVERT: H 170 ASP cc_start: 0.8759 (t70) cc_final: 0.8380 (t70) REVERT: H 187 ASP cc_start: 0.8086 (t0) cc_final: 0.7750 (t0) REVERT: H 243 PHE cc_start: 0.7589 (m-10) cc_final: 0.6659 (t80) REVERT: I 25 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7618 (mtmt) REVERT: I 41 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: I 71 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7650 (mm-30) REVERT: I 86 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: I 109 ASP cc_start: 0.8086 (t0) cc_final: 0.7589 (m-30) REVERT: I 110 TYR cc_start: 0.8588 (t80) cc_final: 0.8299 (t80) REVERT: I 120 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: J 6 MET cc_start: 0.8625 (tmm) cc_final: 0.7979 (tmt) REVERT: J 86 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: J 106 SER cc_start: 0.8389 (m) cc_final: 0.8133 (m) REVERT: J 174 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: J 187 ASP cc_start: 0.8067 (t70) cc_final: 0.7733 (t70) REVERT: J 240 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7988 (ttmm) REVERT: K 10 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7595 (mm-30) REVERT: K 17 ASP cc_start: 0.8396 (t70) cc_final: 0.8191 (t70) REVERT: K 62 LYS cc_start: 0.8013 (tppt) cc_final: 0.7663 (tppt) REVERT: K 120 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: K 170 ASP cc_start: 0.8546 (t70) cc_final: 0.8285 (t70) REVERT: K 180 ASP cc_start: 0.8399 (t0) cc_final: 0.7941 (t0) REVERT: K 197 GLU cc_start: 0.7689 (tt0) cc_final: 0.7433 (tt0) REVERT: L 10 GLU cc_start: 0.7727 (mp0) cc_final: 0.6822 (tp30) REVERT: L 49 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7810 (mtp180) REVERT: L 62 LYS cc_start: 0.7825 (tptm) cc_final: 0.7392 (ttpt) REVERT: L 86 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7557 (mp0) REVERT: L 113 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7729 (mm-30) REVERT: L 120 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7460 (mm-30) REVERT: L 156 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7391 (mp0) REVERT: L 180 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8157 (t0) REVERT: M 6 MET cc_start: 0.8295 (tpt) cc_final: 0.7377 (pp-130) REVERT: M 27 ASP cc_start: 0.7829 (m-30) cc_final: 0.7589 (m-30) REVERT: M 48 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8916 (mmp) REVERT: M 71 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: M 86 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: M 96 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7526 (mt-10) REVERT: M 147 GLU cc_start: 0.7946 (tt0) cc_final: 0.7628 (tt0) REVERT: M 170 ASP cc_start: 0.8588 (t70) cc_final: 0.8257 (t70) REVERT: M 187 ASP cc_start: 0.8172 (t70) cc_final: 0.7859 (t70) REVERT: M 220 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7579 (ttpt) REVERT: N 10 GLU cc_start: 0.8008 (mp0) cc_final: 0.7531 (mp0) REVERT: N 49 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7756 (mtp180) REVERT: N 187 ASP cc_start: 0.8287 (t0) cc_final: 0.7960 (t70) REVERT: N 204 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7622 (mtmt) REVERT: O 27 ASP cc_start: 0.7935 (m-30) cc_final: 0.7601 (m-30) REVERT: O 38 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7897 (pttp) REVERT: O 62 LYS cc_start: 0.7756 (mmmm) cc_final: 0.7503 (tppt) REVERT: O 86 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: O 109 ASP cc_start: 0.7932 (t0) cc_final: 0.7561 (t0) REVERT: O 113 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7816 (mm-30) REVERT: O 147 GLU cc_start: 0.7963 (tt0) cc_final: 0.7644 (tt0) REVERT: O 170 ASP cc_start: 0.8754 (t70) cc_final: 0.8476 (t70) REVERT: O 180 ASP cc_start: 0.8357 (t70) cc_final: 0.7997 (t0) REVERT: P 10 GLU cc_start: 0.7632 (mp0) cc_final: 0.7186 (mp0) REVERT: P 113 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7483 (mm-30) REVERT: P 156 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7451 (mp0) REVERT: P 204 LYS cc_start: 0.8200 (tppp) cc_final: 0.7829 (mtmm) outliers start: 88 outliers final: 18 residues processed: 613 average time/residue: 0.7167 time to fit residues: 510.3664 Evaluate side-chains 570 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 527 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 180 ASP Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 86 GLU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain N residue 247 LEU Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 378 optimal weight: 0.6980 chunk 198 optimal weight: 0.4980 chunk 189 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN I 24 GLN J 131 GLN N 24 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.105081 restraints weight = 33219.048| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.82 r_work: 0.3186 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31814 Z= 0.117 Angle : 0.432 8.404 42512 Z= 0.228 Chirality : 0.030 0.148 4720 Planarity : 0.003 0.026 5456 Dihedral : 3.378 55.058 4284 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 1.98 % Allowed : 25.64 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.25 (0.12), residues: 3952 helix: 3.64 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.45 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 245 TYR 0.023 0.002 TYR B 79 PHE 0.018 0.002 PHE H 77 HIS 0.004 0.001 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00228 (31776) covalent geometry : angle 0.43215 (42512) hydrogen bonds : bond 0.04742 ( 3041) hydrogen bonds : angle 2.87847 ( 9123) metal coordination : bond 0.00287 ( 38) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 538 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7949 (ttmm) REVERT: A 41 GLU cc_start: 0.7903 (pt0) cc_final: 0.7437 (pp20) REVERT: A 187 ASP cc_start: 0.8070 (t0) cc_final: 0.7656 (t0) REVERT: B 38 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8344 (ttmm) REVERT: B 62 LYS cc_start: 0.8052 (tttm) cc_final: 0.7563 (ttpt) REVERT: B 143 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7635 (mttp) REVERT: B 187 ASP cc_start: 0.8080 (t0) cc_final: 0.7758 (t70) REVERT: B 208 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: C 24 GLN cc_start: 0.8088 (mt0) cc_final: 0.7753 (mt0) REVERT: C 86 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: C 113 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7868 (mm-30) REVERT: C 170 ASP cc_start: 0.8783 (t70) cc_final: 0.8327 (t70) REVERT: D 6 MET cc_start: 0.7776 (pmm) cc_final: 0.7527 (ptm) REVERT: D 63 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 109 ASP cc_start: 0.8092 (t70) cc_final: 0.7817 (t0) REVERT: D 113 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7940 (mm-30) REVERT: D 245 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6332 (mtt90) REVERT: E 71 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7769 (mm-30) REVERT: E 86 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: E 170 ASP cc_start: 0.8789 (t70) cc_final: 0.8406 (t70) REVERT: E 240 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7881 (tttm) REVERT: F 24 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: F 86 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: F 170 ASP cc_start: 0.8663 (t70) cc_final: 0.8144 (t70) REVERT: F 174 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7612 (mm-30) REVERT: F 187 ASP cc_start: 0.8083 (t0) cc_final: 0.7575 (t0) REVERT: G 17 ASP cc_start: 0.8386 (t70) cc_final: 0.8124 (t70) REVERT: G 48 MET cc_start: 0.8896 (mmm) cc_final: 0.8689 (mmm) REVERT: G 86 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: G 120 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: G 174 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7726 (mm-30) REVERT: G 187 ASP cc_start: 0.8262 (t0) cc_final: 0.7858 (t0) REVERT: H 109 ASP cc_start: 0.8180 (t0) cc_final: 0.7795 (t0) REVERT: H 113 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7518 (mm-30) REVERT: H 170 ASP cc_start: 0.8789 (t70) cc_final: 0.8407 (t70) REVERT: H 187 ASP cc_start: 0.8065 (t0) cc_final: 0.7730 (t0) REVERT: H 243 PHE cc_start: 0.7535 (m-10) cc_final: 0.6714 (t80) REVERT: I 25 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7633 (mtmt) REVERT: I 41 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: I 71 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7685 (mm-30) REVERT: I 86 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: I 109 ASP cc_start: 0.8177 (t0) cc_final: 0.7730 (m-30) REVERT: I 110 TYR cc_start: 0.8567 (t80) cc_final: 0.8362 (t80) REVERT: I 120 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: J 6 MET cc_start: 0.8635 (tmm) cc_final: 0.8032 (tmt) REVERT: J 72 MET cc_start: 0.8925 (mtt) cc_final: 0.8629 (mtt) REVERT: J 86 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: J 106 SER cc_start: 0.8442 (m) cc_final: 0.8179 (m) REVERT: J 174 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: J 187 ASP cc_start: 0.8087 (t70) cc_final: 0.7770 (t70) REVERT: J 240 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8011 (ttmm) REVERT: J 243 PHE cc_start: 0.7553 (m-10) cc_final: 0.6772 (t80) REVERT: K 10 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7634 (mm-30) REVERT: K 17 ASP cc_start: 0.8427 (t70) cc_final: 0.8227 (t70) REVERT: K 62 LYS cc_start: 0.7943 (tppt) cc_final: 0.7584 (tppt) REVERT: K 120 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: K 170 ASP cc_start: 0.8555 (t70) cc_final: 0.8288 (t70) REVERT: K 180 ASP cc_start: 0.8441 (t0) cc_final: 0.7975 (t0) REVERT: K 197 GLU cc_start: 0.7716 (tt0) cc_final: 0.7473 (tt0) REVERT: L 10 GLU cc_start: 0.7758 (mp0) cc_final: 0.6810 (tp30) REVERT: L 49 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7858 (mtp180) REVERT: L 62 LYS cc_start: 0.7865 (tptm) cc_final: 0.7415 (ttpt) REVERT: L 86 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7605 (mp0) REVERT: L 113 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7734 (mm-30) REVERT: L 156 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7415 (mp0) REVERT: L 180 ASP cc_start: 0.8395 (t70) cc_final: 0.8184 (t0) REVERT: L 243 PHE cc_start: 0.7756 (m-10) cc_final: 0.6923 (t80) REVERT: M 6 MET cc_start: 0.8113 (tpt) cc_final: 0.7446 (pp-130) REVERT: M 27 ASP cc_start: 0.7871 (m-30) cc_final: 0.7630 (m-30) REVERT: M 48 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8904 (mmp) REVERT: M 71 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: M 96 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7512 (mt-10) REVERT: M 147 GLU cc_start: 0.7966 (tt0) cc_final: 0.7647 (tt0) REVERT: M 170 ASP cc_start: 0.8593 (t70) cc_final: 0.8259 (t70) REVERT: M 187 ASP cc_start: 0.8205 (t70) cc_final: 0.7916 (t70) REVERT: M 220 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7561 (ttpt) REVERT: N 10 GLU cc_start: 0.7984 (mp0) cc_final: 0.7467 (mp0) REVERT: N 49 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7815 (mtp180) REVERT: N 187 ASP cc_start: 0.8287 (t0) cc_final: 0.7985 (t70) REVERT: N 204 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7656 (mtmt) REVERT: N 243 PHE cc_start: 0.7464 (m-10) cc_final: 0.6874 (t80) REVERT: O 38 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7930 (pttp) REVERT: O 62 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7492 (tppt) REVERT: O 86 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: O 109 ASP cc_start: 0.7901 (t0) cc_final: 0.7463 (m-30) REVERT: O 147 GLU cc_start: 0.7986 (tt0) cc_final: 0.7642 (tt0) REVERT: O 170 ASP cc_start: 0.8768 (t70) cc_final: 0.8484 (t70) REVERT: O 180 ASP cc_start: 0.8366 (t70) cc_final: 0.8019 (t0) REVERT: P 10 GLU cc_start: 0.7638 (mp0) cc_final: 0.7199 (mp0) REVERT: P 96 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7493 (mt-10) REVERT: P 113 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7481 (mm-30) REVERT: P 156 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7534 (mp0) REVERT: P 204 LYS cc_start: 0.8226 (tppp) cc_final: 0.7859 (mtmm) outliers start: 62 outliers final: 17 residues processed: 576 average time/residue: 0.7280 time to fit residues: 489.0218 Evaluate side-chains 554 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 515 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain I residue 25 LYS Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 207 LEU Chi-restraints excluded: chain P residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 375 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 362 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 273 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 315 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN F 231 HIS I 24 GLN J 131 GLN O 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102969 restraints weight = 32629.743| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.81 r_work: 0.3120 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.644 31814 Z= 0.184 Angle : 0.469 8.468 42512 Z= 0.247 Chirality : 0.031 0.149 4720 Planarity : 0.003 0.026 5456 Dihedral : 3.417 55.473 4284 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.69 % Allowed : 25.80 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.16 (0.12), residues: 3952 helix: 3.58 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 245 TYR 0.028 0.002 TYR B 79 PHE 0.017 0.002 PHE G 77 HIS 0.004 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00299 (31776) covalent geometry : angle 0.46935 (42512) hydrogen bonds : bond 0.05333 ( 3041) hydrogen bonds : angle 2.93562 ( 9123) metal coordination : bond 0.10459 ( 38) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 532 time to evaluate : 1.196 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: A 38 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7919 (ttmm) REVERT: A 41 GLU cc_start: 0.7917 (pt0) cc_final: 0.7422 (pp20) REVERT: A 187 ASP cc_start: 0.8103 (t0) cc_final: 0.7671 (t0) REVERT: B 38 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8309 (ttmm) REVERT: B 62 LYS cc_start: 0.8070 (tttm) cc_final: 0.7570 (ttpt) REVERT: B 96 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7614 (mp0) REVERT: B 187 ASP cc_start: 0.8160 (t0) cc_final: 0.7806 (t70) REVERT: B 208 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: C 24 GLN cc_start: 0.8090 (mt0) cc_final: 0.7751 (mt0) REVERT: C 86 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: C 113 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7872 (mm-30) REVERT: C 170 ASP cc_start: 0.8766 (t70) cc_final: 0.8309 (t70) REVERT: D 86 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: D 109 ASP cc_start: 0.8128 (t70) cc_final: 0.7799 (t0) REVERT: D 113 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7882 (mm-30) REVERT: D 245 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6213 (mtt90) REVERT: E 71 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7666 (mm-30) REVERT: E 86 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: F 24 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7779 (mt0) REVERT: F 86 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: F 170 ASP cc_start: 0.8640 (t70) cc_final: 0.8335 (t70) REVERT: F 174 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7597 (mm-30) REVERT: F 180 ASP cc_start: 0.8354 (t70) cc_final: 0.8112 (t0) REVERT: F 187 ASP cc_start: 0.8123 (t0) cc_final: 0.7607 (t0) REVERT: G 17 ASP cc_start: 0.8337 (t70) cc_final: 0.8073 (t70) REVERT: G 24 GLN cc_start: 0.8179 (mt0) cc_final: 0.7841 (mt0) REVERT: G 174 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7674 (mm-30) REVERT: G 187 ASP cc_start: 0.8285 (t0) cc_final: 0.7881 (t0) REVERT: H 109 ASP cc_start: 0.8215 (t0) cc_final: 0.7592 (m-30) REVERT: H 113 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7634 (mm-30) REVERT: H 170 ASP cc_start: 0.8746 (t70) cc_final: 0.8348 (t70) REVERT: H 187 ASP cc_start: 0.8136 (t0) cc_final: 0.7768 (t0) REVERT: H 243 PHE cc_start: 0.7610 (m-10) cc_final: 0.6598 (t80) REVERT: I 41 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: I 71 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7730 (mm-30) REVERT: I 109 ASP cc_start: 0.8122 (t0) cc_final: 0.7633 (m-30) REVERT: I 110 TYR cc_start: 0.8579 (t80) cc_final: 0.8316 (t80) REVERT: I 120 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: J 6 MET cc_start: 0.8598 (tmm) cc_final: 0.7214 (tmt) REVERT: J 10 GLU cc_start: 0.7752 (mp0) cc_final: 0.7128 (mp0) REVERT: J 72 MET cc_start: 0.8937 (mtt) cc_final: 0.8648 (mtt) REVERT: J 86 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: J 106 SER cc_start: 0.8419 (m) cc_final: 0.8131 (m) REVERT: J 174 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: J 187 ASP cc_start: 0.8084 (t70) cc_final: 0.7750 (t70) REVERT: J 240 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7954 (ttmm) REVERT: K 10 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7596 (mm-30) REVERT: K 17 ASP cc_start: 0.8453 (t70) cc_final: 0.8248 (t70) REVERT: K 62 LYS cc_start: 0.7981 (tppt) cc_final: 0.7629 (tppt) REVERT: K 120 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: K 170 ASP cc_start: 0.8540 (t70) cc_final: 0.8258 (t70) REVERT: K 180 ASP cc_start: 0.8402 (t0) cc_final: 0.7928 (t0) REVERT: K 197 GLU cc_start: 0.7664 (tt0) cc_final: 0.7396 (tt0) REVERT: L 10 GLU cc_start: 0.7754 (mp0) cc_final: 0.6820 (tp30) REVERT: L 49 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7791 (mtp180) REVERT: L 62 LYS cc_start: 0.7822 (tptm) cc_final: 0.7385 (ttpt) REVERT: L 86 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7764 (mm-30) REVERT: L 113 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7741 (mm-30) REVERT: L 156 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7445 (mp0) REVERT: L 180 ASP cc_start: 0.8385 (t70) cc_final: 0.8148 (t0) REVERT: L 243 PHE cc_start: 0.7824 (m-10) cc_final: 0.6913 (t80) REVERT: M 6 MET cc_start: 0.8071 (tpt) cc_final: 0.6980 (pp-130) REVERT: M 10 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7442 (mp0) REVERT: M 27 ASP cc_start: 0.7908 (m-30) cc_final: 0.7625 (m-30) REVERT: M 48 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8814 (mmp) REVERT: M 71 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: M 96 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7573 (mt-10) REVERT: M 147 GLU cc_start: 0.7837 (tt0) cc_final: 0.7523 (tt0) REVERT: M 170 ASP cc_start: 0.8564 (t70) cc_final: 0.8228 (t70) REVERT: M 187 ASP cc_start: 0.8217 (t70) cc_final: 0.7902 (t70) REVERT: M 220 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7612 (ttpt) REVERT: M 240 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7777 (ttmm) REVERT: N 6 MET cc_start: 0.8282 (tmt) cc_final: 0.7272 (ppp) REVERT: N 10 GLU cc_start: 0.7987 (mp0) cc_final: 0.7594 (mp0) REVERT: N 96 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7509 (mp0) REVERT: N 170 ASP cc_start: 0.8515 (t70) cc_final: 0.8309 (t70) REVERT: N 187 ASP cc_start: 0.8343 (t0) cc_final: 0.8015 (t70) REVERT: N 204 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7571 (mtmt) REVERT: O 27 ASP cc_start: 0.7925 (m-30) cc_final: 0.7592 (m-30) REVERT: O 38 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7839 (pttp) REVERT: O 62 LYS cc_start: 0.7753 (mmmm) cc_final: 0.7492 (tppt) REVERT: O 86 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: O 147 GLU cc_start: 0.7926 (tt0) cc_final: 0.7615 (tt0) REVERT: O 170 ASP cc_start: 0.8757 (t70) cc_final: 0.8474 (t70) REVERT: O 180 ASP cc_start: 0.8387 (t70) cc_final: 0.8039 (t0) REVERT: P 10 GLU cc_start: 0.7661 (mp0) cc_final: 0.6933 (tp30) REVERT: P 113 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7453 (mm-30) REVERT: P 156 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7535 (mp0) REVERT: P 204 LYS cc_start: 0.8203 (tppp) cc_final: 0.7772 (mtmt) outliers start: 53 outliers final: 19 residues processed: 569 average time/residue: 0.6894 time to fit residues: 458.8447 Evaluate side-chains 559 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 521 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain M residue 240 LYS Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 316 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 313 optimal weight: 0.9980 chunk 266 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 310 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN H 23 HIS I 24 GLN J 131 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100080 restraints weight = 32515.560| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.82 r_work: 0.3098 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.374 31814 Z= 0.176 Angle : 0.501 8.530 42512 Z= 0.263 Chirality : 0.033 0.175 4720 Planarity : 0.003 0.027 5456 Dihedral : 3.488 57.118 4284 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.63 % Allowed : 26.12 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.03 (0.12), residues: 3952 helix: 3.50 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 245 TYR 0.033 0.002 TYR B 79 PHE 0.017 0.002 PHE O 77 HIS 0.005 0.001 HIS O 21 Details of bonding type rmsd covalent geometry : bond 0.00365 (31776) covalent geometry : angle 0.50099 (42512) hydrogen bonds : bond 0.05946 ( 3041) hydrogen bonds : angle 3.02328 ( 9123) metal coordination : bond 0.06085 ( 38) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 543 time to evaluate : 1.189 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: A 38 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8059 (ttmm) REVERT: A 41 GLU cc_start: 0.8008 (pt0) cc_final: 0.7520 (pp20) REVERT: A 109 ASP cc_start: 0.8106 (t0) cc_final: 0.7650 (m-30) REVERT: A 187 ASP cc_start: 0.8163 (t0) cc_final: 0.7718 (t0) REVERT: B 38 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (ttmm) REVERT: B 208 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: C 24 GLN cc_start: 0.8228 (mt0) cc_final: 0.7913 (mt0) REVERT: C 86 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: C 113 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7915 (mm-30) REVERT: C 170 ASP cc_start: 0.8796 (t70) cc_final: 0.8328 (t70) REVERT: D 63 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 86 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: D 109 ASP cc_start: 0.8182 (t70) cc_final: 0.7840 (t0) REVERT: D 113 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7880 (mm-30) REVERT: D 245 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6308 (mtt90) REVERT: E 10 GLU cc_start: 0.7915 (mp0) cc_final: 0.7473 (mp0) REVERT: E 71 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7822 (mm-30) REVERT: E 86 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: E 170 ASP cc_start: 0.8777 (t70) cc_final: 0.8441 (t70) REVERT: F 24 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: F 86 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: F 170 ASP cc_start: 0.8637 (t70) cc_final: 0.8341 (t70) REVERT: F 174 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7699 (mm-30) REVERT: F 187 ASP cc_start: 0.8194 (t0) cc_final: 0.7672 (t0) REVERT: G 17 ASP cc_start: 0.8413 (t70) cc_final: 0.8163 (t70) REVERT: G 24 GLN cc_start: 0.8365 (mt0) cc_final: 0.8048 (mt0) REVERT: G 174 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7756 (mm-30) REVERT: H 109 ASP cc_start: 0.8262 (t0) cc_final: 0.7653 (m-30) REVERT: H 187 ASP cc_start: 0.8200 (t0) cc_final: 0.7829 (t0) REVERT: I 41 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: I 71 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7899 (mm-30) REVERT: I 109 ASP cc_start: 0.8117 (t0) cc_final: 0.7623 (m-30) REVERT: I 110 TYR cc_start: 0.8717 (t80) cc_final: 0.8474 (t80) REVERT: J 6 MET cc_start: 0.8585 (tmm) cc_final: 0.7351 (tpt) REVERT: J 10 GLU cc_start: 0.7850 (mp0) cc_final: 0.7238 (mp0) REVERT: J 72 MET cc_start: 0.9021 (mtt) cc_final: 0.8687 (mtt) REVERT: J 86 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: J 106 SER cc_start: 0.8443 (m) cc_final: 0.8145 (m) REVERT: J 174 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7633 (mm-30) REVERT: J 187 ASP cc_start: 0.8164 (t70) cc_final: 0.7821 (t70) REVERT: J 240 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8132 (ttmm) REVERT: K 10 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7721 (mm-30) REVERT: K 62 LYS cc_start: 0.8023 (tppt) cc_final: 0.7674 (tppt) REVERT: K 170 ASP cc_start: 0.8579 (t70) cc_final: 0.8274 (t70) REVERT: K 180 ASP cc_start: 0.8469 (t0) cc_final: 0.8000 (t0) REVERT: K 197 GLU cc_start: 0.7774 (tt0) cc_final: 0.7488 (tm-30) REVERT: L 10 GLU cc_start: 0.7848 (mp0) cc_final: 0.6932 (tp30) REVERT: L 48 MET cc_start: 0.8966 (mmm) cc_final: 0.8684 (mmp) REVERT: L 49 ARG cc_start: 0.8057 (ttm-80) cc_final: 0.7758 (mtp180) REVERT: L 62 LYS cc_start: 0.7948 (tptm) cc_final: 0.7504 (ttpt) REVERT: L 113 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7829 (mm-30) REVERT: L 156 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7500 (mp0) REVERT: L 180 ASP cc_start: 0.8495 (t70) cc_final: 0.8228 (t0) REVERT: M 6 MET cc_start: 0.8004 (tpt) cc_final: 0.7083 (pp-130) REVERT: M 10 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7602 (mp0) REVERT: M 27 ASP cc_start: 0.7994 (m-30) cc_final: 0.7730 (m-30) REVERT: M 48 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8870 (mmp) REVERT: M 71 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: M 96 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7683 (mt-10) REVERT: M 147 GLU cc_start: 0.7913 (tt0) cc_final: 0.7615 (tt0) REVERT: M 170 ASP cc_start: 0.8626 (t70) cc_final: 0.8283 (t70) REVERT: M 187 ASP cc_start: 0.8217 (t70) cc_final: 0.7906 (t70) REVERT: M 220 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7759 (ttpt) REVERT: M 240 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7844 (ttmm) REVERT: N 10 GLU cc_start: 0.8043 (mp0) cc_final: 0.7606 (mp0) REVERT: N 86 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7687 (mm-30) REVERT: N 187 ASP cc_start: 0.8422 (t0) cc_final: 0.8078 (t70) REVERT: N 204 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7656 (mtmt) REVERT: O 10 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7581 (mp0) REVERT: O 27 ASP cc_start: 0.8001 (m-30) cc_final: 0.7646 (m-30) REVERT: O 38 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7910 (pttp) REVERT: O 53 TYR cc_start: 0.8843 (t80) cc_final: 0.8460 (t80) REVERT: O 62 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7575 (tppt) REVERT: O 86 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: O 109 ASP cc_start: 0.7795 (t0) cc_final: 0.7229 (m-30) REVERT: O 147 GLU cc_start: 0.8016 (tt0) cc_final: 0.7708 (tt0) REVERT: O 170 ASP cc_start: 0.8767 (t70) cc_final: 0.8468 (t70) REVERT: O 180 ASP cc_start: 0.8461 (t70) cc_final: 0.8132 (t0) REVERT: P 10 GLU cc_start: 0.7752 (mp0) cc_final: 0.7006 (tp30) REVERT: P 113 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7615 (mm-30) REVERT: P 156 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7516 (mp0) REVERT: P 204 LYS cc_start: 0.8270 (tppp) cc_final: 0.7836 (mtmt) outliers start: 51 outliers final: 24 residues processed: 579 average time/residue: 0.6434 time to fit residues: 437.0506 Evaluate side-chains 571 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 530 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain J residue 86 GLU Chi-restraints excluded: chain J residue 174 GLU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 86 GLU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 62 LYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 220 LYS Chi-restraints excluded: chain M residue 240 LYS Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 97 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 236 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 375 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN B 24 GLN B 131 GLN F 131 GLN H 24 GLN I 24 GLN J 131 GLN O 24 GLN O 131 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099851 restraints weight = 32618.789| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.79 r_work: 0.3091 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31814 Z= 0.169 Angle : 0.511 9.445 42512 Z= 0.268 Chirality : 0.033 0.207 4720 Planarity : 0.003 0.026 5456 Dihedral : 3.517 57.275 4284 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.63 % Allowed : 26.18 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.92 (0.12), residues: 3952 helix: 3.43 (0.07), residues: 3696 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 245 TYR 0.035 0.002 TYR B 79 PHE 0.017 0.002 PHE I 77 HIS 0.005 0.001 HIS O 21 Details of bonding type rmsd covalent geometry : bond 0.00388 (31776) covalent geometry : angle 0.51123 (42512) hydrogen bonds : bond 0.06064 ( 3041) hydrogen bonds : angle 3.05378 ( 9123) metal coordination : bond 0.00359 ( 38) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11804.37 seconds wall clock time: 201 minutes 14.10 seconds (12074.10 seconds total)