Starting phenix.real_space_refine on Sun Aug 9 07:51:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcu_28993/08_2026/8fcu_28993.map" } resolution = 3.19 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= 0.069 sd= 0.876 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 859 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 159 5.49 5 Mg 1 5.21 5 S 121 5.16 5 C 20442 2.51 5 N 5567 2.21 5 O 6402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32692 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1745 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1702 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "C" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "D" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "E" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2330 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "G" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "H" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2323 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "I" Number of atoms: 4147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4147 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 13, 'TRANS': 480} Chain: "J" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "L" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 917 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1342 Classifications: {'RNAv2': 63} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 16, 'rna3p_pyr': 21} Link IDs: {'rna2p': 26, 'rna3p': 36} Chain: "N" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1282 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "O" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 620 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "P" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2618 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 15, 'TRANS': 311} Chain: "Q" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2508 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.43, per 1000 atoms: 0.20 Number of scatterers: 32692 At special positions: 0 Unit cell: (105.4, 168.64, 254.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 121 16.00 P 159 15.00 Mg 1 11.99 O 6402 8.00 N 5567 7.00 C 20442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6750 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 49 sheets defined 42.9% alpha, 18.0% beta 56 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 32 through 44 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.634A pdb=" N THR B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.617A pdb=" N ILE C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 196 through 206 removed outlier: 3.873A pdb=" N MET C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.897A pdb=" N GLY C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 277 through 285 removed outlier: 3.610A pdb=" N GLN C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.535A pdb=" N MET C 305 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.644A pdb=" N MET D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.751A pdb=" N GLY D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 277 through 284 removed outlier: 4.019A pdb=" N ASP D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 301 through 318 removed outlier: 3.612A pdb=" N MET D 305 " --> pdb=" O ASN D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.586A pdb=" N ILE E 60 " --> pdb=" O GLY E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 196 through 206 removed outlier: 3.772A pdb=" N MET E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 277 through 285 removed outlier: 3.910A pdb=" N ASP E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 301 through 318 removed outlier: 3.644A pdb=" N MET E 305 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.634A pdb=" N ILE F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 196 through 206 removed outlier: 3.932A pdb=" N MET F 200 " --> pdb=" O ARG F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.716A pdb=" N ASP F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 301 through 318 removed outlier: 3.542A pdb=" N MET F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.749A pdb=" N ILE G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 206 removed outlier: 3.670A pdb=" N MET G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.517A pdb=" N ILE G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.949A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 296 Processing helix chain 'G' and resid 301 through 317 Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 56 through 71 removed outlier: 3.526A pdb=" N ILE H 60 " --> pdb=" O GLY H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 206 removed outlier: 3.671A pdb=" N MET H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.886A pdb=" N GLY H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 270 No H-bonds generated for 'chain 'H' and resid 268 through 270' Processing helix chain 'H' and resid 277 through 284 removed outlier: 3.946A pdb=" N ASP H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 296 Processing helix chain 'H' and resid 301 through 318 Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.595A pdb=" N ARG I 46 " --> pdb=" O SER I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.940A pdb=" N ALA I 70 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 152 through 157 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'I' and resid 253 through 257 removed outlier: 3.572A pdb=" N PHE I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 257' Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 312 through 325 Processing helix chain 'I' and resid 342 through 355 removed outlier: 3.641A pdb=" N SER I 346 " --> pdb=" O ASN I 342 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 367 Processing helix chain 'I' and resid 373 through 393 removed outlier: 3.957A pdb=" N GLN I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLU I 384 " --> pdb=" O PHE I 380 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY I 385 " --> pdb=" O SER I 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 421 removed outlier: 4.544A pdb=" N TYR I 399 " --> pdb=" O GLU I 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 443 Processing helix chain 'I' and resid 445 through 461 removed outlier: 3.756A pdb=" N GLY I 461 " --> pdb=" O LEU I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 469 Processing helix chain 'I' and resid 469 through 480 Processing helix chain 'I' and resid 481 through 495 Processing helix chain 'J' and resid 5 through 33 Processing helix chain 'J' and resid 41 through 54 Processing helix chain 'J' and resid 58 through 73 removed outlier: 6.086A pdb=" N TYR J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY J 73 " --> pdb=" O LEU J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 81 Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 108 Processing helix chain 'J' and resid 109 through 112 Processing helix chain 'K' and resid 5 through 33 Processing helix chain 'K' and resid 41 through 54 Processing helix chain 'K' and resid 58 through 73 removed outlier: 6.029A pdb=" N TYR K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 3.769A pdb=" N HIS K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 91 removed outlier: 4.059A pdb=" N ILE K 85 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 109 removed outlier: 4.502A pdb=" N LYS K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 33 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 57 through 73 removed outlier: 3.800A pdb=" N GLY L 73 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 81 removed outlier: 3.549A pdb=" N HIS L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 Processing helix chain 'L' and resid 93 through 107 Processing helix chain 'P' and resid 36 through 48 Processing helix chain 'P' and resid 51 through 65 removed outlier: 4.670A pdb=" N ALA P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 69 through 74 Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 78 through 83 Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 95 through 110 Processing helix chain 'P' and resid 113 through 118 removed outlier: 3.603A pdb=" N THR P 118 " --> pdb=" O ARG P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 123 Processing helix chain 'P' and resid 139 through 149 Processing helix chain 'P' and resid 156 through 161 Processing helix chain 'P' and resid 214 through 235 removed outlier: 4.557A pdb=" N VAL P 219 " --> pdb=" O GLU P 215 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN P 220 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR P 231 " --> pdb=" O LEU P 227 " (cutoff:3.500A) Proline residue: P 232 - end of helix removed outlier: 4.452A pdb=" N GLY P 235 " --> pdb=" O THR P 231 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 261 Processing helix chain 'P' and resid 263 through 281 removed outlier: 3.831A pdb=" N ASP P 267 " --> pdb=" O LYS P 263 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY P 270 " --> pdb=" O GLY P 266 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE P 271 " --> pdb=" O ASP P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 292 through 300 Processing helix chain 'P' and resid 303 through 310 Processing helix chain 'P' and resid 311 through 323 Processing helix chain 'Q' and resid 8 through 13 removed outlier: 3.716A pdb=" N LEU Q 12 " --> pdb=" O LEU Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 25 Processing helix chain 'Q' and resid 30 through 46 Processing helix chain 'Q' and resid 62 through 83 Proline residue: Q 80 - end of helix removed outlier: 4.384A pdb=" N GLU Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 117 removed outlier: 3.787A pdb=" N TYR Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 164 Processing helix chain 'Q' and resid 172 through 178 removed outlier: 3.534A pdb=" N LYS Q 178 " --> pdb=" O HIS Q 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 198 removed outlier: 4.237A pdb=" N GLN Q 186 " --> pdb=" O GLY Q 182 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET Q 198 " --> pdb=" O SER Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 214 Processing helix chain 'Q' and resid 217 through 224 removed outlier: 3.904A pdb=" N LEU Q 221 " --> pdb=" O LEU Q 217 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG Q 224 " --> pdb=" O GLN Q 220 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 254 Processing helix chain 'Q' and resid 266 through 273 removed outlier: 3.575A pdb=" N ARG Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 295 Processing helix chain 'Q' and resid 301 through 308 removed outlier: 3.868A pdb=" N ARG Q 308 " --> pdb=" O ASP Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 75 removed outlier: 3.984A pdb=" N LYS A 66 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 59 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 163 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 160 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A 186 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 150 removed outlier: 6.994A pdb=" N ILE A 6 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP A 104 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A 8 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 102 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 10 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 100 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.490A pdb=" N LYS B 72 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 150 removed outlier: 6.294A pdb=" N PHE B 177 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU B 119 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 43 through 45 removed outlier: 5.555A pdb=" N SER C 53 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 276 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 Processing sheet with id=AB4, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.280A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 45 removed outlier: 5.280A pdb=" N SER D 53 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 225 " --> pdb=" O LEU D 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 276 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 Processing sheet with id=AB8, first strand: chain 'D' and resid 155 through 156 Processing sheet with id=AB9, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AC1, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.620A pdb=" N SER E 225 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 276 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=AC4, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.565A pdb=" N LYS E 50 " --> pdb=" O TRP E 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'E' and resid 155 through 159 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 5.451A pdb=" N SER F 53 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 180 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 182 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR F 15 " --> pdb=" O TRP F 230 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP F 230 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR F 17 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE F 228 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR F 19 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU F 226 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 21 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 276 " --> pdb=" O TYR F 299 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.689A pdb=" N GLU F 174 " --> pdb=" O THR F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AD3, first strand: chain 'G' and resid 43 through 45 removed outlier: 5.398A pdb=" N SER G 53 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 183 " --> pdb=" O ASN G 143 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA G 145 " --> pdb=" O GLN G 181 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN G 181 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 180 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 225 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.782A pdb=" N GLY G 25 " --> pdb=" O THR G 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'G' and resid 77 through 80 Processing sheet with id=AD7, first strand: chain 'G' and resid 106 through 107 removed outlier: 4.048A pdb=" N PHE G 106 " --> pdb=" O ARG G 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 43 through 45 removed outlier: 5.307A pdb=" N SER H 53 " --> pdb=" O SER H 147 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR H 180 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR H 15 " --> pdb=" O TRP H 230 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TRP H 230 " --> pdb=" O TYR H 15 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR H 17 " --> pdb=" O PHE H 228 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE H 228 " --> pdb=" O TYR H 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR H 19 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU H 226 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU H 21 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY H 276 " --> pdb=" O TYR H 299 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AE3, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AE4, first strand: chain 'I' and resid 9 through 12 removed outlier: 4.081A pdb=" N ILE I 9 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 61 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 11 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 79 through 81 Processing sheet with id=AE6, first strand: chain 'I' and resid 120 through 131 removed outlier: 6.591A pdb=" N GLN I 121 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER I 143 " --> pdb=" O GLY I 123 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE I 125 " --> pdb=" O TYR I 141 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR I 141 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN I 127 " --> pdb=" O TYR I 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR I 139 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU I 129 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL I 137 " --> pdb=" O GLU I 129 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE8, first strand: chain 'I' and resid 258 through 259 removed outlier: 8.376A pdb=" N VAL I 259 " --> pdb=" O TYR I 211 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU I 213 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG I 228 " --> pdb=" O LEU I 214 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER I 304 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU I 291 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU I 302 " --> pdb=" O GLU I 291 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 332 through 333 Processing sheet with id=AF1, first strand: chain 'P' and resid 7 through 8 removed outlier: 3.544A pdb=" N TRP P 8 " --> pdb=" O THR Q 27 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR Q 27 " --> pdb=" O TRP P 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 166 through 167 removed outlier: 3.612A pdb=" N GLN P 172 " --> pdb=" O CYS P 167 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 55 through 57 Processing sheet with id=AF4, first strand: chain 'Q' and resid 91 through 95 removed outlier: 6.646A pdb=" N VAL Q 92 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP Q 171 " --> pdb=" O VAL Q 92 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE Q 94 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE Q 168 " --> pdb=" O CYS Q 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 1321 hydrogen bonds defined for protein. 3669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9809 1.34 - 1.46: 9111 1.46 - 1.59: 14378 1.59 - 1.71: 309 1.71 - 1.84: 187 Bond restraints: 33794 Sorted by residual: bond pdb=" C3' DT O 47 " pdb=" C2' DT O 47 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DT N 20 " pdb=" C2' DT N 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.43e+00 bond pdb=" C3' DG O 10 " pdb=" C2' DG O 10 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.31e+00 bond pdb=" O3' DC N 50 " pdb=" P DT N 51 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.20e-02 6.94e+03 6.93e+00 bond pdb=" C3' DA N 30 " pdb=" C2' DA N 30 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.22e+00 ... (remaining 33789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 45058 2.01 - 4.02: 1122 4.02 - 6.03: 148 6.03 - 8.05: 21 8.05 - 10.06: 2 Bond angle restraints: 46351 Sorted by residual: angle pdb=" O4' DC N 55 " pdb=" C4' DC N 55 " pdb=" C3' DC N 55 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 angle pdb=" N LEU J 103 " pdb=" CA LEU J 103 " pdb=" C LEU J 103 " ideal model delta sigma weight residual 110.97 105.85 5.12 1.09e+00 8.42e-01 2.20e+01 angle pdb=" O4' DA N 41 " pdb=" C4' DA N 41 " pdb=" C3' DA N 41 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT N 27 " pdb=" C4 DT N 27 " pdb=" O4 DT N 27 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N TYR K 108 " pdb=" CA TYR K 108 " pdb=" C TYR K 108 " ideal model delta sigma weight residual 112.90 107.11 5.79 1.31e+00 5.83e-01 1.96e+01 ... (remaining 46346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 18639 34.52 - 69.04: 1096 69.04 - 103.56: 70 103.56 - 138.07: 3 138.07 - 172.59: 3 Dihedral angle restraints: 19811 sinusoidal: 9291 harmonic: 10520 Sorted by residual: dihedral pdb=" C4' A M 37 " pdb=" C3' A M 37 " pdb=" C2' A M 37 " pdb=" C1' A M 37 " ideal model delta sinusoidal sigma weight residual 36.34 -37.89 74.24 1 3.10e+00 1.04e-01 7.28e+02 dihedral pdb=" C4' U M 49 " pdb=" C3' U M 49 " pdb=" C2' U M 49 " pdb=" C1' U M 49 " ideal model delta sinusoidal sigma weight residual 36.35 -37.30 73.64 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' G M 48 " pdb=" C3' G M 48 " pdb=" C2' G M 48 " pdb=" C1' G M 48 " ideal model delta sinusoidal sigma weight residual 36.35 -36.99 73.34 1 3.10e+00 1.04e-01 7.12e+02 ... (remaining 19808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4253 0.061 - 0.122: 609 0.122 - 0.183: 37 0.183 - 0.244: 66 0.244 - 0.305: 46 Chirality restraints: 5011 Sorted by residual: chirality pdb=" P C M 4 " pdb=" OP1 C M 4 " pdb=" OP2 C M 4 " pdb=" O5' C M 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" P A M 36 " pdb=" OP1 A M 36 " pdb=" OP2 A M 36 " pdb=" O5' A M 36 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' A M 7 " pdb=" C3' A M 7 " pdb=" O2' A M 7 " pdb=" C1' A M 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5008 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 246 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO F 247 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 247 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 247 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 61 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C PHE J 61 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE J 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS J 62 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 61 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C PHE K 61 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE K 61 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS K 62 " -0.018 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 407 2.58 - 3.16: 27945 3.16 - 3.74: 55156 3.74 - 4.32: 76341 4.32 - 4.90: 121425 Nonbonded interactions: 281274 Sorted by model distance: nonbonded pdb=" O3B ATP Q 600 " pdb="MG MG Q 601 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR Q 64 " pdb="MG MG Q 601 " model vdw 2.052 2.170 nonbonded pdb=" O4 U M 35 " pdb=" N6 A M 36 " model vdw 2.163 3.120 nonbonded pdb=" O4 U M 23 " pdb=" N6 A M 24 " model vdw 2.165 3.120 nonbonded pdb=" OG SER E 28 " pdb=" O GLU E 174 " model vdw 2.211 3.040 ... (remaining 281269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 12 through 109 or resid 133 through 319)) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.400 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.003 0.059 33794 Z= 0.228 Angle : 0.708 10.058 46351 Z= 0.426 Chirality : 0.055 0.305 5011 Planarity : 0.004 0.088 5356 Dihedral : 19.375 172.592 13061 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.59 % Favored : 92.93 % Rotamer: Outliers : 0.72 % Allowed : 20.38 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.06 (0.14), residues: 3552 helix: 1.26 (0.14), residues: 1332 sheet: -0.91 (0.20), residues: 640 loop : -0.72 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.038 0.001 TYR C 244 PHE 0.019 0.001 PHE G 234 TRP 0.038 0.001 TRP I 63 HIS 0.008 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.23 (33794) covalent geometry : angle 0.70827 / 0.43 (46351) hydrogen bonds : bond 0.17445 / 11.61 ( 1407) hydrogen bonds : angle 6.70653 / 4.60 ( 3939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 414 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6431 (tpt) cc_final: 0.6144 (tpt) REVERT: A 116 LEU cc_start: 0.9273 (tp) cc_final: 0.9016 (tp) REVERT: A 166 ASP cc_start: 0.7416 (t0) cc_final: 0.7192 (t0) REVERT: A 202 ASP cc_start: 0.8014 (p0) cc_final: 0.7730 (p0) REVERT: A 209 GLN cc_start: 0.8822 (tt0) cc_final: 0.8542 (mt0) REVERT: B 43 HIS cc_start: 0.8980 (t70) cc_final: 0.8729 (t70) REVERT: B 118 ARG cc_start: 0.5291 (tmt170) cc_final: 0.4076 (mtp180) REVERT: B 213 ARG cc_start: 0.4448 (tpp80) cc_final: 0.3944 (tpp80) REVERT: C 227 VAL cc_start: 0.9296 (t) cc_final: 0.9057 (p) REVERT: E 256 GLN cc_start: 0.8592 (tp40) cc_final: 0.8300 (tp-100) REVERT: F 260 ASP cc_start: 0.9096 (t0) cc_final: 0.8865 (t0) REVERT: I 358 TRP cc_start: 0.5735 (OUTLIER) cc_final: 0.5470 (p90) REVERT: J 37 LYS cc_start: 0.7961 (pttt) cc_final: 0.7733 (pttp) REVERT: J 87 LEU cc_start: 0.9233 (tp) cc_final: 0.8988 (tp) REVERT: K 5 SER cc_start: 0.8481 (t) cc_final: 0.8213 (p) REVERT: K 20 GLN cc_start: 0.8797 (tp40) cc_final: 0.8421 (tp40) REVERT: P 132 PHE cc_start: 0.7367 (m-80) cc_final: 0.7034 (m-10) REVERT: Q 79 LEU cc_start: 0.7910 (tp) cc_final: 0.7547 (mt) REVERT: Q 95 GLU cc_start: 0.4823 (tt0) cc_final: 0.4519 (pp20) REVERT: Q 124 HIS cc_start: 0.7081 (m-70) cc_final: 0.6790 (m-70) REVERT: Q 164 HIS cc_start: 0.8634 (t-90) cc_final: 0.8340 (t70) REVERT: Q 176 PHE cc_start: 0.6010 (m-80) cc_final: 0.5673 (m-80) REVERT: Q 321 GLU cc_start: 0.4913 (tt0) cc_final: 0.4625 (mm-30) outliers start: 23 outliers final: 6 residues processed: 428 average time/residue: 0.2021 time to fit residues: 141.3010 Evaluate side-chains 292 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 285 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain P residue 110 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN B 193 GLN B 195 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 342 ASN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.104229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.068278 restraints weight = 95243.315| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.84 r_work: 0.2910 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 33794 Z= 0.409 Angle : 1.013 19.344 46351 Z= 0.477 Chirality : 0.074 1.116 5011 Planarity : 0.006 0.094 5356 Dihedral : 18.214 171.806 5770 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.01 % Favored : 92.54 % Rotamer: Outliers : 3.83 % Allowed : 18.87 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -0.15 (0.14), residues: 3552 helix: 1.20 (0.14), residues: 1344 sheet: -1.07 (0.21), residues: 589 loop : -0.78 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 302 TYR 0.024 0.002 TYR D 183 PHE 0.021 0.002 PHE G 234 TRP 0.024 0.002 TRP I 63 HIS 0.009 0.002 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.41 (33794) covalent geometry : angle 1.01302 / 0.48 (46351) hydrogen bonds : bond 0.05508 / 3.74 ( 1407) hydrogen bonds : angle 5.39878 / 3.74 ( 3939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 271 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6986 (tm-30) REVERT: A 202 ASP cc_start: 0.8382 (p0) cc_final: 0.7977 (p0) REVERT: B 118 ARG cc_start: 0.4925 (tmt170) cc_final: 0.3558 (ttt-90) REVERT: D 136 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7356 (ttt90) REVERT: E 77 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8538 (ttp-170) REVERT: E 152 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8848 (p0) REVERT: E 256 GLN cc_start: 0.8405 (tp40) cc_final: 0.8086 (tp-100) REVERT: F 30 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8017 (m110) REVERT: F 137 MET cc_start: 0.8495 (tpp) cc_final: 0.8199 (tpp) REVERT: G 77 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7597 (mtm-85) REVERT: G 229 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: H 251 GLU cc_start: 0.8268 (mp0) cc_final: 0.7899 (mp0) REVERT: I 62 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: I 152 PHE cc_start: 0.8171 (t80) cc_final: 0.7868 (t80) REVERT: I 358 TRP cc_start: 0.5693 (OUTLIER) cc_final: 0.5408 (p90) REVERT: L 103 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9156 (mm) REVERT: Q 14 ARG cc_start: 0.7151 (mmm-85) cc_final: 0.6890 (mmm160) REVERT: Q 95 GLU cc_start: 0.5975 (tt0) cc_final: 0.5527 (pp20) outliers start: 122 outliers final: 47 residues processed: 377 average time/residue: 0.1944 time to fit residues: 121.0321 Evaluate side-chains 302 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 229 GLN Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 238 ASP Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 253 VAL Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 311 optimal weight: 20.0000 chunk 274 optimal weight: 0.9980 chunk 348 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.107075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071570 restraints weight = 93371.807| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.77 r_work: 0.3012 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33794 Z= 0.164 Angle : 0.781 14.205 46351 Z= 0.377 Chirality : 0.062 1.107 5011 Planarity : 0.005 0.095 5356 Dihedral : 18.277 172.164 5764 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.78 % Favored : 92.79 % Rotamer: Outliers : 2.98 % Allowed : 18.93 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.05 (0.14), residues: 3552 helix: 1.43 (0.14), residues: 1342 sheet: -1.04 (0.21), residues: 600 loop : -0.67 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 98 TYR 0.020 0.002 TYR G 182 PHE 0.024 0.001 PHE Q 270 TRP 0.025 0.001 TRP I 63 HIS 0.008 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (33794) covalent geometry : angle 0.78115 / 0.38 (46351) hydrogen bonds : bond 0.04288 / 2.84 ( 1407) hydrogen bonds : angle 4.86882 / 3.37 ( 3939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 298 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6632 (tpt) cc_final: 0.6131 (tpt) REVERT: A 140 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 146 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7793 (tttp) REVERT: A 202 ASP cc_start: 0.8291 (p0) cc_final: 0.7772 (p0) REVERT: A 209 GLN cc_start: 0.8888 (mt0) cc_final: 0.8623 (mt0) REVERT: B 43 HIS cc_start: 0.9067 (t70) cc_final: 0.8808 (t70) REVERT: B 118 ARG cc_start: 0.4526 (tmt170) cc_final: 0.3529 (ttt180) REVERT: C 179 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8146 (ptp90) REVERT: C 244 TYR cc_start: 0.7010 (t80) cc_final: 0.6640 (t80) REVERT: E 181 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.9025 (pt0) REVERT: E 256 GLN cc_start: 0.8419 (tp40) cc_final: 0.8031 (tp-100) REVERT: F 28 SER cc_start: 0.8892 (m) cc_final: 0.8564 (m) REVERT: F 77 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8635 (ttp-170) REVERT: F 137 MET cc_start: 0.8432 (tpp) cc_final: 0.7991 (tpt) REVERT: G 77 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8434 (ttp-170) REVERT: G 160 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8573 (mmtp) REVERT: H 251 GLU cc_start: 0.8431 (mp0) cc_final: 0.7867 (mp0) REVERT: H 302 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8347 (mtt90) REVERT: H 305 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8353 (tpp) REVERT: I 62 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: I 152 PHE cc_start: 0.8101 (t80) cc_final: 0.7778 (t80) REVERT: I 358 TRP cc_start: 0.5644 (OUTLIER) cc_final: 0.5340 (p90) REVERT: I 451 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8770 (tp30) REVERT: K 20 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8673 (tp40) REVERT: L 103 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9095 (mm) REVERT: P 132 PHE cc_start: 0.7221 (m-80) cc_final: 0.6830 (m-10) REVERT: P 154 TYR cc_start: 0.8252 (p90) cc_final: 0.7786 (p90) REVERT: Q 95 GLU cc_start: 0.5271 (tt0) cc_final: 0.4899 (pp20) REVERT: Q 123 ASP cc_start: 0.9043 (p0) cc_final: 0.8789 (t0) REVERT: Q 176 PHE cc_start: 0.7794 (m-80) cc_final: 0.7576 (m-80) outliers start: 95 outliers final: 44 residues processed: 369 average time/residue: 0.2062 time to fit residues: 126.6755 Evaluate side-chains 319 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 281 ASP Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 224 ARG Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 240 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 315 optimal weight: 5.9990 chunk 262 optimal weight: 0.2980 chunk 268 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 GLN B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.107438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072066 restraints weight = 92980.366| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.81 r_work: 0.3003 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33794 Z= 0.150 Angle : 0.734 13.499 46351 Z= 0.355 Chirality : 0.058 1.054 5011 Planarity : 0.005 0.095 5356 Dihedral : 18.111 171.885 5759 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.31 % Favored : 93.30 % Rotamer: Outliers : 3.14 % Allowed : 19.15 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.14 (0.15), residues: 3552 helix: 1.48 (0.14), residues: 1341 sheet: -0.92 (0.21), residues: 590 loop : -0.63 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 98 TYR 0.023 0.001 TYR C 17 PHE 0.022 0.001 PHE Q 54 TRP 0.028 0.001 TRP I 63 HIS 0.008 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (33794) covalent geometry : angle 0.73375 / 0.36 (46351) hydrogen bonds : bond 0.03848 / 2.57 ( 1407) hydrogen bonds : angle 4.63862 / 3.21 ( 3939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 282 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8038 (tpp) cc_final: 0.7808 (tpt) REVERT: A 92 TYR cc_start: 0.9029 (m-80) cc_final: 0.8753 (m-80) REVERT: A 146 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7588 (tttp) REVERT: A 202 ASP cc_start: 0.8260 (p0) cc_final: 0.7744 (p0) REVERT: A 209 GLN cc_start: 0.8819 (mt0) cc_final: 0.8556 (mt0) REVERT: B 43 HIS cc_start: 0.9040 (t70) cc_final: 0.8779 (t70) REVERT: B 99 TYR cc_start: 0.8193 (m-80) cc_final: 0.7835 (m-80) REVERT: B 118 ARG cc_start: 0.4328 (tmt170) cc_final: 0.3347 (ttt180) REVERT: C 179 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8057 (ptp90) REVERT: C 244 TYR cc_start: 0.6944 (t80) cc_final: 0.6546 (t80) REVERT: E 152 ASP cc_start: 0.9033 (p0) cc_final: 0.8591 (p0) REVERT: E 256 GLN cc_start: 0.8394 (tp40) cc_final: 0.7986 (tp-100) REVERT: F 28 SER cc_start: 0.8879 (m) cc_final: 0.8589 (m) REVERT: F 30 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7608 (m110) REVERT: F 77 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8722 (ttp-170) REVERT: F 137 MET cc_start: 0.8339 (tpp) cc_final: 0.7985 (tpp) REVERT: F 181 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8716 (tt0) REVERT: G 77 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7706 (mtm-85) REVERT: H 251 GLU cc_start: 0.8436 (mp0) cc_final: 0.7867 (mp0) REVERT: H 305 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8294 (tpp) REVERT: I 62 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7188 (m-10) REVERT: I 152 PHE cc_start: 0.8074 (t80) cc_final: 0.7764 (t80) REVERT: I 358 TRP cc_start: 0.5640 (OUTLIER) cc_final: 0.5297 (p90) REVERT: I 451 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8774 (tp30) REVERT: K 20 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8585 (tp40) REVERT: K 95 GLN cc_start: 0.9075 (mp10) cc_final: 0.8872 (mp10) REVERT: K 107 SER cc_start: 0.8394 (p) cc_final: 0.7702 (t) REVERT: L 82 GLN cc_start: 0.8086 (mt0) cc_final: 0.7779 (mt0) REVERT: L 103 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9084 (mm) REVERT: P 132 PHE cc_start: 0.7171 (m-80) cc_final: 0.6809 (m-10) REVERT: Q 95 GLU cc_start: 0.5246 (tt0) cc_final: 0.4898 (pp20) outliers start: 100 outliers final: 43 residues processed: 363 average time/residue: 0.1955 time to fit residues: 117.5434 Evaluate side-chains 313 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 349 optimal weight: 20.0000 chunk 325 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN I 256 GLN ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN Q 124 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.107035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071715 restraints weight = 93720.371| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.77 r_work: 0.3016 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33794 Z= 0.163 Angle : 0.717 12.949 46351 Z= 0.350 Chirality : 0.057 1.063 5011 Planarity : 0.004 0.096 5356 Dihedral : 18.060 172.034 5759 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.48 % Favored : 93.13 % Rotamer: Outliers : 2.89 % Allowed : 19.59 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.19 (0.15), residues: 3552 helix: 1.55 (0.14), residues: 1335 sheet: -0.89 (0.21), residues: 590 loop : -0.63 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 98 TYR 0.024 0.001 TYR C 17 PHE 0.021 0.001 PHE Q 54 TRP 0.027 0.001 TRP I 63 HIS 0.009 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33794) covalent geometry : angle 0.71749 / 0.35 (46351) hydrogen bonds : bond 0.03724 / 2.49 ( 1407) hydrogen bonds : angle 4.55977 / 3.16 ( 3939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 279 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6391 (tpt) cc_final: 0.5648 (tpt) REVERT: A 24 MET cc_start: 0.8139 (tpp) cc_final: 0.7922 (tpp) REVERT: A 39 MET cc_start: 0.9356 (tmm) cc_final: 0.9112 (tmm) REVERT: A 202 ASP cc_start: 0.8302 (p0) cc_final: 0.7782 (p0) REVERT: A 209 GLN cc_start: 0.8836 (mt0) cc_final: 0.8557 (mt0) REVERT: B 43 HIS cc_start: 0.9083 (t70) cc_final: 0.8834 (t70) REVERT: B 99 TYR cc_start: 0.8221 (m-80) cc_final: 0.7877 (m-80) REVERT: B 118 ARG cc_start: 0.4263 (tmt170) cc_final: 0.3275 (ttt180) REVERT: B 213 ARG cc_start: 0.4272 (tpp80) cc_final: 0.2972 (tpm170) REVERT: C 244 TYR cc_start: 0.6991 (t80) cc_final: 0.6607 (t80) REVERT: E 152 ASP cc_start: 0.9066 (p0) cc_final: 0.8627 (p0) REVERT: E 181 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8973 (pt0) REVERT: E 256 GLN cc_start: 0.8461 (tp40) cc_final: 0.8042 (tp-100) REVERT: F 77 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8799 (ttp-170) REVERT: F 137 MET cc_start: 0.8314 (tpp) cc_final: 0.7950 (tpp) REVERT: F 181 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8793 (tt0) REVERT: G 77 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7711 (mtm-85) REVERT: H 251 GLU cc_start: 0.8458 (mp0) cc_final: 0.7875 (mp0) REVERT: H 305 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8331 (tpp) REVERT: I 62 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: I 152 PHE cc_start: 0.8125 (t80) cc_final: 0.7810 (t80) REVERT: I 358 TRP cc_start: 0.5559 (OUTLIER) cc_final: 0.5278 (p90) REVERT: I 451 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8792 (tp30) REVERT: J 112 ASP cc_start: 0.6125 (OUTLIER) cc_final: 0.4917 (p0) REVERT: K 20 GLN cc_start: 0.9063 (tp-100) cc_final: 0.8579 (tp40) REVERT: K 49 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8816 (tmm-80) REVERT: K 95 GLN cc_start: 0.9098 (mp10) cc_final: 0.8871 (mp10) REVERT: K 107 SER cc_start: 0.8306 (p) cc_final: 0.7520 (t) REVERT: L 82 GLN cc_start: 0.8076 (mt0) cc_final: 0.7734 (mt0) REVERT: L 103 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9105 (mm) REVERT: P 40 TYR cc_start: 0.8758 (t80) cc_final: 0.8490 (t80) REVERT: Q 95 GLU cc_start: 0.5086 (tt0) cc_final: 0.4740 (pp20) REVERT: Q 271 TYR cc_start: 0.0403 (OUTLIER) cc_final: -0.0266 (m-10) outliers start: 92 outliers final: 58 residues processed: 352 average time/residue: 0.1966 time to fit residues: 114.6220 Evaluate side-chains 329 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 259 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 181 GLN Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 62 PHE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 49 ARG Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 297 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 333 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.104897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069263 restraints weight = 93765.595| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.67 r_work: 0.2964 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33794 Z= 0.246 Angle : 0.757 12.986 46351 Z= 0.369 Chirality : 0.057 1.112 5011 Planarity : 0.005 0.099 5356 Dihedral : 18.037 172.241 5759 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.70 % Favored : 92.91 % Rotamer: Outliers : 3.30 % Allowed : 19.62 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.16 (0.15), residues: 3552 helix: 1.55 (0.14), residues: 1328 sheet: -0.99 (0.21), residues: 597 loop : -0.61 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 42 TYR 0.029 0.002 TYR C 17 PHE 0.024 0.001 PHE Q 54 TRP 0.031 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (33794) covalent geometry : angle 0.75684 / 0.37 (46351) hydrogen bonds : bond 0.03937 / 2.66 ( 1407) hydrogen bonds : angle 4.60793 / 3.20 ( 3939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 265 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6368 (tpt) cc_final: 0.5619 (tpt) REVERT: A 39 MET cc_start: 0.9348 (tmm) cc_final: 0.9131 (tmm) REVERT: A 202 ASP cc_start: 0.8335 (p0) cc_final: 0.7865 (p0) REVERT: B 43 HIS cc_start: 0.9122 (t70) cc_final: 0.8878 (t70) REVERT: B 99 TYR cc_start: 0.8214 (m-80) cc_final: 0.7648 (m-80) REVERT: B 118 ARG cc_start: 0.4302 (tmt170) cc_final: 0.3191 (tpt-90) REVERT: B 187 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 179 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8299 (ptp90) REVERT: C 244 TYR cc_start: 0.7134 (t80) cc_final: 0.6642 (t80) REVERT: E 152 ASP cc_start: 0.9119 (p0) cc_final: 0.8729 (p0) REVERT: E 181 GLN cc_start: 0.9325 (OUTLIER) cc_final: 0.9012 (pt0) REVERT: E 256 GLN cc_start: 0.8493 (tp40) cc_final: 0.8080 (tp-100) REVERT: F 77 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8788 (ttp-170) REVERT: F 136 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6929 (mmm-85) REVERT: G 77 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7784 (mtm-85) REVERT: G 160 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8889 (mmtp) REVERT: H 101 ASP cc_start: 0.8524 (m-30) cc_final: 0.8302 (m-30) REVERT: H 251 GLU cc_start: 0.8510 (mp0) cc_final: 0.7924 (mp0) REVERT: H 305 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8294 (tpp) REVERT: I 152 PHE cc_start: 0.8088 (t80) cc_final: 0.7826 (t80) REVERT: I 358 TRP cc_start: 0.5696 (OUTLIER) cc_final: 0.5431 (p90) REVERT: I 451 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8793 (tp30) REVERT: J 20 GLN cc_start: 0.9385 (tp40) cc_final: 0.8816 (tm-30) REVERT: K 20 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8740 (tp40) REVERT: K 95 GLN cc_start: 0.9178 (mp10) cc_final: 0.8893 (mp10) REVERT: K 107 SER cc_start: 0.8338 (p) cc_final: 0.7467 (t) REVERT: L 82 GLN cc_start: 0.8138 (mt0) cc_final: 0.7753 (mt0) REVERT: L 103 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9183 (mm) REVERT: Q 95 GLU cc_start: 0.5158 (tt0) cc_final: 0.4831 (pp20) REVERT: Q 271 TYR cc_start: 0.0519 (OUTLIER) cc_final: -0.0104 (m-80) outliers start: 105 outliers final: 62 residues processed: 347 average time/residue: 0.2047 time to fit residues: 117.5130 Evaluate side-chains 326 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 284 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 72 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 338 optimal weight: 40.0000 chunk 179 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 196 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 311 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Q 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.106325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.070920 restraints weight = 93581.536| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.78 r_work: 0.2999 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33794 Z= 0.158 Angle : 0.711 12.715 46351 Z= 0.347 Chirality : 0.055 1.062 5011 Planarity : 0.004 0.099 5356 Dihedral : 17.938 172.080 5757 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.70 % Favored : 92.91 % Rotamer: Outliers : 3.27 % Allowed : 19.50 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.25 (0.15), residues: 3552 helix: 1.61 (0.14), residues: 1329 sheet: -0.92 (0.21), residues: 593 loop : -0.57 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 42 TYR 0.027 0.001 TYR C 17 PHE 0.026 0.001 PHE Q 54 TRP 0.031 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (33794) covalent geometry : angle 0.71119 / 0.35 (46351) hydrogen bonds : bond 0.03660 / 2.45 ( 1407) hydrogen bonds : angle 4.47211 / 3.10 ( 3939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 280 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6384 (tpt) cc_final: 0.5660 (tpt) REVERT: A 39 MET cc_start: 0.9289 (tmm) cc_final: 0.9059 (tmm) REVERT: A 202 ASP cc_start: 0.8323 (p0) cc_final: 0.7848 (p0) REVERT: B 43 HIS cc_start: 0.9113 (t70) cc_final: 0.8859 (t70) REVERT: B 99 TYR cc_start: 0.8209 (m-80) cc_final: 0.7648 (m-80) REVERT: B 118 ARG cc_start: 0.4149 (tmt170) cc_final: 0.3254 (ttt180) REVERT: B 187 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 213 ARG cc_start: 0.4207 (tpp80) cc_final: 0.2851 (tpm170) REVERT: C 179 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8087 (ptp90) REVERT: C 244 TYR cc_start: 0.7103 (t80) cc_final: 0.6751 (t80) REVERT: C 294 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8008 (t0) REVERT: D 77 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8867 (ttp-170) REVERT: D 209 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8628 (pttp) REVERT: E 152 ASP cc_start: 0.9081 (p0) cc_final: 0.8668 (p0) REVERT: E 181 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8990 (pt0) REVERT: E 247 PRO cc_start: 0.7758 (Cg_exo) cc_final: 0.7550 (Cg_endo) REVERT: E 256 GLN cc_start: 0.8509 (tp40) cc_final: 0.8090 (tp-100) REVERT: F 28 SER cc_start: 0.8937 (m) cc_final: 0.8624 (m) REVERT: F 30 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7642 (m110) REVERT: F 77 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8805 (ttp-170) REVERT: G 77 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7768 (mtm-85) REVERT: G 160 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8800 (mmtp) REVERT: H 101 ASP cc_start: 0.8522 (m-30) cc_final: 0.8285 (m-30) REVERT: H 251 GLU cc_start: 0.8458 (mp0) cc_final: 0.7882 (mp0) REVERT: H 305 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8324 (tpp) REVERT: I 26 MET cc_start: 0.8874 (mmm) cc_final: 0.8270 (mmt) REVERT: I 152 PHE cc_start: 0.8042 (t80) cc_final: 0.7774 (t80) REVERT: I 358 TRP cc_start: 0.5671 (OUTLIER) cc_final: 0.5438 (p90) REVERT: I 451 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8746 (tp30) REVERT: J 112 ASP cc_start: 0.6125 (OUTLIER) cc_final: 0.4863 (p0) REVERT: K 20 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8747 (tp40) REVERT: K 95 GLN cc_start: 0.9167 (mp10) cc_final: 0.8876 (mp10) REVERT: K 107 SER cc_start: 0.8351 (p) cc_final: 0.7375 (t) REVERT: L 82 GLN cc_start: 0.8116 (mt0) cc_final: 0.7683 (mt0) REVERT: L 103 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9156 (mm) REVERT: P 54 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7606 (ttmm) REVERT: P 154 TYR cc_start: 0.8304 (p90) cc_final: 0.7769 (p90) REVERT: Q 271 TYR cc_start: 0.0772 (OUTLIER) cc_final: 0.0143 (m-80) outliers start: 104 outliers final: 65 residues processed: 359 average time/residue: 0.1909 time to fit residues: 113.3326 Evaluate side-chains 337 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 257 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 ASN Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 160 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 358 TRP Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 30 TYR Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 124 HIS Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 139 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 328 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 296 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068948 restraints weight = 94472.075| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.78 r_work: 0.2959 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 33794 Z= 0.260 Angle : 0.759 12.752 46351 Z= 0.371 Chirality : 0.056 1.118 5011 Planarity : 0.005 0.101 5356 Dihedral : 17.932 171.948 5757 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.81 % Favored : 92.79 % Rotamer: Outliers : 2.89 % Allowed : 20.13 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.17 (0.15), residues: 3552 helix: 1.54 (0.14), residues: 1329 sheet: -0.97 (0.21), residues: 592 loop : -0.61 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 42 TYR 0.027 0.002 TYR C 17 PHE 0.034 0.002 PHE Q 54 TRP 0.032 0.001 TRP I 63 HIS 0.025 0.001 HIS Q 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.26 (33794) covalent geometry : angle 0.75908 / 0.37 (46351) hydrogen bonds : bond 0.03897 / 2.63 ( 1407) hydrogen bonds : angle 4.56425 / 3.17 ( 3939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 262 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6371 (tpt) cc_final: 0.5690 (tpt) REVERT: A 24 MET cc_start: 0.8215 (tpp) cc_final: 0.7980 (tpp) REVERT: A 92 TYR cc_start: 0.9020 (m-80) cc_final: 0.8750 (m-80) REVERT: A 202 ASP cc_start: 0.8321 (p0) cc_final: 0.7942 (p0) REVERT: B 99 TYR cc_start: 0.8246 (m-80) cc_final: 0.7707 (m-80) REVERT: B 118 ARG cc_start: 0.4280 (tmt170) cc_final: 0.3234 (tpt-90) REVERT: B 187 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7780 (tm-30) REVERT: C 179 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8256 (ptp90) REVERT: C 244 TYR cc_start: 0.7215 (t80) cc_final: 0.6751 (t80) REVERT: E 152 ASP cc_start: 0.9144 (p0) cc_final: 0.8772 (p0) REVERT: E 181 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.9019 (pt0) REVERT: E 256 GLN cc_start: 0.8490 (tp40) cc_final: 0.8071 (tp-100) REVERT: F 77 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8813 (ttp-170) REVERT: F 136 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6971 (mmm-85) REVERT: F 137 MET cc_start: 0.8626 (tpt) cc_final: 0.8247 (tpt) REVERT: G 77 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7790 (mtm-85) REVERT: G 164 GLU cc_start: 0.9187 (tp30) cc_final: 0.8961 (pm20) REVERT: H 101 ASP cc_start: 0.8540 (m-30) cc_final: 0.8284 (m-30) REVERT: H 251 GLU cc_start: 0.8507 (mp0) cc_final: 0.7885 (mp0) REVERT: H 305 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8268 (tpp) REVERT: I 152 PHE cc_start: 0.8075 (t80) cc_final: 0.7810 (t80) REVERT: J 20 GLN cc_start: 0.9394 (tp40) cc_final: 0.8853 (tm-30) REVERT: J 112 ASP cc_start: 0.6081 (OUTLIER) cc_final: 0.4828 (p0) REVERT: K 20 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8724 (tp40) REVERT: L 82 GLN cc_start: 0.8129 (mt0) cc_final: 0.7923 (mp10) REVERT: L 95 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8935 (mp10) REVERT: L 103 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9195 (mm) REVERT: P 154 TYR cc_start: 0.8424 (p90) cc_final: 0.7911 (p90) REVERT: Q 271 TYR cc_start: 0.0796 (OUTLIER) cc_final: 0.0131 (m-80) outliers start: 92 outliers final: 68 residues processed: 331 average time/residue: 0.2025 time to fit residues: 111.0171 Evaluate side-chains 333 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 180 ILE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 331 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 10 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.104477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.069026 restraints weight = 93331.452| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.77 r_work: 0.2950 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33794 Z= 0.246 Angle : 0.759 12.762 46351 Z= 0.371 Chirality : 0.056 1.118 5011 Planarity : 0.005 0.103 5356 Dihedral : 17.909 171.869 5755 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.90 % Favored : 92.68 % Rotamer: Outliers : 2.83 % Allowed : 20.31 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.16 (0.15), residues: 3552 helix: 1.48 (0.14), residues: 1333 sheet: -0.93 (0.21), residues: 587 loop : -0.58 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 42 TYR 0.047 0.002 TYR A 37 PHE 0.037 0.001 PHE Q 54 TRP 0.037 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (33794) covalent geometry : angle 0.75852 / 0.37 (46351) hydrogen bonds : bond 0.03883 / 2.62 ( 1407) hydrogen bonds : angle 4.57165 / 3.18 ( 3939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 263 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6409 (tpt) cc_final: 0.5738 (tpt) REVERT: A 24 MET cc_start: 0.8289 (tpp) cc_final: 0.8014 (tpp) REVERT: A 92 TYR cc_start: 0.9041 (m-80) cc_final: 0.8730 (m-80) REVERT: A 202 ASP cc_start: 0.8307 (p0) cc_final: 0.7929 (p0) REVERT: B 99 TYR cc_start: 0.8290 (m-80) cc_final: 0.7649 (m-80) REVERT: B 118 ARG cc_start: 0.4101 (tmt170) cc_final: 0.3105 (tpt-90) REVERT: B 187 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 179 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8268 (ptp90) REVERT: C 244 TYR cc_start: 0.7227 (t80) cc_final: 0.6785 (t80) REVERT: D 156 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9013 (tptt) REVERT: D 209 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8729 (pttp) REVERT: E 152 ASP cc_start: 0.9161 (p0) cc_final: 0.8769 (p0) REVERT: E 256 GLN cc_start: 0.8518 (tp40) cc_final: 0.8097 (tp-100) REVERT: F 77 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8826 (ttp-170) REVERT: F 137 MET cc_start: 0.8611 (tpt) cc_final: 0.8286 (tpt) REVERT: G 77 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7763 (mtm-85) REVERT: G 164 GLU cc_start: 0.9191 (tp30) cc_final: 0.8963 (pm20) REVERT: H 101 ASP cc_start: 0.8555 (m-30) cc_final: 0.8292 (m-30) REVERT: H 251 GLU cc_start: 0.8486 (mp0) cc_final: 0.7898 (mp0) REVERT: H 305 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8297 (tpp) REVERT: I 26 MET cc_start: 0.8941 (mmm) cc_final: 0.8381 (mmt) REVERT: I 152 PHE cc_start: 0.8103 (t80) cc_final: 0.7830 (t80) REVERT: I 396 ASP cc_start: 0.7108 (t0) cc_final: 0.6587 (t70) REVERT: I 451 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8733 (tp30) REVERT: J 20 GLN cc_start: 0.9398 (tp40) cc_final: 0.8854 (tm-30) REVERT: J 112 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.4840 (p0) REVERT: K 20 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8725 (tp40) REVERT: L 95 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8840 (mp10) REVERT: L 103 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9182 (mm) REVERT: P 54 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7616 (ttmm) REVERT: P 154 TYR cc_start: 0.8499 (p90) cc_final: 0.8040 (p90) REVERT: Q 42 ARG cc_start: 0.7636 (tpt90) cc_final: 0.6990 (ptp-110) REVERT: Q 95 GLU cc_start: 0.5146 (tt0) cc_final: 0.4823 (pp20) REVERT: Q 271 TYR cc_start: 0.0793 (OUTLIER) cc_final: 0.0568 (m-10) outliers start: 90 outliers final: 69 residues processed: 329 average time/residue: 0.1982 time to fit residues: 107.7165 Evaluate side-chains 334 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 254 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 245 CYS Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 142 MET Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 315 LEU Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 451 GLU Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 10 GLN Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain P residue 329 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 124 HIS Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 96 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 117 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 170 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.105986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070795 restraints weight = 93516.839| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.69 r_work: 0.2998 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33794 Z= 0.149 Angle : 0.726 12.630 46351 Z= 0.355 Chirality : 0.054 1.048 5011 Planarity : 0.004 0.103 5356 Dihedral : 17.849 171.917 5755 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.76 % Favored : 92.85 % Rotamer: Outliers : 2.32 % Allowed : 21.07 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.27 (0.15), residues: 3552 helix: 1.55 (0.14), residues: 1335 sheet: -0.86 (0.22), residues: 587 loop : -0.51 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 42 TYR 0.045 0.002 TYR A 37 PHE 0.041 0.001 PHE Q 54 TRP 0.038 0.001 TRP I 63 HIS 0.024 0.001 HIS Q 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (33794) covalent geometry : angle 0.72591 / 0.36 (46351) hydrogen bonds : bond 0.03707 / 2.47 ( 1407) hydrogen bonds : angle 4.46381 / 3.10 ( 3939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7104 Ramachandran restraints generated. 3552 Oldfield, 0 Emsley, 3552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 277 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6389 (tpt) cc_final: 0.5746 (tpt) REVERT: A 24 MET cc_start: 0.8293 (tpp) cc_final: 0.8082 (tpp) REVERT: A 92 TYR cc_start: 0.9025 (m-80) cc_final: 0.8758 (m-80) REVERT: A 202 ASP cc_start: 0.8343 (p0) cc_final: 0.7874 (p0) REVERT: B 99 TYR cc_start: 0.8308 (m-80) cc_final: 0.7678 (m-80) REVERT: B 118 ARG cc_start: 0.4180 (tmt170) cc_final: 0.3307 (ttt180) REVERT: B 187 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 213 ARG cc_start: 0.4290 (tpp80) cc_final: 0.2911 (tpm170) REVERT: C 179 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8361 (ptm160) REVERT: C 244 TYR cc_start: 0.7182 (t80) cc_final: 0.6764 (t80) REVERT: C 294 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8122 (t0) REVERT: D 156 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9003 (tptt) REVERT: E 137 MET cc_start: 0.9090 (tpp) cc_final: 0.8871 (tpp) REVERT: E 152 ASP cc_start: 0.9079 (p0) cc_final: 0.8676 (p0) REVERT: E 181 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8990 (pt0) REVERT: E 256 GLN cc_start: 0.8502 (tp40) cc_final: 0.8074 (tp-100) REVERT: F 28 SER cc_start: 0.8831 (m) cc_final: 0.8583 (m) REVERT: F 77 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8824 (ttp-170) REVERT: F 136 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6941 (mmm-85) REVERT: F 137 MET cc_start: 0.8529 (tpt) cc_final: 0.8135 (tpp) REVERT: F 247 PRO cc_start: 0.9046 (Cg_exo) cc_final: 0.8833 (Cg_endo) REVERT: G 77 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8035 (mtm-85) REVERT: G 152 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8694 (p0) REVERT: G 164 GLU cc_start: 0.9162 (tp30) cc_final: 0.8955 (pm20) REVERT: H 101 ASP cc_start: 0.8558 (m-30) cc_final: 0.8291 (m-30) REVERT: H 251 GLU cc_start: 0.8442 (mp0) cc_final: 0.7861 (mp0) REVERT: H 305 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8334 (tpp) REVERT: I 26 MET cc_start: 0.8897 (mmm) cc_final: 0.8312 (mmt) REVERT: I 152 PHE cc_start: 0.8003 (t80) cc_final: 0.7725 (t80) REVERT: I 396 ASP cc_start: 0.7002 (t0) cc_final: 0.6427 (t70) REVERT: J 112 ASP cc_start: 0.6108 (OUTLIER) cc_final: 0.4777 (p0) REVERT: K 20 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8741 (tp40) REVERT: L 95 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8830 (mp10) REVERT: L 103 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9154 (mm) REVERT: P 154 TYR cc_start: 0.8429 (p90) cc_final: 0.8024 (p90) REVERT: Q 42 ARG cc_start: 0.7744 (tpt90) cc_final: 0.7100 (ptp-110) REVERT: Q 271 TYR cc_start: 0.0819 (OUTLIER) cc_final: 0.0196 (m-80) outliers start: 74 outliers final: 52 residues processed: 333 average time/residue: 0.2049 time to fit residues: 112.5568 Evaluate side-chains 328 residues out of total 3185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 264 CYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 264 CYS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 302 ARG Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 132 PHE Chi-restraints excluded: chain I residue 232 VAL Chi-restraints excluded: chain I residue 417 ILE Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain J residue 70 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 112 ASP Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 241 ILE Chi-restraints excluded: chain P residue 271 ILE Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 77 LEU Chi-restraints excluded: chain Q residue 226 VAL Chi-restraints excluded: chain Q residue 265 ASP Chi-restraints excluded: chain Q residue 271 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 160 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 272 optimal weight: 0.4980 chunk 309 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 GLN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.105567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070379 restraints weight = 93600.906| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.65 r_work: 0.2992 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33794 Z= 0.177 Angle : 0.734 26.323 46351 Z= 0.356 Chirality : 0.054 1.076 5011 Planarity : 0.005 0.188 5356 Dihedral : 17.814 171.720 5755 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.62 % Favored : 92.99 % Rotamer: Outliers : 2.39 % Allowed : 21.32 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: 0.30 (0.15), residues: 3552 helix: 1.55 (0.14), residues: 1339 sheet: -0.81 (0.22), residues: 576 loop : -0.50 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 42 TYR 0.050 0.002 TYR A 37 PHE 0.038 0.001 PHE Q 54 TRP 0.037 0.001 TRP I 63 HIS 0.006 0.001 HIS Q 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (33794) covalent geometry : angle 0.73436 / 0.36 (46351) hydrogen bonds : bond 0.03705 / 2.49 ( 1407) hydrogen bonds : angle 4.47873 / 3.11 ( 3939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9697.03 seconds wall clock time: 166 minutes 47.38 seconds (10007.38 seconds total)