Starting phenix.real_space_refine on Thu Feb 5 05:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1w_62756/02_2026/9l1w_62756.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1w_62756/02_2026/9l1w_62756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l1w_62756/02_2026/9l1w_62756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1w_62756/02_2026/9l1w_62756.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1w_62756/02_2026/9l1w_62756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1w_62756/02_2026/9l1w_62756.cif" } resolution = 3.1 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= 0.000 sd= 0.023 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 Fe 9 7.16 5 S 69 5.16 5 C 9462 2.51 5 N 2655 2.21 5 O 2805 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15000 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 1 Chain: "B" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1453 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "C" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 1 Chain: "D" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1453 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "E" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 1 Chain: "F" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1453 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {'FE2': 1, 'FES': 1, 'HCI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {'FE2': 1, 'FES': 1, 'HCI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {'FE2': 1, 'FES': 1, 'HCI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 692 SG CYS A 85 30.797 55.670 33.252 1.00 68.79 S ATOM 851 SG CYS A 105 31.295 56.854 36.760 1.00 53.78 S ATOM 5676 SG CYS C 85 81.078 43.349 33.239 1.00 72.70 S ATOM 5835 SG CYS C 105 79.822 43.201 36.764 1.00 55.54 S ATOM 10660 SG CYS E 85 66.611 93.067 33.252 1.00 68.39 S ATOM 10819 SG CYS E 105 67.387 92.047 36.761 1.00 53.44 S Time building chain proxies: 2.99, per 1000 atoms: 0.20 Number of scatterers: 15000 At special positions: 0 Unit cell: (120.701, 116.167, 97.4672, 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) Fe 9 26.01 S 69 16.00 O 2805 8.00 N 2655 7.00 C 9462 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: 6.82 Conformation dependent library (CDL) restraints added in 397.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 502 " pdb="FE2 FES A 502 " - pdb=" ND1 HIS A 108 " pdb="FE2 FES A 502 " - pdb=" ND1 HIS A 87 " pdb="FE1 FES A 502 " - pdb=" SG CYS A 105 " pdb="FE1 FES A 502 " - pdb=" SG CYS A 85 " pdb=" FES C 502 " pdb="FE1 FES C 502 " - pdb=" ND1 HIS C 108 " pdb="FE1 FES C 502 " - pdb=" ND1 HIS C 87 " pdb="FE2 FES C 502 " - pdb=" SG CYS C 85 " pdb="FE2 FES C 502 " - pdb=" SG CYS C 105 " pdb=" FES E 502 " pdb="FE2 FES E 502 " - pdb=" ND1 HIS E 108 " pdb="FE2 FES E 502 " - pdb=" ND1 HIS E 87 " pdb="FE1 FES E 502 " - pdb=" SG CYS E 105 " pdb="FE1 FES E 502 " - pdb=" SG CYS E 85 " Number of angles added : 9 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 21 sheets defined 37.9% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.679A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 8 through 12' Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 27 through 42 removed outlier: 4.450A pdb=" N PHE A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 169 through 179 removed outlier: 3.815A pdb=" N TYR A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.690A pdb=" N ALA A 204 " --> pdb=" O TRP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.572A pdb=" N LEU A 215 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.357A pdb=" N THR A 248 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.689A pdb=" N ALA A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 346 through 361 Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.931A pdb=" N ASP A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.013A pdb=" N SER A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 436 through 453 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 28 through 35 Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.552A pdb=" N LEU B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.734A pdb=" N GLU B 90 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.774A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 8 through 12' Processing helix chain 'C' and resid 22 through 26 Processing helix chain 'C' and resid 27 through 42 removed outlier: 4.426A pdb=" N PHE C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 169 through 179 removed outlier: 3.819A pdb=" N TYR C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY C 176 " --> pdb=" O TRP C 172 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.705A pdb=" N ALA C 204 " --> pdb=" O TRP C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.598A pdb=" N LEU C 215 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.070A pdb=" N THR C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 287 through 295 removed outlier: 3.690A pdb=" N ALA C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 346 through 361 Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.935A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 4.024A pdb=" N SER C 390 " --> pdb=" O ALA C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 433 Processing helix chain 'C' and resid 436 through 453 removed outlier: 3.522A pdb=" N LYS C 453 " --> pdb=" O GLN C 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 51 through 58 Processing helix chain 'D' and resid 70 through 84 removed outlier: 3.550A pdb=" N LEU D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.821A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 12' Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 27 through 42 removed outlier: 4.411A pdb=" N PHE E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 162 through 168 Processing helix chain 'E' and resid 169 through 179 removed outlier: 3.810A pdb=" N TYR E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY E 176 " --> pdb=" O TRP E 172 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 210 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.527A pdb=" N ALA E 214 " --> pdb=" O GLN E 211 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 215 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 244 through 249 removed outlier: 4.023A pdb=" N THR E 248 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 removed outlier: 5.205A pdb=" N ALA E 289 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLU E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 346 through 361 Processing helix chain 'E' and resid 367 through 382 removed outlier: 3.937A pdb=" N ASP E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 removed outlier: 4.038A pdb=" N SER E 390 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 433 Processing helix chain 'E' and resid 436 through 453 Processing helix chain 'F' and resid 6 through 26 Processing helix chain 'F' and resid 28 through 35 Processing helix chain 'F' and resid 51 through 58 Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.558A pdb=" N LEU F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY F 84 " --> pdb=" O ARG F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.729A pdb=" N GLU F 90 " --> pdb=" O TRP F 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.763A pdb=" N ILE A 152 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 144 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 82 removed outlier: 4.411A pdb=" N ASP A 57 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 98 " --> pdb=" O PHE A 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.700A pdb=" N GLY A 113 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 118 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.956A pdb=" N THR A 321 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 316 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 256 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A 411 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.458A pdb=" N MET B 44 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 68 " --> pdb=" O TYR B 42 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR B 42 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP B 37 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 152 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 39 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ARG B 154 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG B 41 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE B 156 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 43 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 158 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 45 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS B 140 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 154 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B 138 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE B 156 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR B 136 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU B 158 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL B 134 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL B 112 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU B 106 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 114 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 104 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 116 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS B 102 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA9, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.759A pdb=" N ILE C 152 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS C 144 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 82 removed outlier: 4.419A pdb=" N ASP C 57 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 98 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 102 through 104 removed outlier: 6.713A pdb=" N GLY C 113 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 118 " --> pdb=" O GLY C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AB4, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.959A pdb=" N THR C 321 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 316 " --> pdb=" O THR C 321 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 256 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 411 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 65 through 69 removed outlier: 6.461A pdb=" N MET D 44 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN D 68 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR D 42 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP D 37 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU D 152 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU D 39 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG D 154 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG D 41 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 156 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR D 43 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU D 158 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ARG D 45 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS D 140 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG D 154 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE D 138 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE D 156 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR D 136 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU D 158 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N VAL D 134 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL D 112 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU D 106 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA D 114 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE D 104 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG D 116 " --> pdb=" O CYS D 102 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS D 102 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB7, first strand: chain 'E' and resid 44 through 48 removed outlier: 6.763A pdb=" N ILE E 152 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS E 144 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 78 through 82 removed outlier: 4.418A pdb=" N ASP E 57 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY E 98 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 102 through 104 removed outlier: 6.675A pdb=" N GLY E 113 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU E 118 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'E' and resid 185 through 187 removed outlier: 3.984A pdb=" N THR E 321 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 316 " --> pdb=" O THR E 321 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP E 315 " --> pdb=" O ASN E 307 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 256 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE E 411 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.457A pdb=" N MET F 44 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN F 68 " --> pdb=" O TYR F 42 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR F 42 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP F 37 " --> pdb=" O ARG F 150 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU F 152 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLU F 39 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG F 154 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG F 41 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE F 156 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR F 43 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU F 158 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ARG F 45 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS F 140 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG F 154 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE F 138 " --> pdb=" O ARG F 154 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE F 156 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 136 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU F 158 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL F 134 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL F 112 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLU F 106 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA F 114 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE F 104 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG F 116 " --> pdb=" O CYS F 102 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS F 102 " --> pdb=" O ARG F 116 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1824 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: 2.29 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 6813 1.42 - 1.62: 8457 1.62 - 1.81: 93 1.81 - 2.01: 0 2.01 - 2.20: 12 Bond restraints: 15375 Sorted by residual: bond pdb=" N ARG A 88 " pdb=" CA ARG A 88 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.77e-02 3.19e+03 1.17e+00 bond pdb=" N ARG C 88 " pdb=" CA ARG C 88 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.77e-02 3.19e+03 1.16e+00 bond pdb=" N ARG E 88 " pdb=" CA ARG E 88 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.77e-02 3.19e+03 1.14e+00 bond pdb=" CA ASN B 68 " pdb=" C ASN B 68 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.10e+00 bond pdb=" CA ASN D 68 " pdb=" C ASN D 68 " ideal model delta sigma weight residual 1.529 1.518 0.011 1.04e-02 9.25e+03 1.05e+00 ... (remaining 15370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 19887 1.22 - 2.44: 803 2.44 - 3.66: 129 3.66 - 4.88: 17 4.88 - 6.10: 14 Bond angle restraints: 20850 Sorted by residual: angle pdb=" N SER E 209 " pdb=" CA SER E 209 " pdb=" C SER E 209 " ideal model delta sigma weight residual 110.61 115.22 -4.61 1.25e+00 6.40e-01 1.36e+01 angle pdb=" N SER C 209 " pdb=" CA SER C 209 " pdb=" C SER C 209 " ideal model delta sigma weight residual 111.71 116.37 -4.66 1.34e+00 5.57e-01 1.21e+01 angle pdb=" N THR C 312 " pdb=" CA THR C 312 " pdb=" C THR C 312 " ideal model delta sigma weight residual 110.61 114.43 -3.82 1.25e+00 6.40e-01 9.33e+00 angle pdb=" N THR A 312 " pdb=" CA THR A 312 " pdb=" C THR A 312 " ideal model delta sigma weight residual 110.06 114.21 -4.15 1.43e+00 4.89e-01 8.42e+00 angle pdb=" N SER A 209 " pdb=" CA SER A 209 " pdb=" C SER A 209 " ideal model delta sigma weight residual 111.71 115.29 -3.58 1.34e+00 5.57e-01 7.16e+00 ... (remaining 20845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 8266 14.37 - 28.75: 592 28.75 - 43.12: 128 43.12 - 57.50: 42 57.50 - 71.87: 14 Dihedral angle restraints: 9042 sinusoidal: 3708 harmonic: 5334 Sorted by residual: dihedral pdb=" CA PRO E 311 " pdb=" C PRO E 311 " pdb=" N THR E 312 " pdb=" CA THR E 312 " ideal model delta harmonic sigma weight residual 180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY E 189 " pdb=" C GLY E 189 " pdb=" N GLY E 190 " pdb=" CA GLY E 190 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY C 189 " pdb=" C GLY C 189 " pdb=" N GLY C 190 " pdb=" CA GLY C 190 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 9039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1266 0.028 - 0.056: 555 0.056 - 0.084: 200 0.084 - 0.112: 97 0.112 - 0.140: 51 Chirality restraints: 2169 Sorted by residual: chirality pdb=" CA VAL E 191 " pdb=" N VAL E 191 " pdb=" C VAL E 191 " pdb=" CB VAL E 191 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE C 78 " pdb=" N ILE C 78 " pdb=" C ILE C 78 " pdb=" CB ILE C 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 2166 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 310 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO C 311 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 311 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 311 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 310 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 311 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 310 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO E 311 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.020 5.00e-02 4.00e+02 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 245 2.69 - 3.24: 13329 3.24 - 3.79: 21238 3.79 - 4.35: 29810 4.35 - 4.90: 52443 Nonbonded interactions: 117065 Sorted by model distance: nonbonded pdb=" O PRO A 122 " pdb=" OH TYR E 212 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR A 212 " pdb=" O PRO C 122 " model vdw 2.159 3.040 nonbonded pdb=" OH TYR C 212 " pdb=" O PRO E 122 " model vdw 2.164 3.040 nonbonded pdb=" OE2 GLU F 89 " pdb=" OG SER F 169 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU B 89 " pdb=" OG SER B 169 " model vdw 2.224 3.040 ... (remaining 117060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 5.170 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.480 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.004 0.042 15387 Z= 0.170 Angle : 0.615 15.307 20859 Z= 0.338 Chirality : 0.042 0.140 2169 Planarity : 0.004 0.044 2742 Dihedral : 11.440 71.869 5610 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.95 % Allowed : 4.64 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.37 (0.19), residues: 1827 helix: 1.38 (0.22), residues: 564 sheet: 0.99 (0.26), residues: 360 loop : -0.81 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 91 TYR 0.018 0.001 TYR B 42 PHE 0.017 0.002 PHE E 338 TRP 0.016 0.001 TRP A 428 HIS 0.006 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00379 (15375) covalent geometry : angle 0.58474 (20850) hydrogen bonds : bond 0.15206 ( 654) hydrogen bonds : angle 5.39884 ( 1824) metal coordination : bond 0.02407 ( 12) metal coordination : angle 9.21267 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.389 Fit side-chains REVERT: A 54 LYS cc_start: 0.8040 (mttt) cc_final: 0.7562 (mmmm) REVERT: A 57 ASP cc_start: 0.8376 (m-30) cc_final: 0.8115 (m-30) REVERT: A 292 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 293 GLN cc_start: 0.7643 (tt0) cc_final: 0.7389 (mm110) REVERT: B 35 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: C 54 LYS cc_start: 0.8059 (mttt) cc_final: 0.7556 (mmmm) REVERT: C 57 ASP cc_start: 0.8342 (m-30) cc_final: 0.8094 (m-30) REVERT: C 128 TYR cc_start: 0.7943 (m-80) cc_final: 0.7607 (m-80) REVERT: C 293 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 35 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: E 13 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8259 (pp) REVERT: E 54 LYS cc_start: 0.8087 (mttt) cc_final: 0.7600 (mmmm) REVERT: E 57 ASP cc_start: 0.8371 (m-30) cc_final: 0.8135 (m-30) REVERT: F 35 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6964 (mp10) outliers start: 15 outliers final: 5 residues processed: 202 average time/residue: 0.1098 time to fit residues: 32.1500 Evaluate side-chains 156 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain F residue 35 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 213 HIS C 213 HIS C 223 GLN E 192 GLN E 213 HIS E 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114131 restraints weight = 16937.211| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.36 r_work: 0.3207 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15387 Z= 0.124 Angle : 0.559 15.708 20859 Z= 0.287 Chirality : 0.042 0.140 2169 Planarity : 0.004 0.044 2742 Dihedral : 6.760 71.069 2087 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.40 % Allowed : 6.49 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.60 (0.19), residues: 1827 helix: 1.70 (0.22), residues: 567 sheet: 0.99 (0.26), residues: 369 loop : -0.73 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 126 TYR 0.022 0.001 TYR E 128 PHE 0.014 0.002 PHE E 338 TRP 0.014 0.001 TRP C 194 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00274 (15375) covalent geometry : angle 0.52107 (20850) hydrogen bonds : bond 0.05195 ( 654) hydrogen bonds : angle 4.64474 ( 1824) metal coordination : bond 0.01917 ( 12) metal coordination : angle 9.81104 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.560 Fit side-chains REVERT: A 54 LYS cc_start: 0.8076 (mttt) cc_final: 0.7791 (mmmm) REVERT: A 292 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 293 GLN cc_start: 0.7639 (tt0) cc_final: 0.7363 (mm110) REVERT: B 35 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: B 130 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8418 (mt-10) REVERT: B 146 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5604 (p0) REVERT: C 54 LYS cc_start: 0.8054 (mttt) cc_final: 0.7526 (mmmm) REVERT: C 57 ASP cc_start: 0.8468 (m-30) cc_final: 0.8170 (m-30) REVERT: C 128 TYR cc_start: 0.7993 (m-80) cc_final: 0.7596 (m-80) REVERT: C 185 THR cc_start: 0.8558 (p) cc_final: 0.8217 (p) REVERT: C 293 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7513 (tm-30) REVERT: D 35 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: E 13 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8283 (pp) REVERT: E 54 LYS cc_start: 0.8077 (mttt) cc_final: 0.7579 (mmmm) REVERT: E 57 ASP cc_start: 0.8427 (m-30) cc_final: 0.8127 (m-30) REVERT: F 35 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: F 146 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.5613 (p0) outliers start: 22 outliers final: 14 residues processed: 182 average time/residue: 0.1246 time to fit residues: 33.1861 Evaluate side-chains 172 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 84 GLN A 192 GLN C 84 GLN C 223 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113479 restraints weight = 17067.355| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.16 r_work: 0.3168 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15387 Z= 0.262 Angle : 0.678 15.484 20859 Z= 0.355 Chirality : 0.047 0.144 2169 Planarity : 0.005 0.048 2742 Dihedral : 7.232 78.498 2087 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.04 % Allowed : 7.57 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.12 (0.19), residues: 1827 helix: 1.26 (0.22), residues: 567 sheet: 0.61 (0.27), residues: 360 loop : -0.92 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 88 TYR 0.019 0.002 TYR B 42 PHE 0.020 0.003 PHE E 338 TRP 0.015 0.002 TRP C 194 HIS 0.007 0.002 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00651 (15375) covalent geometry : angle 0.65014 (20850) hydrogen bonds : bond 0.07211 ( 654) hydrogen bonds : angle 4.84996 ( 1824) metal coordination : bond 0.03279 ( 12) metal coordination : angle 9.28004 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.599 Fit side-chains REVERT: A 54 LYS cc_start: 0.8310 (mttt) cc_final: 0.8073 (mmmm) REVERT: A 292 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8251 (tm-30) REVERT: A 293 GLN cc_start: 0.7693 (tt0) cc_final: 0.7436 (mm110) REVERT: B 35 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: B 146 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5711 (p0) REVERT: C 54 LYS cc_start: 0.8277 (mttt) cc_final: 0.7778 (mmmm) REVERT: C 57 ASP cc_start: 0.8474 (m-30) cc_final: 0.8226 (m-30) REVERT: C 128 TYR cc_start: 0.8148 (m-80) cc_final: 0.7820 (m-80) REVERT: C 293 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7635 (tm-30) REVERT: D 35 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: D 146 ASP cc_start: 0.6104 (OUTLIER) cc_final: 0.5821 (p0) REVERT: E 13 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8399 (pp) REVERT: E 54 LYS cc_start: 0.8362 (mttt) cc_final: 0.7846 (mmmm) REVERT: E 57 ASP cc_start: 0.8399 (m-30) cc_final: 0.8153 (m-30) REVERT: F 35 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: F 146 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5719 (p0) outliers start: 32 outliers final: 21 residues processed: 184 average time/residue: 0.1071 time to fit residues: 29.8284 Evaluate side-chains 180 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 83 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 152 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 355 ASN C 355 ASN E 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118959 restraints weight = 16726.354| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.01 r_work: 0.3242 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15387 Z= 0.099 Angle : 0.533 15.730 20859 Z= 0.270 Chirality : 0.041 0.142 2169 Planarity : 0.003 0.044 2742 Dihedral : 6.776 71.261 2087 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 9.16 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.53 (0.19), residues: 1827 helix: 1.73 (0.22), residues: 570 sheet: 0.88 (0.27), residues: 369 loop : -0.81 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 126 TYR 0.008 0.001 TYR E 112 PHE 0.011 0.001 PHE E 338 TRP 0.015 0.001 TRP E 194 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00201 (15375) covalent geometry : angle 0.48887 (20850) hydrogen bonds : bond 0.04163 ( 654) hydrogen bonds : angle 4.53276 ( 1824) metal coordination : bond 0.01574 ( 12) metal coordination : angle 10.20039 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.567 Fit side-chains REVERT: A 54 LYS cc_start: 0.8154 (mttt) cc_final: 0.7921 (mmmm) REVERT: A 292 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 293 GLN cc_start: 0.7651 (tt0) cc_final: 0.7400 (mm110) REVERT: B 28 LYS cc_start: 0.8837 (mttm) cc_final: 0.8575 (mttp) REVERT: B 35 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: B 146 ASP cc_start: 0.5919 (OUTLIER) cc_final: 0.5624 (p0) REVERT: C 54 LYS cc_start: 0.8173 (mttt) cc_final: 0.7676 (mmmm) REVERT: C 57 ASP cc_start: 0.8397 (m-30) cc_final: 0.8120 (m-30) REVERT: C 128 TYR cc_start: 0.8046 (m-80) cc_final: 0.7831 (m-80) REVERT: C 185 THR cc_start: 0.8577 (p) cc_final: 0.8252 (p) REVERT: C 293 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7607 (tm-30) REVERT: D 35 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: D 146 ASP cc_start: 0.5884 (OUTLIER) cc_final: 0.5575 (p0) REVERT: E 13 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8265 (pp) REVERT: E 54 LYS cc_start: 0.8172 (mttt) cc_final: 0.7831 (mmtp) REVERT: F 35 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: F 146 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5500 (p0) outliers start: 27 outliers final: 18 residues processed: 181 average time/residue: 0.1186 time to fit residues: 31.8179 Evaluate side-chains 176 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114376 restraints weight = 17030.257| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.14 r_work: 0.3181 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15387 Z= 0.179 Angle : 0.588 14.945 20859 Z= 0.304 Chirality : 0.044 0.140 2169 Planarity : 0.004 0.039 2742 Dihedral : 6.875 72.375 2087 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.48 % Allowed : 9.48 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.38 (0.19), residues: 1827 helix: 1.57 (0.22), residues: 567 sheet: 0.83 (0.27), residues: 369 loop : -0.89 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 126 TYR 0.013 0.001 TYR D 42 PHE 0.016 0.002 PHE E 338 TRP 0.013 0.001 TRP C 194 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00438 (15375) covalent geometry : angle 0.55631 (20850) hydrogen bonds : bond 0.05605 ( 654) hydrogen bonds : angle 4.57600 ( 1824) metal coordination : bond 0.02768 ( 12) metal coordination : angle 9.25796 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.594 Fit side-chains REVERT: A 54 LYS cc_start: 0.8241 (mttt) cc_final: 0.8012 (mmmm) REVERT: A 292 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 293 GLN cc_start: 0.7656 (tt0) cc_final: 0.7404 (mm110) REVERT: B 35 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: B 146 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5634 (p0) REVERT: C 54 LYS cc_start: 0.8293 (mttt) cc_final: 0.7595 (mmmm) REVERT: C 57 ASP cc_start: 0.8462 (m-30) cc_final: 0.8097 (m-30) REVERT: C 128 TYR cc_start: 0.8093 (m-80) cc_final: 0.7692 (m-80) REVERT: C 185 THR cc_start: 0.8620 (p) cc_final: 0.8291 (p) REVERT: C 293 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7599 (tm-30) REVERT: D 35 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: D 146 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5563 (p0) REVERT: E 13 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8307 (pp) REVERT: E 54 LYS cc_start: 0.8118 (mttt) cc_final: 0.7799 (mmtp) REVERT: E 400 GLN cc_start: 0.8410 (mp10) cc_final: 0.7927 (mp10) REVERT: F 35 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: F 146 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.5567 (p0) outliers start: 39 outliers final: 28 residues processed: 197 average time/residue: 0.1109 time to fit residues: 33.1651 Evaluate side-chains 189 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN C 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113769 restraints weight = 16964.816| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.14 r_work: 0.3174 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15387 Z= 0.183 Angle : 0.599 15.208 20859 Z= 0.310 Chirality : 0.044 0.141 2169 Planarity : 0.004 0.040 2742 Dihedral : 7.014 74.237 2087 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.54 % Allowed : 9.99 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.26 (0.19), residues: 1827 helix: 1.50 (0.22), residues: 567 sheet: 0.74 (0.27), residues: 363 loop : -0.95 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 126 TYR 0.013 0.001 TYR F 42 PHE 0.016 0.002 PHE E 338 TRP 0.014 0.001 TRP E 194 HIS 0.006 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00447 (15375) covalent geometry : angle 0.56653 (20850) hydrogen bonds : bond 0.05762 ( 654) hydrogen bonds : angle 4.62181 ( 1824) metal coordination : bond 0.02846 ( 12) metal coordination : angle 9.41833 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.556 Fit side-chains REVERT: A 54 LYS cc_start: 0.8266 (mttt) cc_final: 0.8039 (mmmm) REVERT: A 292 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8157 (tm-30) REVERT: A 293 GLN cc_start: 0.7662 (tt0) cc_final: 0.7409 (mm110) REVERT: B 35 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: B 85 MET cc_start: 0.8496 (mmm) cc_final: 0.7825 (mtm) REVERT: B 146 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5671 (p0) REVERT: C 54 LYS cc_start: 0.8303 (mttt) cc_final: 0.7612 (mmmm) REVERT: C 57 ASP cc_start: 0.8453 (m-30) cc_final: 0.8083 (m-30) REVERT: C 185 THR cc_start: 0.8656 (p) cc_final: 0.8325 (p) REVERT: C 293 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7581 (tm-30) REVERT: D 35 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: D 146 ASP cc_start: 0.5921 (OUTLIER) cc_final: 0.5604 (p0) REVERT: E 13 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8304 (pp) REVERT: E 400 GLN cc_start: 0.8426 (mp10) cc_final: 0.7940 (mp10) REVERT: F 35 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: F 146 ASP cc_start: 0.5850 (OUTLIER) cc_final: 0.5576 (p0) outliers start: 40 outliers final: 30 residues processed: 189 average time/residue: 0.1214 time to fit residues: 34.6817 Evaluate side-chains 188 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 12 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN C 17 ASN C 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.158208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119300 restraints weight = 16828.801| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.19 r_work: 0.3234 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15387 Z= 0.098 Angle : 0.517 14.956 20859 Z= 0.260 Chirality : 0.041 0.142 2169 Planarity : 0.003 0.041 2742 Dihedral : 6.595 68.258 2087 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.04 % Allowed : 10.62 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.56 (0.19), residues: 1827 helix: 1.80 (0.22), residues: 570 sheet: 0.92 (0.26), residues: 375 loop : -0.86 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 126 TYR 0.012 0.001 TYR C 128 PHE 0.011 0.001 PHE E 338 TRP 0.016 0.001 TRP A 194 HIS 0.003 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00212 (15375) covalent geometry : angle 0.47568 (20850) hydrogen bonds : bond 0.03974 ( 654) hydrogen bonds : angle 4.41972 ( 1824) metal coordination : bond 0.01666 ( 12) metal coordination : angle 9.70724 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.570 Fit side-chains REVERT: A 54 LYS cc_start: 0.8173 (mttt) cc_final: 0.7949 (mmmm) REVERT: A 293 GLN cc_start: 0.7651 (tt0) cc_final: 0.7447 (mm110) REVERT: B 35 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: B 85 MET cc_start: 0.8467 (mmm) cc_final: 0.7983 (mtm) REVERT: C 54 LYS cc_start: 0.8211 (mttt) cc_final: 0.7539 (mmmm) REVERT: C 57 ASP cc_start: 0.8394 (m-30) cc_final: 0.8036 (m-30) REVERT: C 128 TYR cc_start: 0.8183 (m-80) cc_final: 0.7755 (m-80) REVERT: C 185 THR cc_start: 0.8536 (p) cc_final: 0.8206 (p) REVERT: C 293 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7578 (tm-30) REVERT: D 35 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: D 146 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5584 (p0) REVERT: E 13 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8181 (pp) REVERT: E 400 GLN cc_start: 0.8324 (mp10) cc_final: 0.7825 (mp10) REVERT: F 35 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: F 146 ASP cc_start: 0.5784 (OUTLIER) cc_final: 0.5503 (p0) outliers start: 32 outliers final: 24 residues processed: 177 average time/residue: 0.1209 time to fit residues: 32.0494 Evaluate side-chains 178 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 1 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.3980 chunk 69 optimal weight: 0.0870 chunk 134 optimal weight: 0.0970 chunk 173 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN C 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114528 restraints weight = 16815.290| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.22 r_work: 0.3213 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15387 Z= 0.112 Angle : 0.528 14.238 20859 Z= 0.268 Chirality : 0.042 0.139 2169 Planarity : 0.003 0.039 2742 Dihedral : 6.484 67.800 2087 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 10.88 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1827 helix: 1.82 (0.22), residues: 570 sheet: 0.94 (0.26), residues: 375 loop : -0.86 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.011 0.001 TYR C 128 PHE 0.013 0.002 PHE E 338 TRP 0.014 0.001 TRP C 194 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00256 (15375) covalent geometry : angle 0.49245 (20850) hydrogen bonds : bond 0.04341 ( 654) hydrogen bonds : angle 4.37395 ( 1824) metal coordination : bond 0.02043 ( 12) metal coordination : angle 9.13877 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.574 Fit side-chains REVERT: A 54 LYS cc_start: 0.8113 (mttt) cc_final: 0.7859 (mmmm) REVERT: A 267 THR cc_start: 0.8276 (m) cc_final: 0.8013 (p) REVERT: A 293 GLN cc_start: 0.7621 (tt0) cc_final: 0.7403 (mm110) REVERT: B 35 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: B 85 MET cc_start: 0.8393 (mmm) cc_final: 0.7683 (mtm) REVERT: B 146 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5555 (p0) REVERT: C 54 LYS cc_start: 0.8149 (mttt) cc_final: 0.7442 (mmmm) REVERT: C 57 ASP cc_start: 0.8445 (m-30) cc_final: 0.8016 (m-30) REVERT: C 128 TYR cc_start: 0.8129 (m-80) cc_final: 0.7674 (m-80) REVERT: C 293 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 35 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: D 146 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5529 (p0) REVERT: E 13 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8095 (pp) REVERT: E 400 GLN cc_start: 0.8174 (mp10) cc_final: 0.7676 (mp10) REVERT: F 35 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: F 146 ASP cc_start: 0.5751 (OUTLIER) cc_final: 0.5452 (p0) outliers start: 36 outliers final: 24 residues processed: 181 average time/residue: 0.1196 time to fit residues: 32.5499 Evaluate side-chains 178 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 393 CYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 181 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 161 optimal weight: 0.0010 chunk 146 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN C 17 ASN C 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117542 restraints weight = 16906.391| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.15 r_work: 0.3208 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15387 Z= 0.117 Angle : 0.535 14.196 20859 Z= 0.271 Chirality : 0.042 0.140 2169 Planarity : 0.003 0.039 2742 Dihedral : 6.345 68.413 2085 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.10 % Allowed : 11.13 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1827 helix: 1.83 (0.22), residues: 570 sheet: 0.93 (0.26), residues: 375 loop : -0.87 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.011 0.001 TYR C 128 PHE 0.013 0.002 PHE C 338 TRP 0.014 0.001 TRP A 194 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00269 (15375) covalent geometry : angle 0.50020 (20850) hydrogen bonds : bond 0.04384 ( 654) hydrogen bonds : angle 4.37033 ( 1824) metal coordination : bond 0.02093 ( 12) metal coordination : angle 9.12693 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.588 Fit side-chains REVERT: A 54 LYS cc_start: 0.8183 (mttt) cc_final: 0.7960 (mmmm) REVERT: A 293 GLN cc_start: 0.7636 (tt0) cc_final: 0.7422 (mm110) REVERT: B 35 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: B 85 MET cc_start: 0.8480 (mmm) cc_final: 0.7808 (mtm) REVERT: B 146 ASP cc_start: 0.5912 (OUTLIER) cc_final: 0.5580 (p0) REVERT: C 54 LYS cc_start: 0.8225 (mttt) cc_final: 0.7727 (mmmm) REVERT: C 57 ASP cc_start: 0.8425 (m-30) cc_final: 0.8127 (m-30) REVERT: C 128 TYR cc_start: 0.8180 (m-80) cc_final: 0.7729 (m-80) REVERT: C 293 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7567 (tm-30) REVERT: D 35 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: D 146 ASP cc_start: 0.5904 (OUTLIER) cc_final: 0.5567 (p0) REVERT: E 13 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8154 (pp) REVERT: E 400 GLN cc_start: 0.8263 (mp10) cc_final: 0.7773 (mp10) REVERT: F 35 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7221 (mp10) REVERT: F 146 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5434 (p0) outliers start: 33 outliers final: 25 residues processed: 174 average time/residue: 0.1198 time to fit residues: 31.3902 Evaluate side-chains 178 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 71 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 14 optimal weight: 0.0670 chunk 102 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 ASN C 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117723 restraints weight = 16918.602| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.17 r_work: 0.3222 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15387 Z= 0.116 Angle : 0.537 14.192 20859 Z= 0.273 Chirality : 0.042 0.139 2169 Planarity : 0.003 0.039 2742 Dihedral : 6.242 68.795 2083 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.10 % Allowed : 11.01 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1827 helix: 1.83 (0.23), residues: 570 sheet: 0.93 (0.26), residues: 375 loop : -0.87 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.011 0.001 TYR C 128 PHE 0.013 0.002 PHE C 338 TRP 0.014 0.001 TRP E 194 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00268 (15375) covalent geometry : angle 0.50267 (20850) hydrogen bonds : bond 0.04378 ( 654) hydrogen bonds : angle 4.37837 ( 1824) metal coordination : bond 0.02084 ( 12) metal coordination : angle 9.12073 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.608 Fit side-chains REVERT: A 54 LYS cc_start: 0.8207 (mttt) cc_final: 0.7973 (mmmm) REVERT: A 293 GLN cc_start: 0.7629 (tt0) cc_final: 0.7403 (mm110) REVERT: B 35 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7386 (mp10) REVERT: B 85 MET cc_start: 0.8483 (mmm) cc_final: 0.7813 (mtm) REVERT: B 146 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5549 (p0) REVERT: C 54 LYS cc_start: 0.8236 (mttt) cc_final: 0.7748 (mmmm) REVERT: C 57 ASP cc_start: 0.8433 (m-30) cc_final: 0.8144 (m-30) REVERT: C 128 TYR cc_start: 0.8167 (m-80) cc_final: 0.7706 (m-80) REVERT: C 293 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 35 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: D 146 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5553 (p0) REVERT: E 13 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8151 (pp) REVERT: E 400 GLN cc_start: 0.8233 (mp10) cc_final: 0.7742 (mp10) REVERT: F 35 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: F 146 ASP cc_start: 0.5711 (OUTLIER) cc_final: 0.5416 (p0) outliers start: 33 outliers final: 26 residues processed: 174 average time/residue: 0.1181 time to fit residues: 30.9419 Evaluate side-chains 180 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 393 CYS Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 393 CYS Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 451 VAL Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain F residue 35 GLN Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 125 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 134 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN C 17 ASN C 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.156623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118203 restraints weight = 16832.797| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.16 r_work: 0.3231 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15387 Z= 0.098 Angle : 0.514 13.871 20859 Z= 0.260 Chirality : 0.041 0.140 2169 Planarity : 0.003 0.039 2742 Dihedral : 6.033 68.258 2083 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.97 % Allowed : 11.20 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1827 helix: 1.93 (0.23), residues: 570 sheet: 0.99 (0.26), residues: 375 loop : -0.83 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.011 0.001 TYR C 128 PHE 0.011 0.001 PHE E 338 TRP 0.016 0.001 TRP E 194 HIS 0.003 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00217 (15375) covalent geometry : angle 0.47827 (20850) hydrogen bonds : bond 0.03885 ( 654) hydrogen bonds : angle 4.32859 ( 1824) metal coordination : bond 0.01744 ( 12) metal coordination : angle 9.09604 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3900.57 seconds wall clock time: 67 minutes 35.91 seconds (4055.91 seconds total)