Starting phenix.real_space_refine on Sun Oct 25 03:24:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/37xd_78594/10_2026/37xd_78594.cif Found real_map, /net/cci-nas-00/data/ceres_data/37xd_78594/10_2026/37xd_78594.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/37xd_78594/10_2026/37xd_78594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/37xd_78594/10_2026/37xd_78594.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/37xd_78594/10_2026/37xd_78594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/37xd_78594/10_2026/37xd_78594.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= -0.001 sd= 0.018 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 10 6.06 5 S 110 5.16 5 C 9530 2.51 5 N 2720 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15200 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "D" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "E" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "F" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "G" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "I" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "J" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1518 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 656 SG CYS A 170 66.641 94.307 48.602 1.00140.24 S ATOM 1225 SG CYS A 241 68.754 91.854 46.627 1.00153.35 S ATOM 2174 SG CYS B 170 35.589 74.361 48.599 1.00142.17 S ATOM 2743 SG CYS B 241 38.577 75.616 46.629 1.00146.57 S ATOM 3692 SG CYS C 170 44.953 38.657 48.595 1.00145.90 S ATOM 4261 SG CYS C 241 44.689 41.888 46.628 1.00153.64 S ATOM 5210 SG CYS D 170 81.808 36.537 48.598 1.00143.79 S ATOM 5779 SG CYS D 241 78.657 37.286 46.627 1.00150.79 S ATOM 6728 SG CYS E 170 95.211 70.929 48.596 1.00140.74 S ATOM 7297 SG CYS E 241 93.523 68.163 46.627 1.00155.46 S ATOM 8246 SG CYS F 170 63.040 94.307 30.322 1.00140.97 S ATOM 8815 SG CYS F 241 60.927 91.853 32.294 1.00154.26 S ATOM 9764 SG CYS G 170 94.092 74.361 30.324 1.00143.97 S ATOM 10333 SG CYS G 241 91.103 75.616 32.292 1.00149.23 S ATOM 11282 SG CYS H 170 84.733 38.651 30.328 1.00145.77 S ATOM 11851 SG CYS H 241 84.999 41.887 32.286 1.00154.85 S ATOM 12800 SG CYS I 170 47.873 36.538 30.324 1.00142.22 S ATOM 13369 SG CYS I 241 51.025 37.286 32.294 1.00152.64 S ATOM 14318 SG CYS J 170 34.470 70.930 30.326 1.00139.33 S ATOM 14887 SG CYS J 241 36.158 68.163 32.295 1.00154.84 S Time building chain proxies: 2.84, per 1000 atoms: 0.19 Number of scatterers: 15200 At special positions: 0 Unit cell: (130.66, 125.02, 79.9, 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 10 29.99 S 110 16.00 O 2830 8.00 N 2720 7.00 C 9530 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: 1.16 Conformation dependent library (CDL) restraints added in 672.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 173 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 241 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 170 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 173 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 241 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 170 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 173 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 241 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 170 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 173 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 170 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 241 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 173 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 170 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 241 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 173 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 241 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 170 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 173 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 241 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 170 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 173 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 241 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 170 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 173 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 241 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 170 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 173 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 241 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 170 " 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 2 sheets defined 53.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 91 through 112 removed outlier: 3.626A pdb=" N GLY A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.882A pdb=" N LEU A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 140 removed outlier: 3.938A pdb=" N TYR A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.529A pdb=" N ARG A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.694A pdb=" N ARG A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 112 removed outlier: 3.627A pdb=" N GLY B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.886A pdb=" N LEU B 121 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 140 removed outlier: 3.935A pdb=" N TYR B 138 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 193 through 206 removed outlier: 3.533A pdb=" N ARG B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.694A pdb=" N ARG B 270 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 112 removed outlier: 3.627A pdb=" N GLY C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.884A pdb=" N LEU C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR C 138 " --> pdb=" O PHE C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 193 through 206 removed outlier: 3.523A pdb=" N ARG C 206 " --> pdb=" O GLU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.696A pdb=" N ARG C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 112 removed outlier: 3.628A pdb=" N GLY D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.884A pdb=" N LEU D 121 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR D 138 " --> pdb=" O PHE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.529A pdb=" N ARG D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 266 through 279 removed outlier: 3.695A pdb=" N ARG D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 112 removed outlier: 3.622A pdb=" N GLY E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.886A pdb=" N LEU E 121 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 140 removed outlier: 3.935A pdb=" N TYR E 138 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 193 through 206 removed outlier: 3.528A pdb=" N ARG E 206 " --> pdb=" O GLU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 Processing helix chain 'E' and resid 262 through 266 Processing helix chain 'E' and resid 266 through 279 removed outlier: 3.694A pdb=" N ARG E 270 " --> pdb=" O GLN E 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 112 removed outlier: 3.627A pdb=" N GLY F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 removed outlier: 3.882A pdb=" N LEU F 121 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR F 138 " --> pdb=" O PHE F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 193 through 206 removed outlier: 3.529A pdb=" N ARG F 206 " --> pdb=" O GLU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 266 through 279 removed outlier: 3.695A pdb=" N ARG F 270 " --> pdb=" O GLN F 266 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 279 " --> pdb=" O THR F 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.628A pdb=" N GLY G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.885A pdb=" N LEU G 121 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR G 138 " --> pdb=" O PHE G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 Processing helix chain 'G' and resid 193 through 206 removed outlier: 3.526A pdb=" N ARG G 206 " --> pdb=" O GLU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 226 Processing helix chain 'G' and resid 262 through 266 Processing helix chain 'G' and resid 266 through 279 removed outlier: 3.692A pdb=" N ARG G 270 " --> pdb=" O GLN G 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG G 279 " --> pdb=" O THR G 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 112 removed outlier: 3.623A pdb=" N GLY H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 121 removed outlier: 3.884A pdb=" N LEU H 121 " --> pdb=" O GLU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR H 138 " --> pdb=" O PHE H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 Processing helix chain 'H' and resid 193 through 206 removed outlier: 3.523A pdb=" N ARG H 206 " --> pdb=" O GLU H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 266 through 279 removed outlier: 3.695A pdb=" N ARG H 270 " --> pdb=" O GLN H 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 279 " --> pdb=" O THR H 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 112 removed outlier: 3.628A pdb=" N GLY I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 121 removed outlier: 3.883A pdb=" N LEU I 121 " --> pdb=" O GLU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 147 Processing helix chain 'I' and resid 193 through 206 removed outlier: 3.523A pdb=" N ARG I 206 " --> pdb=" O GLU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 Processing helix chain 'I' and resid 262 through 266 Processing helix chain 'I' and resid 266 through 279 removed outlier: 3.695A pdb=" N ARG I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG I 279 " --> pdb=" O THR I 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 112 removed outlier: 3.626A pdb=" N GLY J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 121 removed outlier: 3.885A pdb=" N LEU J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 140 removed outlier: 3.936A pdb=" N TYR J 138 " --> pdb=" O PHE J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 147 Processing helix chain 'J' and resid 193 through 206 removed outlier: 3.532A pdb=" N ARG J 206 " --> pdb=" O GLU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 Processing helix chain 'J' and resid 262 through 266 Processing helix chain 'J' and resid 266 through 279 removed outlier: 3.694A pdb=" N ARG J 270 " --> pdb=" O GLN J 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG J 279 " --> pdb=" O THR J 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 169 removed outlier: 5.132A pdb=" N ILE A 160 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR A 185 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG A 162 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A 183 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 179 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE A 178 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY A 230 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET E 158 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE E 160 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR E 185 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG E 162 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE E 183 " --> pdb=" O ARG E 162 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY E 179 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE E 178 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY E 230 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 158 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE D 160 " --> pdb=" O TYR D 185 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR D 185 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG D 162 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE D 183 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 179 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE D 178 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY D 230 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET C 158 " --> pdb=" O SER D 257 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE C 160 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR C 185 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG C 162 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 183 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 179 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 178 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 230 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 158 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE B 160 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR B 185 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG B 162 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 183 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 179 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 178 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY B 230 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 158 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 158 through 169 removed outlier: 5.134A pdb=" N ILE F 160 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR F 185 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG F 162 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE F 183 " --> pdb=" O ARG F 162 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY F 179 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE F 178 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY F 230 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET J 158 " --> pdb=" O SER F 257 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE J 160 " --> pdb=" O TYR J 185 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR J 185 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG J 162 " --> pdb=" O ILE J 183 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE J 183 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY J 179 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE J 178 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY J 230 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET I 158 " --> pdb=" O SER J 257 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE I 160 " --> pdb=" O TYR I 185 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR I 185 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG I 162 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE I 183 " --> pdb=" O ARG I 162 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY I 179 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE I 178 " --> pdb=" O THR I 238 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY I 230 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET H 158 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE H 160 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR H 185 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG H 162 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE H 183 " --> pdb=" O ARG H 162 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY H 179 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE H 178 " --> pdb=" O THR H 238 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY H 230 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET G 158 " --> pdb=" O SER H 257 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE G 160 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR G 185 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG G 162 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE G 183 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY G 179 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE G 178 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY G 230 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET F 158 " --> pdb=" O SER G 257 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2583 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: 2.10 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4384 1.33 - 1.45: 2158 1.45 - 1.57: 8668 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 15390 Sorted by residual: bond pdb=" C ALA D 128 " pdb=" N ARG D 129 " ideal model delta sigma weight residual 1.334 1.417 -0.082 1.33e-02 5.65e+03 3.82e+01 bond pdb=" C ALA J 128 " pdb=" N ARG J 129 " ideal model delta sigma weight residual 1.334 1.416 -0.082 1.33e-02 5.65e+03 3.81e+01 bond pdb=" C ALA E 128 " pdb=" N ARG E 129 " ideal model delta sigma weight residual 1.334 1.416 -0.082 1.33e-02 5.65e+03 3.81e+01 bond pdb=" C ALA F 128 " pdb=" N ARG F 129 " ideal model delta sigma weight residual 1.334 1.416 -0.082 1.33e-02 5.65e+03 3.79e+01 bond pdb=" C ALA H 128 " pdb=" N ARG H 129 " ideal model delta sigma weight residual 1.334 1.416 -0.082 1.33e-02 5.65e+03 3.79e+01 ... (remaining 15385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20138 2.01 - 4.01: 396 4.01 - 6.02: 85 6.02 - 8.03: 2 8.03 - 10.03: 29 Bond angle restraints: 20650 Sorted by residual: angle pdb=" N TYR A 127 " pdb=" CA TYR A 127 " pdb=" C TYR A 127 " ideal model delta sigma weight residual 111.75 105.44 6.31 1.28e+00 6.10e-01 2.43e+01 angle pdb=" C PHE J 134 " pdb=" N THR J 135 " pdb=" CA THR J 135 " ideal model delta sigma weight residual 122.79 114.50 8.29 1.70e+00 3.46e-01 2.38e+01 angle pdb=" C PHE H 134 " pdb=" N THR H 135 " pdb=" CA THR H 135 " ideal model delta sigma weight residual 122.79 114.51 8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" C PHE A 134 " pdb=" N THR A 135 " pdb=" CA THR A 135 " ideal model delta sigma weight residual 122.79 114.53 8.26 1.70e+00 3.46e-01 2.36e+01 angle pdb=" C PHE F 134 " pdb=" N THR F 135 " pdb=" CA THR F 135 " ideal model delta sigma weight residual 122.79 114.53 8.26 1.70e+00 3.46e-01 2.36e+01 ... (remaining 20645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8430 17.52 - 35.04: 860 35.04 - 52.56: 250 52.56 - 70.08: 10 70.08 - 87.60: 10 Dihedral angle restraints: 9560 sinusoidal: 4040 harmonic: 5520 Sorted by residual: dihedral pdb=" CA LEU D 132 " pdb=" CB LEU D 132 " pdb=" CG LEU D 132 " pdb=" CD1 LEU D 132 " ideal model delta sinusoidal sigma weight residual 60.00 0.67 59.33 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU G 132 " pdb=" CB LEU G 132 " pdb=" CG LEU G 132 " pdb=" CD1 LEU G 132 " ideal model delta sinusoidal sigma weight residual 60.00 0.67 59.33 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU E 132 " pdb=" CB LEU E 132 " pdb=" CG LEU E 132 " pdb=" CD1 LEU E 132 " ideal model delta sinusoidal sigma weight residual 60.00 0.68 59.32 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1755 0.050 - 0.099: 429 0.099 - 0.149: 126 0.149 - 0.198: 10 0.198 - 0.248: 20 Chirality restraints: 2340 Sorted by residual: chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU E 197 " pdb=" CB LEU E 197 " pdb=" CD1 LEU E 197 " pdb=" CD2 LEU E 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU F 197 " pdb=" CB LEU F 197 " pdb=" CD1 LEU F 197 " pdb=" CD2 LEU F 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2337 not shown) Planarity restraints: 2650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 126 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ARG A 126 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG A 126 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR A 127 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 128 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C ALA B 128 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA B 128 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 128 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.45e+00 pdb=" C ALA D 128 " 0.027 2.00e-02 2.50e+03 pdb=" O ALA D 128 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG D 129 " -0.009 2.00e-02 2.50e+03 ... (remaining 2647 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 51 2.62 - 3.19: 13151 3.19 - 3.76: 24226 3.76 - 4.33: 32759 4.33 - 4.90: 53991 Nonbonded interactions: 124178 Sorted by model distance: nonbonded pdb="ZN ZN E 301 " pdb=" O HOH E 401 " model vdw 2.049 2.230 nonbonded pdb="ZN ZN H 301 " pdb=" O HOH H 401 " model vdw 2.049 2.230 nonbonded pdb="ZN ZN I 301 " pdb=" O HOH I 401 " model vdw 2.049 2.230 nonbonded pdb="ZN ZN F 301 " pdb=" O HOH F 401 " model vdw 2.050 2.230 nonbonded pdb="ZN ZN J 301 " pdb=" O HOH J 401 " model vdw 2.050 2.230 ... (remaining 124173 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.530 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.007 0.210 15420 Z= 0.334 Angle : 0.740 10.033 20650 Z= 0.404 Chirality : 0.051 0.248 2340 Planarity : 0.003 0.034 2650 Dihedral : 15.032 87.600 5980 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.61 % Allowed : 7.74 % Favored : 91.65 % 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: -1.34 (0.19), residues: 1870 helix: 0.02 (0.17), residues: 890 sheet: -1.50 (0.26), residues: 460 loop : -1.59 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 213 TYR 0.007 0.001 TYR H 133 PHE 0.015 0.002 PHE E 134 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.28 (15390) covalent geometry : angle 0.73964 / 0.40 (20650) hydrogen bonds : bond 0.18489 / 12.12 ( 881) hydrogen bonds : angle 7.92503 / 5.61 ( 2583) metal coordination : bond 0.12206 / 7.83 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 527 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7177 (tptt) REVERT: A 109 GLU cc_start: 0.8485 (tt0) cc_final: 0.8152 (mm-30) REVERT: A 127 TYR cc_start: 0.8059 (t80) cc_final: 0.7839 (t80) REVERT: A 189 LYS cc_start: 0.8277 (tmmt) cc_final: 0.7989 (tmmt) REVERT: A 266 GLN cc_start: 0.7767 (mp10) cc_final: 0.7487 (mp10) REVERT: B 105 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7025 (mmtt) REVERT: B 109 GLU cc_start: 0.8445 (tt0) cc_final: 0.8055 (mm-30) REVERT: B 152 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7488 (mp0) REVERT: B 189 LYS cc_start: 0.8289 (tmmt) cc_final: 0.7740 (tmmt) REVERT: B 271 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8302 (tp30) REVERT: C 105 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7096 (mmtt) REVERT: C 109 GLU cc_start: 0.8481 (tt0) cc_final: 0.8053 (mm-30) REVERT: C 152 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7728 (mp0) REVERT: C 189 LYS cc_start: 0.8326 (tmmt) cc_final: 0.7919 (tmmt) REVERT: C 212 GLU cc_start: 0.8085 (pm20) cc_final: 0.7826 (pm20) REVERT: D 105 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7064 (mmtt) REVERT: D 109 GLU cc_start: 0.8453 (tt0) cc_final: 0.8202 (mm-30) REVERT: D 152 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7672 (mp0) REVERT: D 189 LYS cc_start: 0.8281 (tmmt) cc_final: 0.7838 (tmmt) REVERT: D 212 GLU cc_start: 0.8042 (pm20) cc_final: 0.7756 (pm20) REVERT: E 105 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7191 (tptt) REVERT: E 109 GLU cc_start: 0.8591 (tt0) cc_final: 0.8210 (mm-30) REVERT: E 152 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7565 (mp0) REVERT: E 189 LYS cc_start: 0.8319 (tmmt) cc_final: 0.7819 (tmmt) REVERT: E 266 GLN cc_start: 0.7782 (mp10) cc_final: 0.7551 (mp10) REVERT: E 271 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8335 (tp30) REVERT: F 105 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7243 (tptt) REVERT: F 109 GLU cc_start: 0.8556 (tt0) cc_final: 0.8258 (mm-30) REVERT: F 152 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7611 (mp0) REVERT: F 189 LYS cc_start: 0.8302 (tmmt) cc_final: 0.7726 (tmmt) REVERT: F 266 GLN cc_start: 0.7758 (mp10) cc_final: 0.7405 (mp10) REVERT: F 267 GLN cc_start: 0.7644 (mp10) cc_final: 0.7344 (mp10) REVERT: G 105 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7188 (mmtt) REVERT: G 109 GLU cc_start: 0.8460 (tt0) cc_final: 0.8119 (mm-30) REVERT: G 127 TYR cc_start: 0.7711 (t80) cc_final: 0.7505 (t80) REVERT: G 189 LYS cc_start: 0.8348 (tmmt) cc_final: 0.8027 (tmmt) REVERT: G 215 THR cc_start: 0.8683 (m) cc_final: 0.8443 (p) REVERT: G 266 GLN cc_start: 0.7741 (mp10) cc_final: 0.7504 (mp10) REVERT: H 105 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7266 (mmtt) REVERT: H 109 GLU cc_start: 0.8421 (tt0) cc_final: 0.8073 (mm-30) REVERT: H 152 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7756 (mp0) REVERT: H 189 LYS cc_start: 0.8382 (tmmt) cc_final: 0.7974 (tmmt) REVERT: H 212 GLU cc_start: 0.8011 (pm20) cc_final: 0.7754 (pm20) REVERT: I 105 LYS cc_start: 0.7948 (mmmm) cc_final: 0.7090 (mmtt) REVERT: I 109 GLU cc_start: 0.8481 (tt0) cc_final: 0.8210 (mm-30) REVERT: I 152 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7669 (mp0) REVERT: I 189 LYS cc_start: 0.8243 (tmmt) cc_final: 0.7825 (tmmt) REVERT: I 271 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8408 (tp30) REVERT: J 105 LYS cc_start: 0.8166 (mmmm) cc_final: 0.7247 (mmtt) REVERT: J 109 GLU cc_start: 0.8559 (tt0) cc_final: 0.8191 (mm-30) REVERT: J 152 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7650 (mp0) REVERT: J 189 LYS cc_start: 0.8275 (tmmt) cc_final: 0.7780 (tmmt) REVERT: J 271 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8379 (tp30) outliers start: 10 outliers final: 8 residues processed: 528 average time/residue: 0.5919 time to fit residues: 342.3748 Evaluate side-chains 378 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 370 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain J residue 132 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 GLN B 209 GLN C 209 GLN D 209 GLN E 209 GLN F 209 GLN G 209 GLN H 209 GLN I 209 GLN J 209 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.140608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.110720 restraints weight = 23255.077| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.52 r_work: 0.3519 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15420 Z= 0.206 Angle : 0.697 7.688 20650 Z= 0.354 Chirality : 0.047 0.214 2340 Planarity : 0.003 0.027 2650 Dihedral : 5.884 59.248 2136 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.54 % Allowed : 22.26 % Favored : 74.21 % 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: -0.90 (0.19), residues: 1870 helix: 0.63 (0.17), residues: 890 sheet: -1.28 (0.25), residues: 460 loop : -1.88 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 117 TYR 0.015 0.002 TYR I 138 PHE 0.017 0.002 PHE E 151 HIS 0.008 0.001 HIS H 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (15390) covalent geometry : angle 0.69696 / 0.35 (20650) hydrogen bonds : bond 0.04035 / 2.72 ( 881) hydrogen bonds : angle 4.87663 / 3.42 ( 2583) metal coordination : bond 0.00430 / 0.27 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 404 time to evaluate : 0.511 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 105 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7241 (mmtt) REVERT: A 109 GLU cc_start: 0.8515 (tt0) cc_final: 0.8175 (mm-30) REVERT: A 152 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7943 (mt-10) REVERT: A 189 LYS cc_start: 0.8385 (tmmt) cc_final: 0.7597 (tptp) REVERT: A 203 MET cc_start: 0.8833 (tmt) cc_final: 0.8616 (tmm) REVERT: A 212 GLU cc_start: 0.8234 (pm20) cc_final: 0.7885 (pm20) REVERT: B 105 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7219 (mmtt) REVERT: B 109 GLU cc_start: 0.8539 (tt0) cc_final: 0.8175 (mm-30) REVERT: B 152 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7565 (mp0) REVERT: B 189 LYS cc_start: 0.8475 (tmmt) cc_final: 0.8017 (tmmt) REVERT: C 105 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7326 (mmtt) REVERT: C 109 GLU cc_start: 0.8563 (tt0) cc_final: 0.8173 (mm-30) REVERT: C 138 TYR cc_start: 0.7315 (t80) cc_final: 0.7063 (t80) REVERT: C 152 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7712 (mp0) REVERT: C 155 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7237 (m90) REVERT: C 189 LYS cc_start: 0.8373 (tmmt) cc_final: 0.7882 (tmmt) REVERT: C 212 GLU cc_start: 0.8255 (pm20) cc_final: 0.7990 (pm20) REVERT: D 105 LYS cc_start: 0.8032 (mmmm) cc_final: 0.7201 (mmtt) REVERT: D 109 GLU cc_start: 0.8471 (tt0) cc_final: 0.8201 (mm-30) REVERT: D 152 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7735 (mp0) REVERT: D 171 GLU cc_start: 0.7990 (pt0) cc_final: 0.7781 (pt0) REVERT: D 189 LYS cc_start: 0.8455 (tmmt) cc_final: 0.7982 (tmmt) REVERT: D 220 MET cc_start: 0.8851 (mmm) cc_final: 0.8509 (mmm) REVERT: D 227 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7809 (mmmt) REVERT: E 105 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7371 (mmtt) REVERT: E 109 GLU cc_start: 0.8566 (tt0) cc_final: 0.8171 (mm-30) REVERT: E 152 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7577 (mp0) REVERT: E 189 LYS cc_start: 0.8470 (tmmt) cc_final: 0.8076 (tmtt) REVERT: E 227 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7852 (mmmt) REVERT: F 105 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7222 (mmtt) REVERT: F 109 GLU cc_start: 0.8595 (tt0) cc_final: 0.8213 (mm-30) REVERT: F 189 LYS cc_start: 0.8401 (tmmt) cc_final: 0.8077 (tmmt) REVERT: F 266 GLN cc_start: 0.7542 (mp10) cc_final: 0.7321 (mp10) REVERT: F 267 GLN cc_start: 0.7863 (mp10) cc_final: 0.7583 (mp10) REVERT: G 105 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7239 (mmtt) REVERT: G 109 GLU cc_start: 0.8545 (tt0) cc_final: 0.8172 (mm-30) REVERT: G 152 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7570 (mp0) REVERT: G 155 HIS cc_start: 0.7297 (m90) cc_final: 0.7091 (m90) REVERT: G 189 LYS cc_start: 0.8538 (tmmt) cc_final: 0.8109 (tmmt) REVERT: G 265 ASP cc_start: 0.8912 (m-30) cc_final: 0.8699 (m-30) REVERT: H 105 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7355 (mmtt) REVERT: H 109 GLU cc_start: 0.8550 (tt0) cc_final: 0.8186 (mm-30) REVERT: H 138 TYR cc_start: 0.7377 (t80) cc_final: 0.7095 (t80) REVERT: H 152 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7710 (mp0) REVERT: H 189 LYS cc_start: 0.8399 (tmmt) cc_final: 0.7964 (tmmt) REVERT: H 191 VAL cc_start: 0.8936 (t) cc_final: 0.8633 (p) REVERT: H 212 GLU cc_start: 0.8254 (pm20) cc_final: 0.7976 (pm20) REVERT: I 105 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7272 (mmtt) REVERT: I 109 GLU cc_start: 0.8483 (tt0) cc_final: 0.8221 (mm-30) REVERT: I 152 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7744 (mp0) REVERT: I 171 GLU cc_start: 0.8022 (pt0) cc_final: 0.7770 (pt0) REVERT: I 189 LYS cc_start: 0.8432 (tmmt) cc_final: 0.7935 (tmmt) REVERT: I 220 MET cc_start: 0.8866 (mmm) cc_final: 0.8543 (mmm) REVERT: J 105 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7387 (mmtt) REVERT: J 109 GLU cc_start: 0.8581 (tt0) cc_final: 0.8184 (mm-30) REVERT: J 152 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7627 (mp0) REVERT: J 155 HIS cc_start: 0.7279 (m90) cc_final: 0.7023 (m90) REVERT: J 189 LYS cc_start: 0.8460 (tmmt) cc_final: 0.8040 (tmtt) REVERT: J 265 ASP cc_start: 0.8804 (m-30) cc_final: 0.8603 (m-30) outliers start: 58 outliers final: 7 residues processed: 430 average time/residue: 0.5775 time to fit residues: 271.8852 Evaluate side-chains 359 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 349 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 216 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [74, 172, 46, 79, 160, 111, 144, 67, 1, 73, 59] chunk 74 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN H 266 GLN ** I 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 GLN ** J 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.143950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114856 restraints weight = 22969.988| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.49 r_work: 0.3593 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15420 Z= 0.127 Angle : 0.611 8.019 20650 Z= 0.309 Chirality : 0.045 0.216 2340 Planarity : 0.003 0.020 2650 Dihedral : 4.263 13.575 2120 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.96 % Allowed : 27.07 % Favored : 68.96 % 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: -0.71 (0.19), residues: 1870 helix: 0.84 (0.17), residues: 890 sheet: -1.21 (0.24), residues: 460 loop : -1.91 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 213 TYR 0.019 0.002 TYR G 127 PHE 0.010 0.001 PHE J 177 HIS 0.007 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15390) covalent geometry : angle 0.61056 / 0.31 (20650) hydrogen bonds : bond 0.03255 / 2.22 ( 881) hydrogen bonds : angle 4.31254 / 3.02 ( 2583) metal coordination : bond 0.00118 / 0.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 387 time to evaluate : 0.612 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 105 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7226 (mmtt) REVERT: A 109 GLU cc_start: 0.8488 (tt0) cc_final: 0.8192 (mm-30) REVERT: A 138 TYR cc_start: 0.7221 (t80) cc_final: 0.7012 (t80) REVERT: A 152 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7666 (mp0) REVERT: A 189 LYS cc_start: 0.8458 (tmmt) cc_final: 0.7835 (tmmt) REVERT: A 212 GLU cc_start: 0.8138 (pm20) cc_final: 0.7936 (pm20) REVERT: A 240 MET cc_start: 0.7394 (tmm) cc_final: 0.7130 (tmm) REVERT: B 105 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7095 (mmtt) REVERT: B 109 GLU cc_start: 0.8497 (tt0) cc_final: 0.8118 (mm-30) REVERT: B 152 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7570 (mp0) REVERT: B 189 LYS cc_start: 0.8548 (tmmt) cc_final: 0.8100 (tmmt) REVERT: B 227 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7815 (mmmt) REVERT: B 240 MET cc_start: 0.7477 (tmm) cc_final: 0.6791 (tmm) REVERT: B 267 GLN cc_start: 0.8004 (mp10) cc_final: 0.7784 (mp10) REVERT: C 105 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7259 (mmtt) REVERT: C 109 GLU cc_start: 0.8588 (tt0) cc_final: 0.8211 (mm-30) REVERT: C 138 TYR cc_start: 0.7290 (t80) cc_final: 0.7064 (t80) REVERT: C 152 GLU cc_start: 0.8645 (mt-10) cc_final: 0.7798 (mp0) REVERT: C 189 LYS cc_start: 0.8454 (tmmt) cc_final: 0.8022 (tmmt) REVERT: D 105 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7170 (mmtt) REVERT: D 109 GLU cc_start: 0.8491 (tt0) cc_final: 0.8219 (mm-30) REVERT: D 152 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7764 (mp0) REVERT: D 171 GLU cc_start: 0.8077 (pt0) cc_final: 0.7841 (pt0) REVERT: D 189 LYS cc_start: 0.8528 (tmmt) cc_final: 0.8016 (tmmt) REVERT: D 220 MET cc_start: 0.8820 (mmm) cc_final: 0.8491 (mmm) REVERT: D 227 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7679 (mmmt) REVERT: D 240 MET cc_start: 0.7519 (tmm) cc_final: 0.6774 (tmm) REVERT: E 105 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7294 (mmtt) REVERT: E 109 GLU cc_start: 0.8583 (tt0) cc_final: 0.8214 (mm-30) REVERT: E 152 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7640 (mp0) REVERT: E 189 LYS cc_start: 0.8478 (tmmt) cc_final: 0.8016 (tmmt) REVERT: E 227 LYS cc_start: 0.8096 (mmpt) cc_final: 0.7817 (mmmt) REVERT: E 240 MET cc_start: 0.7527 (tmm) cc_final: 0.7017 (tmm) REVERT: E 265 ASP cc_start: 0.8801 (m-30) cc_final: 0.8401 (m-30) REVERT: E 267 GLN cc_start: 0.7905 (mp10) cc_final: 0.7546 (mp10) REVERT: F 105 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7212 (mmtt) REVERT: F 109 GLU cc_start: 0.8583 (tt0) cc_final: 0.8214 (mm-30) REVERT: F 189 LYS cc_start: 0.8473 (tmmt) cc_final: 0.8127 (tmmt) REVERT: F 212 GLU cc_start: 0.8210 (pm20) cc_final: 0.7961 (pm20) REVERT: F 227 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7803 (mmmt) REVERT: F 267 GLN cc_start: 0.7854 (mp10) cc_final: 0.7569 (mp10) REVERT: G 105 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7115 (mmtt) REVERT: G 109 GLU cc_start: 0.8537 (tt0) cc_final: 0.8179 (mm-30) REVERT: G 152 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7509 (mp0) REVERT: G 155 HIS cc_start: 0.7418 (m90) cc_final: 0.7127 (m90) REVERT: G 189 LYS cc_start: 0.8572 (tmmt) cc_final: 0.8059 (tmmt) REVERT: H 105 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7309 (mmtt) REVERT: H 109 GLU cc_start: 0.8580 (tt0) cc_final: 0.8214 (mm-30) REVERT: H 152 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7793 (mp0) REVERT: H 189 LYS cc_start: 0.8544 (tmmt) cc_final: 0.8076 (tmmt) REVERT: H 212 GLU cc_start: 0.8197 (pm20) cc_final: 0.7922 (pm20) REVERT: H 240 MET cc_start: 0.7229 (tmm) cc_final: 0.6946 (OUTLIER) REVERT: I 105 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7348 (mmtm) REVERT: I 109 GLU cc_start: 0.8533 (tt0) cc_final: 0.8256 (mm-30) REVERT: I 138 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.7117 (t80) REVERT: I 152 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7711 (mp0) REVERT: I 171 GLU cc_start: 0.8092 (pt0) cc_final: 0.7847 (pt0) REVERT: I 189 LYS cc_start: 0.8519 (tmmt) cc_final: 0.7966 (tmmt) REVERT: I 220 MET cc_start: 0.8849 (mmm) cc_final: 0.8513 (mmm) REVERT: J 105 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7331 (mmtt) REVERT: J 109 GLU cc_start: 0.8542 (tt0) cc_final: 0.8189 (mm-30) REVERT: J 152 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7635 (mp0) REVERT: J 155 HIS cc_start: 0.7287 (m90) cc_final: 0.6948 (m90) REVERT: J 189 LYS cc_start: 0.8422 (tmmt) cc_final: 0.7923 (tmmt) REVERT: J 227 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7907 (mmmt) REVERT: J 240 MET cc_start: 0.7371 (tmm) cc_final: 0.6961 (tmm) outliers start: 65 outliers final: 29 residues processed: 424 average time/residue: 0.5185 time to fit residues: 243.2676 Evaluate side-chains 379 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 349 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [148, 117, 42, 11, 54, 53, 162, 165, 71, 83, 78] chunk 148 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 GLN ** I 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114206 restraints weight = 23160.300| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.53 r_work: 0.3568 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15420 Z= 0.131 Angle : 0.614 9.703 20650 Z= 0.308 Chirality : 0.046 0.196 2340 Planarity : 0.003 0.022 2650 Dihedral : 4.245 13.390 2120 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.24 % Allowed : 27.13 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1870 helix: 0.93 (0.17), residues: 890 sheet: -1.18 (0.24), residues: 460 loop : -1.92 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 213 TYR 0.022 0.002 TYR F 127 PHE 0.011 0.001 PHE J 177 HIS 0.002 0.001 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15390) covalent geometry : angle 0.61356 / 0.31 (20650) hydrogen bonds : bond 0.03144 / 2.15 ( 881) hydrogen bonds : angle 4.17962 / 2.92 ( 2583) metal coordination : bond 0.00187 / 0.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 377 time to evaluate : 0.597 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 105 LYS cc_start: 0.7954 (mmmm) cc_final: 0.7137 (mmtm) REVERT: A 109 GLU cc_start: 0.8495 (tt0) cc_final: 0.8111 (mm-30) REVERT: A 152 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7697 (mp0) REVERT: A 189 LYS cc_start: 0.8522 (tmmt) cc_final: 0.7997 (tmmt) REVERT: A 212 GLU cc_start: 0.8177 (pm20) cc_final: 0.7966 (pm20) REVERT: B 105 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7033 (mmtt) REVERT: B 109 GLU cc_start: 0.8505 (tt0) cc_final: 0.8132 (mm-30) REVERT: B 152 GLU cc_start: 0.8533 (mt-10) cc_final: 0.7543 (mp0) REVERT: B 189 LYS cc_start: 0.8631 (tmmt) cc_final: 0.8147 (tmmt) REVERT: B 240 MET cc_start: 0.7457 (tmm) cc_final: 0.6668 (tmm) REVERT: B 271 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8568 (tp30) REVERT: C 105 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7247 (mmtt) REVERT: C 109 GLU cc_start: 0.8578 (tt0) cc_final: 0.8205 (mm-30) REVERT: C 152 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7782 (mp0) REVERT: C 189 LYS cc_start: 0.8520 (tmmt) cc_final: 0.8054 (tmmt) REVERT: C 240 MET cc_start: 0.7437 (tmm) cc_final: 0.7115 (tmm) REVERT: C 242 MET cc_start: 0.6656 (tpt) cc_final: 0.6433 (tpt) REVERT: D 105 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7167 (mmtt) REVERT: D 109 GLU cc_start: 0.8519 (tt0) cc_final: 0.8246 (mm-30) REVERT: D 152 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7773 (mp0) REVERT: D 171 GLU cc_start: 0.8053 (pt0) cc_final: 0.7832 (pt0) REVERT: D 189 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8171 (tmtt) REVERT: D 220 MET cc_start: 0.8827 (mmm) cc_final: 0.8484 (mmm) REVERT: D 227 LYS cc_start: 0.7987 (mmpt) cc_final: 0.7729 (mmmt) REVERT: D 240 MET cc_start: 0.7450 (tmm) cc_final: 0.6689 (tmm) REVERT: E 105 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7244 (mmtt) REVERT: E 109 GLU cc_start: 0.8527 (tt0) cc_final: 0.8142 (mm-30) REVERT: E 138 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6684 (t80) REVERT: E 152 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7666 (mp0) REVERT: E 189 LYS cc_start: 0.8527 (tmmt) cc_final: 0.8074 (tmtt) REVERT: E 227 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7779 (mmmt) REVERT: E 240 MET cc_start: 0.7501 (tmm) cc_final: 0.7197 (tmm) REVERT: E 265 ASP cc_start: 0.8836 (m-30) cc_final: 0.8318 (m-30) REVERT: E 267 GLN cc_start: 0.7974 (mp10) cc_final: 0.7606 (mp10) REVERT: F 105 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7221 (mmtm) REVERT: F 109 GLU cc_start: 0.8568 (tt0) cc_final: 0.8206 (mm-30) REVERT: F 189 LYS cc_start: 0.8514 (tmmt) cc_final: 0.8212 (tmmt) REVERT: F 212 GLU cc_start: 0.8214 (pm20) cc_final: 0.7960 (pm20) REVERT: F 227 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7823 (mmmt) REVERT: F 267 GLN cc_start: 0.7915 (mp10) cc_final: 0.7603 (mp10) REVERT: G 105 LYS cc_start: 0.7887 (mmmm) cc_final: 0.7095 (mmtt) REVERT: G 109 GLU cc_start: 0.8540 (tt0) cc_final: 0.8184 (mm-30) REVERT: G 132 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8009 (mm) REVERT: G 152 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7590 (mp0) REVERT: G 155 HIS cc_start: 0.7478 (m90) cc_final: 0.7156 (m90) REVERT: G 189 LYS cc_start: 0.8603 (tmmt) cc_final: 0.8041 (tmmt) REVERT: H 105 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7347 (mmtt) REVERT: H 109 GLU cc_start: 0.8565 (tt0) cc_final: 0.8200 (mm-30) REVERT: H 138 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6380 (t80) REVERT: H 152 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7787 (mp0) REVERT: H 189 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8142 (tmmt) REVERT: H 212 GLU cc_start: 0.8216 (pm20) cc_final: 0.7938 (pm20) REVERT: H 227 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7674 (mmmt) REVERT: H 240 MET cc_start: 0.7055 (tmm) cc_final: 0.6705 (tmm) REVERT: I 105 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7273 (mmtt) REVERT: I 109 GLU cc_start: 0.8538 (tt0) cc_final: 0.8259 (mm-30) REVERT: I 152 GLU cc_start: 0.8613 (mt-10) cc_final: 0.7764 (mp0) REVERT: I 171 GLU cc_start: 0.8005 (pt0) cc_final: 0.7745 (pt0) REVERT: I 189 LYS cc_start: 0.8607 (tmmt) cc_final: 0.8109 (tmmt) REVERT: I 220 MET cc_start: 0.8826 (mmm) cc_final: 0.8521 (mmm) REVERT: J 105 LYS cc_start: 0.8079 (mmmm) cc_final: 0.7274 (mmtt) REVERT: J 109 GLU cc_start: 0.8544 (tt0) cc_final: 0.8158 (mm-30) REVERT: J 138 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6815 (t80) REVERT: J 152 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7682 (mp0) REVERT: J 155 HIS cc_start: 0.7245 (m90) cc_final: 0.6885 (m90) REVERT: J 189 LYS cc_start: 0.8442 (tmmt) cc_final: 0.8020 (tmmt) REVERT: J 240 MET cc_start: 0.7294 (tmm) cc_final: 0.6731 (tmm) outliers start: 86 outliers final: 28 residues processed: 421 average time/residue: 0.5149 time to fit residues: 240.5253 Evaluate side-chains 373 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 340 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 155 HIS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 216 LYS Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain H residue 138 TYR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [70, 63, 113, 132, 43, 13, 73, 174, 67, 111, 88] chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 0.0570 chunk 132 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 0.0270 chunk 88 optimal weight: 9.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN F 266 GLN ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN ** I 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 GLN ** J 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.146217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116404 restraints weight = 23391.893| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.59 r_work: 0.3626 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15420 Z= 0.114 Angle : 0.621 9.926 20650 Z= 0.307 Chirality : 0.046 0.173 2340 Planarity : 0.003 0.021 2650 Dihedral : 4.257 15.576 2120 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.51 % Allowed : 29.27 % Favored : 66.22 % 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: -0.69 (0.19), residues: 1870 helix: 0.91 (0.17), residues: 890 sheet: -1.13 (0.23), residues: 460 loop : -2.09 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 213 TYR 0.017 0.001 TYR F 127 PHE 0.010 0.001 PHE D 177 HIS 0.002 0.000 HIS B 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15390) covalent geometry : angle 0.62074 / 0.31 (20650) hydrogen bonds : bond 0.02904 / 1.99 ( 881) hydrogen bonds : angle 4.05560 / 2.83 ( 2583) metal coordination : bond 0.00069 / 0.04 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 386 time to evaluate : 0.552 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 105 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7142 (tptt) REVERT: A 109 GLU cc_start: 0.8465 (tt0) cc_final: 0.8113 (mm-30) REVERT: A 152 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7661 (mp0) REVERT: A 158 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6354 (ttp) REVERT: A 189 LYS cc_start: 0.8524 (tmmt) cc_final: 0.7928 (tmmt) REVERT: A 212 GLU cc_start: 0.8166 (pm20) cc_final: 0.7927 (pm20) REVERT: B 105 LYS cc_start: 0.7884 (mmmm) cc_final: 0.7015 (mmtm) REVERT: B 109 GLU cc_start: 0.8477 (tt0) cc_final: 0.8109 (mm-30) REVERT: B 152 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7543 (mp0) REVERT: B 189 LYS cc_start: 0.8591 (tmmt) cc_final: 0.8065 (tmmt) REVERT: B 227 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7535 (mmmt) REVERT: B 240 MET cc_start: 0.7396 (tmm) cc_final: 0.6670 (tmm) REVERT: C 105 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7125 (mmtt) REVERT: C 109 GLU cc_start: 0.8598 (tt0) cc_final: 0.8210 (mm-30) REVERT: C 138 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6625 (t80) REVERT: C 152 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7737 (mp0) REVERT: C 189 LYS cc_start: 0.8550 (tmmt) cc_final: 0.8113 (tmmt) REVERT: C 240 MET cc_start: 0.7198 (tmm) cc_final: 0.6803 (tmm) REVERT: D 105 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7109 (mmtt) REVERT: D 109 GLU cc_start: 0.8513 (tt0) cc_final: 0.8251 (mm-30) REVERT: D 152 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7692 (mp0) REVERT: D 189 LYS cc_start: 0.8588 (tmmt) cc_final: 0.8099 (tmtt) REVERT: D 220 MET cc_start: 0.8785 (mmm) cc_final: 0.8451 (mmm) REVERT: D 227 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7768 (mmmt) REVERT: D 240 MET cc_start: 0.7396 (tmm) cc_final: 0.6633 (tmm) REVERT: D 242 MET cc_start: 0.6442 (tpt) cc_final: 0.6159 (mmm) REVERT: E 105 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7097 (mmtt) REVERT: E 109 GLU cc_start: 0.8606 (tt0) cc_final: 0.8207 (mm-30) REVERT: E 138 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6859 (t80) REVERT: E 152 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7662 (mp0) REVERT: E 189 LYS cc_start: 0.8519 (tmmt) cc_final: 0.8023 (tmmt) REVERT: E 227 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7710 (mmmt) REVERT: E 240 MET cc_start: 0.7252 (tmm) cc_final: 0.6906 (tmm) REVERT: F 105 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7118 (mmtm) REVERT: F 109 GLU cc_start: 0.8550 (tt0) cc_final: 0.8223 (mm-30) REVERT: F 189 LYS cc_start: 0.8534 (tmmt) cc_final: 0.8217 (tmmt) REVERT: F 212 GLU cc_start: 0.8227 (pm20) cc_final: 0.7947 (pm20) REVERT: F 267 GLN cc_start: 0.7895 (mp10) cc_final: 0.7583 (mp10) REVERT: G 105 LYS cc_start: 0.7843 (mmmm) cc_final: 0.6913 (mmtt) REVERT: G 109 GLU cc_start: 0.8513 (tt0) cc_final: 0.8156 (mm-30) REVERT: G 132 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7993 (mm) REVERT: G 152 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7604 (mp0) REVERT: G 155 HIS cc_start: 0.7402 (m90) cc_final: 0.7003 (m90) REVERT: G 189 LYS cc_start: 0.8564 (tmmt) cc_final: 0.8009 (tmmt) REVERT: G 227 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7500 (mmmt) REVERT: H 105 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7157 (mmtt) REVERT: H 109 GLU cc_start: 0.8568 (tt0) cc_final: 0.8174 (mm-30) REVERT: H 138 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6770 (t80) REVERT: H 152 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7730 (mp0) REVERT: H 189 LYS cc_start: 0.8611 (tmmt) cc_final: 0.8187 (tmmt) REVERT: H 212 GLU cc_start: 0.8209 (pm20) cc_final: 0.7949 (pm20) REVERT: H 240 MET cc_start: 0.6912 (tmm) cc_final: 0.6669 (tmm) REVERT: I 105 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7133 (mmtt) REVERT: I 109 GLU cc_start: 0.8527 (tt0) cc_final: 0.8233 (mm-30) REVERT: I 152 GLU cc_start: 0.8614 (mt-10) cc_final: 0.7698 (mp0) REVERT: I 189 LYS cc_start: 0.8529 (tmmt) cc_final: 0.7950 (tmmt) REVERT: I 220 MET cc_start: 0.8847 (mmm) cc_final: 0.8564 (mmm) REVERT: I 242 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6093 (mmm) REVERT: J 105 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7247 (mmtt) REVERT: J 109 GLU cc_start: 0.8545 (tt0) cc_final: 0.8168 (mm-30) REVERT: J 138 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6915 (t80) REVERT: J 152 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7685 (mp0) REVERT: J 155 HIS cc_start: 0.7168 (m90) cc_final: 0.6759 (m90) REVERT: J 189 LYS cc_start: 0.8477 (tmmt) cc_final: 0.8036 (tmmt) REVERT: J 196 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8298 (mmpt) REVERT: J 227 LYS cc_start: 0.7794 (mmpt) cc_final: 0.7543 (mmmt) REVERT: J 240 MET cc_start: 0.7174 (tmm) cc_final: 0.6788 (tmm) outliers start: 74 outliers final: 23 residues processed: 414 average time/residue: 0.5441 time to fit residues: 248.8810 Evaluate side-chains 374 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 227 LYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 138 TYR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 242 MET Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [177, 85, 7, 9, 133, 167, 3, 42, 109, 87, 129] chunk 177 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.140008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.110244 restraints weight = 23246.435| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.50 r_work: 0.3520 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15420 Z= 0.199 Angle : 0.721 9.206 20650 Z= 0.354 Chirality : 0.050 0.281 2340 Planarity : 0.003 0.026 2650 Dihedral : 4.428 15.186 2120 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.43 % Allowed : 30.85 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.19), residues: 1870 helix: 0.81 (0.17), residues: 890 sheet: -1.03 (0.24), residues: 460 loop : -1.96 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 143 TYR 0.021 0.002 TYR F 127 PHE 0.011 0.002 PHE D 151 HIS 0.002 0.001 HIS F 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (15390) covalent geometry : angle 0.72133 / 0.35 (20650) hydrogen bonds : bond 0.03589 / 2.46 ( 881) hydrogen bonds : angle 4.35937 / 3.06 ( 2583) metal coordination : bond 0.00350 / 0.21 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 353 time to evaluate : 0.651 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 105 LYS cc_start: 0.7961 (mmmm) cc_final: 0.7158 (mmtm) REVERT: A 109 GLU cc_start: 0.8578 (tt0) cc_final: 0.8152 (mm-30) REVERT: A 138 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 189 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8286 (tmtt) REVERT: A 212 GLU cc_start: 0.8312 (pm20) cc_final: 0.7997 (pm20) REVERT: B 105 LYS cc_start: 0.7859 (mmmm) cc_final: 0.7028 (mmtt) REVERT: B 109 GLU cc_start: 0.8559 (tt0) cc_final: 0.8176 (mm-30) REVERT: B 152 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7706 (mp0) REVERT: B 189 LYS cc_start: 0.8659 (tmmt) cc_final: 0.8213 (tmmt) REVERT: B 240 MET cc_start: 0.7585 (tmm) cc_final: 0.6821 (tmm) REVERT: C 105 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7324 (mmtm) REVERT: C 109 GLU cc_start: 0.8632 (tt0) cc_final: 0.8269 (mm-30) REVERT: C 138 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6791 (t80) REVERT: C 152 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7762 (mp0) REVERT: C 189 LYS cc_start: 0.8566 (tmmt) cc_final: 0.8097 (tmmt) REVERT: C 191 VAL cc_start: 0.8803 (t) cc_final: 0.8489 (p) REVERT: C 240 MET cc_start: 0.7285 (tmm) cc_final: 0.6889 (tmm) REVERT: D 105 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7325 (mmtt) REVERT: D 109 GLU cc_start: 0.8499 (tt0) cc_final: 0.8249 (mm-30) REVERT: D 138 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6614 (t80) REVERT: D 189 LYS cc_start: 0.8623 (tmmt) cc_final: 0.8329 (tmtt) REVERT: D 227 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7715 (mmmt) REVERT: D 240 MET cc_start: 0.7566 (tmm) cc_final: 0.6735 (tmm) REVERT: E 105 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7278 (mmtt) REVERT: E 109 GLU cc_start: 0.8541 (tt0) cc_final: 0.8163 (mm-30) REVERT: E 138 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6902 (t80) REVERT: E 152 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7747 (mp0) REVERT: E 189 LYS cc_start: 0.8479 (tmmt) cc_final: 0.8053 (tmmt) REVERT: E 240 MET cc_start: 0.7515 (tmm) cc_final: 0.6901 (tmm) REVERT: F 105 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7146 (mmtm) REVERT: F 109 GLU cc_start: 0.8573 (tt0) cc_final: 0.8218 (mm-30) REVERT: F 138 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.7028 (t80) REVERT: F 189 LYS cc_start: 0.8507 (tmmt) cc_final: 0.8259 (tmtt) REVERT: F 212 GLU cc_start: 0.8385 (pm20) cc_final: 0.8037 (pm20) REVERT: F 267 GLN cc_start: 0.7986 (mp10) cc_final: 0.7675 (mp10) REVERT: G 105 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7010 (mmtt) REVERT: G 109 GLU cc_start: 0.8587 (tt0) cc_final: 0.8188 (mm-30) REVERT: G 132 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8107 (mm) REVERT: G 138 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6332 (t80) REVERT: G 155 HIS cc_start: 0.7618 (m90) cc_final: 0.7377 (m90) REVERT: G 189 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8334 (tmmt) REVERT: H 105 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7295 (mmtm) REVERT: H 109 GLU cc_start: 0.8590 (tt0) cc_final: 0.8208 (mm-30) REVERT: H 138 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6907 (t80) REVERT: H 189 LYS cc_start: 0.8659 (tmmt) cc_final: 0.8392 (tmmt) REVERT: H 212 GLU cc_start: 0.8272 (pm20) cc_final: 0.7948 (pm20) REVERT: H 240 MET cc_start: 0.7139 (tmm) cc_final: 0.6810 (tmm) REVERT: I 105 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7293 (mmtt) REVERT: I 109 GLU cc_start: 0.8531 (tt0) cc_final: 0.8270 (mm-30) REVERT: I 138 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6675 (t80) REVERT: I 152 GLU cc_start: 0.8691 (mt-10) cc_final: 0.7772 (mp0) REVERT: I 189 LYS cc_start: 0.8639 (tmmt) cc_final: 0.8183 (tmtt) REVERT: J 105 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7277 (mmtt) REVERT: J 109 GLU cc_start: 0.8572 (tt0) cc_final: 0.8198 (mm-30) REVERT: J 138 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6867 (t80) REVERT: J 152 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7725 (mp0) REVERT: J 155 HIS cc_start: 0.7345 (m90) cc_final: 0.6946 (m90) REVERT: J 189 LYS cc_start: 0.8472 (tmmt) cc_final: 0.8103 (tmtt) REVERT: J 240 MET cc_start: 0.7283 (tmm) cc_final: 0.6698 (tmm) outliers start: 89 outliers final: 33 residues processed: 390 average time/residue: 0.5472 time to fit residues: 235.5035 Evaluate side-chains 383 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 138 TYR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [151, 140, 118, 93, 153, 17, 98, 147, 23, 13, 79] chunk 151 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN I 266 GLN ** J 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.144065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114220 restraints weight = 23352.915| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.61 r_work: 0.3596 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15420 Z= 0.133 Angle : 0.709 11.347 20650 Z= 0.341 Chirality : 0.048 0.207 2340 Planarity : 0.003 0.029 2650 Dihedral : 4.339 16.841 2120 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.94 % Allowed : 32.01 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.19), residues: 1870 helix: 0.84 (0.17), residues: 890 sheet: -0.99 (0.24), residues: 460 loop : -2.05 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 213 TYR 0.011 0.001 TYR A 138 PHE 0.011 0.001 PHE E 177 HIS 0.002 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15390) covalent geometry : angle 0.70935 / 0.34 (20650) hydrogen bonds : bond 0.03122 / 2.13 ( 881) hydrogen bonds : angle 4.11364 / 2.89 ( 2583) metal coordination : bond 0.00079 / 0.04 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 346 time to evaluate : 0.577 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 105 LYS cc_start: 0.7939 (mmmm) cc_final: 0.7136 (mmtm) REVERT: A 109 GLU cc_start: 0.8498 (tt0) cc_final: 0.8097 (mm-30) REVERT: A 121 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8444 (mm) REVERT: A 189 LYS cc_start: 0.8528 (tmmt) cc_final: 0.8248 (tmtt) REVERT: A 212 GLU cc_start: 0.8103 (pm20) cc_final: 0.7824 (pm20) REVERT: B 105 LYS cc_start: 0.7862 (mmmm) cc_final: 0.6907 (mmtt) REVERT: B 109 GLU cc_start: 0.8549 (tt0) cc_final: 0.8183 (mm-30) REVERT: B 189 LYS cc_start: 0.8611 (tmmt) cc_final: 0.8335 (tmmt) REVERT: B 240 MET cc_start: 0.7420 (tmm) cc_final: 0.6678 (tmm) REVERT: C 105 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7221 (mmtt) REVERT: C 109 GLU cc_start: 0.8653 (tt0) cc_final: 0.8286 (mm-30) REVERT: C 152 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7634 (mp0) REVERT: C 189 LYS cc_start: 0.8619 (tmmt) cc_final: 0.8147 (tmmt) REVERT: C 240 MET cc_start: 0.7065 (tmm) cc_final: 0.6686 (tmm) REVERT: D 105 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7199 (mmtt) REVERT: D 109 GLU cc_start: 0.8493 (tt0) cc_final: 0.8218 (mm-30) REVERT: D 158 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6218 (ttp) REVERT: D 189 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8340 (tmtt) REVERT: D 220 MET cc_start: 0.8858 (mmm) cc_final: 0.8520 (mmm) REVERT: D 227 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7786 (mmmt) REVERT: D 240 MET cc_start: 0.7393 (tmm) cc_final: 0.6568 (tmm) REVERT: D 242 MET cc_start: 0.6288 (tpt) cc_final: 0.5958 (mmm) REVERT: E 105 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7249 (mmtt) REVERT: E 109 GLU cc_start: 0.8582 (tt0) cc_final: 0.8169 (mm-30) REVERT: E 121 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8444 (mm) REVERT: E 189 LYS cc_start: 0.8434 (tmmt) cc_final: 0.8210 (tmmt) REVERT: E 240 MET cc_start: 0.7371 (tmm) cc_final: 0.6900 (tmm) REVERT: F 105 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7182 (mmtm) REVERT: F 109 GLU cc_start: 0.8581 (tt0) cc_final: 0.8222 (mm-30) REVERT: F 158 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6904 (ttp) REVERT: F 189 LYS cc_start: 0.8492 (tmmt) cc_final: 0.8248 (tmtt) REVERT: F 212 GLU cc_start: 0.8260 (pm20) cc_final: 0.7972 (pm20) REVERT: F 267 GLN cc_start: 0.7932 (mp10) cc_final: 0.7618 (mp10) REVERT: G 105 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7051 (mmtm) REVERT: G 109 GLU cc_start: 0.8551 (tt0) cc_final: 0.8186 (mm-30) REVERT: G 155 HIS cc_start: 0.7588 (m90) cc_final: 0.7280 (m90) REVERT: G 189 LYS cc_start: 0.8578 (tmmt) cc_final: 0.8284 (tmmt) REVERT: H 105 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7337 (mmtt) REVERT: H 109 GLU cc_start: 0.8573 (tt0) cc_final: 0.8205 (mm-30) REVERT: H 189 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8460 (tmmt) REVERT: H 212 GLU cc_start: 0.8186 (pm20) cc_final: 0.7900 (pm20) REVERT: H 227 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7716 (mmmt) REVERT: H 240 MET cc_start: 0.6878 (tmm) cc_final: 0.6613 (tmm) REVERT: I 105 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7264 (mmtm) REVERT: I 109 GLU cc_start: 0.8533 (tt0) cc_final: 0.8250 (mm-30) REVERT: I 189 LYS cc_start: 0.8661 (tmmt) cc_final: 0.8368 (tmtt) REVERT: I 220 MET cc_start: 0.8850 (mmm) cc_final: 0.8569 (mmm) REVERT: I 242 MET cc_start: 0.6591 (tpt) cc_final: 0.6347 (mmm) REVERT: J 105 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7304 (mmtt) REVERT: J 109 GLU cc_start: 0.8566 (tt0) cc_final: 0.8208 (mm-30) REVERT: J 121 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8491 (mm) REVERT: J 155 HIS cc_start: 0.7307 (m90) cc_final: 0.6892 (m90) REVERT: J 189 LYS cc_start: 0.8457 (tmmt) cc_final: 0.8245 (tmmt) REVERT: J 240 MET cc_start: 0.7104 (tmm) cc_final: 0.6756 (tmm) outliers start: 81 outliers final: 36 residues processed: 392 average time/residue: 0.5360 time to fit residues: 232.2831 Evaluate side-chains 358 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 316 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [43, 4, 90, 126, 102, 165, 116, 151, 146, 60, 0] chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108446 restraints weight = 23628.117| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.54 r_work: 0.3503 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 15420 Z= 0.234 Angle : 0.760 10.828 20650 Z= 0.377 Chirality : 0.049 0.255 2340 Planarity : 0.003 0.030 2650 Dihedral : 4.599 20.946 2120 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.73 % Allowed : 30.79 % Favored : 63.48 % 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: -0.66 (0.19), residues: 1870 helix: 0.79 (0.17), residues: 890 sheet: -0.77 (0.23), residues: 440 loop : -2.12 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 245 TYR 0.020 0.002 TYR D 138 PHE 0.011 0.002 PHE D 151 HIS 0.002 0.001 HIS F 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (15390) covalent geometry : angle 0.75980 / 0.38 (20650) hydrogen bonds : bond 0.03761 / 2.55 ( 881) hydrogen bonds : angle 4.48126 / 3.16 ( 2583) metal coordination : bond 0.00439 / 0.26 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 348 time to evaluate : 0.564 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 105 LYS cc_start: 0.7964 (mmmm) cc_final: 0.7492 (tptt) REVERT: A 121 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8526 (mm) REVERT: A 138 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.7041 (t80) REVERT: A 189 LYS cc_start: 0.8554 (tmmt) cc_final: 0.8307 (tmtt) REVERT: A 212 GLU cc_start: 0.8295 (pm20) cc_final: 0.7969 (pm20) REVERT: B 105 LYS cc_start: 0.7871 (mmmm) cc_final: 0.6990 (mmtt) REVERT: B 109 GLU cc_start: 0.8579 (tt0) cc_final: 0.8193 (mm-30) REVERT: B 189 LYS cc_start: 0.8630 (tmmt) cc_final: 0.8358 (tmmt) REVERT: B 240 MET cc_start: 0.7653 (tmm) cc_final: 0.6916 (tmm) REVERT: C 105 LYS cc_start: 0.8084 (mmmm) cc_final: 0.7294 (mmtm) REVERT: C 109 GLU cc_start: 0.8644 (tt0) cc_final: 0.8199 (mm-30) REVERT: C 138 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6678 (t80) REVERT: C 189 LYS cc_start: 0.8610 (tmmt) cc_final: 0.8345 (tmmt) REVERT: C 191 VAL cc_start: 0.8840 (t) cc_final: 0.8557 (p) REVERT: C 240 MET cc_start: 0.7388 (tmm) cc_final: 0.7142 (tmm) REVERT: D 105 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7371 (mmtm) REVERT: D 109 GLU cc_start: 0.8546 (tt0) cc_final: 0.8269 (mm-30) REVERT: D 138 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6521 (t80) REVERT: D 189 LYS cc_start: 0.8574 (tmmt) cc_final: 0.8268 (tmtt) REVERT: D 220 MET cc_start: 0.8870 (mmm) cc_final: 0.8523 (mmm) REVERT: D 240 MET cc_start: 0.7525 (tmm) cc_final: 0.6776 (tmm) REVERT: E 105 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7313 (mmtt) REVERT: E 109 GLU cc_start: 0.8540 (tt0) cc_final: 0.8155 (mm-30) REVERT: E 121 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8554 (mm) REVERT: E 138 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.7087 (t80) REVERT: E 240 MET cc_start: 0.7465 (tmm) cc_final: 0.7132 (tmm) REVERT: F 105 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7548 (tptt) REVERT: F 121 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8545 (mm) REVERT: F 138 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6951 (t80) REVERT: F 189 LYS cc_start: 0.8473 (tmmt) cc_final: 0.8242 (tmtt) REVERT: F 212 GLU cc_start: 0.8412 (pm20) cc_final: 0.8046 (pm20) REVERT: F 267 GLN cc_start: 0.8020 (mp10) cc_final: 0.7709 (mp10) REVERT: G 105 LYS cc_start: 0.7915 (mmmm) cc_final: 0.7417 (mmtt) REVERT: G 155 HIS cc_start: 0.7721 (m90) cc_final: 0.7483 (m90) REVERT: G 189 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8325 (tmtt) REVERT: H 105 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7728 (mmtt) REVERT: H 138 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6851 (t80) REVERT: H 189 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8423 (tmmt) REVERT: H 191 VAL cc_start: 0.8854 (t) cc_final: 0.8581 (p) REVERT: H 212 GLU cc_start: 0.8353 (pm20) cc_final: 0.8035 (pm20) REVERT: H 240 MET cc_start: 0.7134 (tmm) cc_final: 0.6742 (tmm) REVERT: I 105 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7387 (mmtm) REVERT: I 109 GLU cc_start: 0.8565 (tt0) cc_final: 0.8264 (mm-30) REVERT: I 138 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6526 (t80) REVERT: I 189 LYS cc_start: 0.8662 (tmmt) cc_final: 0.8343 (tmtt) REVERT: I 220 MET cc_start: 0.8855 (mmm) cc_final: 0.8492 (mmm) REVERT: I 240 MET cc_start: 0.7582 (tmm) cc_final: 0.7354 (ttp) REVERT: J 105 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7559 (mmtt) REVERT: J 121 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8541 (mm) REVERT: J 138 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6871 (t80) REVERT: J 155 HIS cc_start: 0.7446 (m90) cc_final: 0.7042 (m90) REVERT: J 240 MET cc_start: 0.7372 (tmm) cc_final: 0.6889 (tmm) outliers start: 94 outliers final: 40 residues processed: 393 average time/residue: 0.5409 time to fit residues: 234.1009 Evaluate side-chains 374 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 322 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 138 TYR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [178, 27, 19, 139, 130, 35, 148, 76, 119, 49, 149] chunk 178 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN I 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.140840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111249 restraints weight = 23583.439| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.56 r_work: 0.3518 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15420 Z= 0.178 Angle : 0.764 10.558 20650 Z= 0.374 Chirality : 0.049 0.262 2340 Planarity : 0.003 0.032 2650 Dihedral : 4.601 20.221 2120 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.51 % Allowed : 32.74 % Favored : 62.74 % 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: -0.65 (0.18), residues: 1870 helix: 0.77 (0.17), residues: 890 sheet: -0.67 (0.23), residues: 440 loop : -2.13 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.017 0.002 TYR F 127 PHE 0.012 0.002 PHE E 177 HIS 0.002 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (15390) covalent geometry : angle 0.76374 / 0.37 (20650) hydrogen bonds : bond 0.03544 / 2.40 ( 881) hydrogen bonds : angle 4.36332 / 3.07 ( 2583) metal coordination : bond 0.00227 / 0.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 337 time to evaluate : 0.421 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 105 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7495 (mmtm) REVERT: A 121 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8471 (mm) REVERT: A 134 PHE cc_start: 0.8154 (m-80) cc_final: 0.7879 (t80) REVERT: A 189 LYS cc_start: 0.8578 (tmmt) cc_final: 0.8299 (tmtt) REVERT: A 203 MET cc_start: 0.8961 (tmt) cc_final: 0.8723 (tmm) REVERT: A 212 GLU cc_start: 0.8207 (pm20) cc_final: 0.7945 (pm20) REVERT: B 105 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7054 (mmtt) REVERT: B 109 GLU cc_start: 0.8604 (tt0) cc_final: 0.8206 (mm-30) REVERT: B 132 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 138 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 189 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8361 (tmmt) REVERT: B 227 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8178 (mmmt) REVERT: B 240 MET cc_start: 0.7581 (tmm) cc_final: 0.6831 (tmm) REVERT: C 105 LYS cc_start: 0.8158 (mmmm) cc_final: 0.7560 (mmtt) REVERT: C 109 GLU cc_start: 0.8607 (tt0) cc_final: 0.8321 (mm-30) REVERT: C 189 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8410 (tmmt) REVERT: C 191 VAL cc_start: 0.8823 (t) cc_final: 0.8522 (p) REVERT: D 105 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7421 (mmtm) REVERT: D 109 GLU cc_start: 0.8557 (tt0) cc_final: 0.8287 (mm-30) REVERT: D 189 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8271 (tmtt) REVERT: D 220 MET cc_start: 0.8841 (mmm) cc_final: 0.8510 (mmm) REVERT: D 240 MET cc_start: 0.7460 (tmm) cc_final: 0.6706 (tmm) REVERT: D 242 MET cc_start: 0.6596 (tpt) cc_final: 0.6366 (mmm) REVERT: E 105 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7289 (mmtt) REVERT: E 109 GLU cc_start: 0.8550 (tt0) cc_final: 0.8124 (mm-30) REVERT: E 121 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8480 (mm) REVERT: E 138 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6965 (t80) REVERT: F 105 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7587 (mmtm) REVERT: F 121 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 189 LYS cc_start: 0.8506 (tmmt) cc_final: 0.8266 (tmtt) REVERT: F 212 GLU cc_start: 0.8304 (pm20) cc_final: 0.8030 (pm20) REVERT: F 267 GLN cc_start: 0.8010 (mp10) cc_final: 0.7690 (mp10) REVERT: G 105 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7474 (mmtt) REVERT: G 132 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8106 (mm) REVERT: G 138 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6387 (t80) REVERT: G 155 HIS cc_start: 0.7688 (m90) cc_final: 0.7457 (m90) REVERT: G 189 LYS cc_start: 0.8653 (tmmt) cc_final: 0.8365 (tmtt) REVERT: G 242 MET cc_start: 0.6570 (tpt) cc_final: 0.6195 (mmm) REVERT: H 105 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7440 (mmtt) REVERT: H 109 GLU cc_start: 0.8581 (tt0) cc_final: 0.8222 (mm-30) REVERT: H 138 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6682 (t80) REVERT: H 189 LYS cc_start: 0.8691 (tmmt) cc_final: 0.8431 (tmmt) REVERT: H 212 GLU cc_start: 0.8239 (pm20) cc_final: 0.7942 (pm20) REVERT: H 240 MET cc_start: 0.7064 (tmm) cc_final: 0.6690 (tmm) REVERT: I 105 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7338 (mmtt) REVERT: I 109 GLU cc_start: 0.8596 (tt0) cc_final: 0.8283 (mm-30) REVERT: I 189 LYS cc_start: 0.8740 (tmmt) cc_final: 0.8388 (tmtt) REVERT: I 220 MET cc_start: 0.8799 (mmm) cc_final: 0.8433 (mmm) REVERT: I 227 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7984 (mmmt) REVERT: I 242 MET cc_start: 0.6719 (tpt) cc_final: 0.5958 (mmm) REVERT: J 105 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7590 (mmtt) REVERT: J 121 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8467 (mm) REVERT: J 138 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6838 (t80) REVERT: J 155 HIS cc_start: 0.7430 (m90) cc_final: 0.6956 (m90) REVERT: J 240 MET cc_start: 0.7369 (tmm) cc_final: 0.6953 (tmm) outliers start: 74 outliers final: 40 residues processed: 378 average time/residue: 0.5388 time to fit residues: 225.0509 Evaluate side-chains 370 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 138 TYR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [18, 172, 21, 104, 94, 10, 95, 8, 131, 100, 33] chunk 18 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 GLN ** G 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN J 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.138474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108079 restraints weight = 24160.231| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.64 r_work: 0.3468 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15420 Z= 0.255 Angle : 0.835 12.677 20650 Z= 0.413 Chirality : 0.051 0.313 2340 Planarity : 0.003 0.034 2650 Dihedral : 4.836 19.256 2120 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.96 % Allowed : 33.60 % Favored : 62.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.19), residues: 1870 helix: 0.65 (0.17), residues: 890 sheet: -0.76 (0.23), residues: 440 loop : -1.81 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.024 0.003 TYR F 127 PHE 0.012 0.002 PHE D 151 HIS 0.004 0.001 HIS I 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.26 (15390) covalent geometry : angle 0.83543 / 0.41 (20650) hydrogen bonds : bond 0.04051 / 2.73 ( 881) hydrogen bonds : angle 4.62914 / 3.26 ( 2583) metal coordination : bond 0.00441 / 0.25 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 0.564 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 105 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7607 (mmtt) REVERT: A 121 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 138 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.7063 (t80) REVERT: A 189 LYS cc_start: 0.8587 (tmmt) cc_final: 0.8301 (tmtt) REVERT: A 212 GLU cc_start: 0.8326 (pm20) cc_final: 0.8007 (pm20) REVERT: B 105 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7514 (mmtm) REVERT: B 138 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6430 (t80) REVERT: B 189 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8283 (tmmt) REVERT: C 105 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7745 (mmtt) REVERT: C 138 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6507 (t80) REVERT: C 189 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8342 (tmmt) REVERT: C 191 VAL cc_start: 0.8854 (t) cc_final: 0.8583 (p) REVERT: D 105 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7710 (mmtm) REVERT: D 138 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6221 (t80) REVERT: D 189 LYS cc_start: 0.8635 (tmmt) cc_final: 0.8328 (tmtt) REVERT: D 220 MET cc_start: 0.8859 (mmm) cc_final: 0.8521 (mmm) REVERT: D 240 MET cc_start: 0.7579 (tmm) cc_final: 0.7138 (tmm) REVERT: D 242 MET cc_start: 0.6751 (tpt) cc_final: 0.6524 (mmm) REVERT: E 105 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7595 (mmtt) REVERT: E 121 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8538 (mm) REVERT: E 138 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7006 (t80) REVERT: E 189 LYS cc_start: 0.8068 (tmmt) cc_final: 0.7865 (tmmt) REVERT: F 105 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7565 (mmtt) REVERT: F 121 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8539 (mm) REVERT: F 138 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6905 (t80) REVERT: F 189 LYS cc_start: 0.8541 (tmmt) cc_final: 0.8317 (tmtt) REVERT: F 212 GLU cc_start: 0.8440 (pm20) cc_final: 0.8095 (pm20) REVERT: F 267 GLN cc_start: 0.8009 (mp10) cc_final: 0.7687 (mp10) REVERT: G 105 LYS cc_start: 0.7967 (mmmm) cc_final: 0.7480 (mmtt) REVERT: G 138 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6452 (t80) REVERT: G 189 LYS cc_start: 0.8658 (tmmt) cc_final: 0.8368 (tmtt) REVERT: G 242 MET cc_start: 0.6627 (tpt) cc_final: 0.6187 (mmm) REVERT: H 105 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7727 (mmtt) REVERT: H 138 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6690 (t80) REVERT: H 189 LYS cc_start: 0.8648 (tmmt) cc_final: 0.8377 (tmmt) REVERT: H 191 VAL cc_start: 0.8864 (t) cc_final: 0.8609 (p) REVERT: H 212 GLU cc_start: 0.8371 (pm20) cc_final: 0.8083 (pm20) REVERT: I 105 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7671 (mmtm) REVERT: I 138 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6418 (t80) REVERT: I 189 LYS cc_start: 0.8702 (tmmt) cc_final: 0.8379 (tmtt) REVERT: I 220 MET cc_start: 0.8847 (mmm) cc_final: 0.8466 (mmm) REVERT: I 240 MET cc_start: 0.6736 (ttp) cc_final: 0.6251 (tmm) REVERT: J 105 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7591 (mmtt) REVERT: J 121 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8525 (mm) REVERT: J 138 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6963 (t80) REVERT: J 155 HIS cc_start: 0.7575 (m90) cc_final: 0.7115 (m90) outliers start: 65 outliers final: 42 residues processed: 366 average time/residue: 0.5310 time to fit residues: 214.9763 Evaluate side-chains 369 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 253 SER Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 TYR Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 138 TYR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 138 TYR Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 253 SER Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 TYR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 222 LEU Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [78, 126, 117, 74, 167, 65, 35, 112, 129, 151, 48] chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 151 optimal weight: 0.0270 chunk 48 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN E 239 HIS H 266 GLN I 239 HIS I 266 GLN J 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.144015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115170 restraints weight = 23741.184| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.57 r_work: 0.3575 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15420 Z= 0.148 Angle : 0.807 13.180 20650 Z= 0.391 Chirality : 0.048 0.230 2340 Planarity : 0.003 0.032 2650 Dihedral : 4.717 19.313 2120 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.68 % Allowed : 35.00 % Favored : 62.32 % 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: -0.57 (0.19), residues: 1870 helix: 0.71 (0.17), residues: 890 sheet: -0.59 (0.23), residues: 440 loop : -1.88 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.014 0.002 TYR C 133 PHE 0.012 0.001 PHE E 177 HIS 0.005 0.001 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (15390) covalent geometry : angle 0.80710 / 0.39 (20650) hydrogen bonds : bond 0.03444 / 2.32 ( 881) hydrogen bonds : angle 4.31365 / 3.03 ( 2583) metal coordination : bond 0.00110 / 0.06 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5788.47 seconds wall clock time: 99 minutes 18.13 seconds (5958.13 seconds total)