Starting phenix.real_space_refine on Sun Sep 13 09:32:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.cif" model { file = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b44_7048/09_2026/6b44_7048.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.757 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 114 5.49 5 S 18 5.16 5 C 13604 2.51 5 N 4284 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22681 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2079 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 310} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1373 Unresolved non-hydrogen angles: 1987 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 392 Planarities with less than four sites: {'GLN:plan1': 29, 'GLU:plan': 24, 'ARG:plan': 29, 'PHE:plan': 11, 'ASP:plan': 20, 'HIS:plan': 9, 'TRP:plan': 9, 'ASN:plan1': 13, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2374 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2561 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2566 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2557 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2569 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 761 Classifications: {'peptide': 189} Incomplete info: {'backbone_only': 173} Link IDs: {'PTRANS': 15, 'TRANS': 173} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 1149 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'ASP:plan': 12, 'HIS:plan': 8, 'TYR:plan': 3, 'ARG:plan': 24, 'GLU:plan': 11, 'PHE:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 414 Chain: "M" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNAv2': 60} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 20, 'rna3p': 39} Chain: "N" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 850 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "O" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 262 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 4.56, per 1000 atoms: 0.20 Number of scatterers: 22681 At special positions: 0 Unit cell: (133.715, 133.715, 182.413, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 114 15.00 O 4661 8.00 N 4284 7.00 C 13604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 973.5 milliseconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 38 sheets defined 29.1% alpha, 16.4% beta 30 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 14 through 28 removed outlier: 3.548A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.892A pdb=" N HIS A 74 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.910A pdb=" N LEU A 115 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.775A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 129 through 134 removed outlier: 4.498A pdb=" N ASN A 132 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 195 through 208 removed outlier: 3.711A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 4.377A pdb=" N ARG A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.265A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 317 through 320 removed outlier: 3.646A pdb=" N GLN A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.961A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 386 through 399 removed outlier: 4.023A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 5.072A pdb=" N GLU A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.973A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.917A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 190 through 196 removed outlier: 3.756A pdb=" N GLN B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.710A pdb=" N LEU B 214 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.616A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.592A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.853A pdb=" N ARG C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 204 removed outlier: 3.849A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.404A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 313 removed outlier: 4.352A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.705A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.507A pdb=" N LEU D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.839A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 removed outlier: 4.601A pdb=" N ASP D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.657A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.906A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN E 129 " --> pdb=" O TYR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.586A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.633A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.993A pdb=" N LEU E 277 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 4.231A pdb=" N SER E 287 " --> pdb=" O PRO E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 4.084A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.566A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 65 through 73 Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.606A pdb=" N ASN F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP F 128 " --> pdb=" O THR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.670A pdb=" N ARG F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.954A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 303 through 313 removed outlier: 4.002A pdb=" N ASP F 309 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.860A pdb=" N HIS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 39 removed outlier: 4.422A pdb=" N GLU G 38 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP G 39 " --> pdb=" O SER G 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 35 through 39' Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.839A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 127 Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.622A pdb=" N ARG G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 204 removed outlier: 3.747A pdb=" N ASP G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU G 198 " --> pdb=" O ALA G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.558A pdb=" N ILE G 260 " --> pdb=" O HIS G 256 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 4.530A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.836A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 removed outlier: 4.274A pdb=" N GLU H 38 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TRP H 39 " --> pdb=" O SER H 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 35 through 39' Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.032A pdb=" N ASP H 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.644A pdb=" N GLN H 120 " --> pdb=" O ASP H 116 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP H 128 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 4.065A pdb=" N ARG H 137 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 204 removed outlier: 4.202A pdb=" N ALA H 194 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 198 " --> pdb=" O ALA H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 removed outlier: 3.513A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 330 " --> pdb=" O VAL H 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 4.813A pdb=" N VAL L 23 " --> pdb=" O GLN L 19 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 4.055A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 77 " --> pdb=" O PRO L 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 73 through 77' Processing helix chain 'L' and resid 78 through 82 removed outlier: 4.240A pdb=" N ASP L 81 " --> pdb=" O GLY L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 removed outlier: 4.429A pdb=" N ARG L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.744A pdb=" N ASP A 107 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 8.376A pdb=" N ARG B 278 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 189 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 280 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.633A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.576A pdb=" N GLN A 241 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 262 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.519A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 106 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 103 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN B 18 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 159 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 185 through 188 removed outlier: 3.571A pdb=" N VAL B 187 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU B 288 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 25 removed outlier: 4.198A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.205A pdb=" N VAL C 79 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.676A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 161 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 216 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 172 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 95 through 96 removed outlier: 3.676A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 161 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE C 216 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 4.223A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.484A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 25 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA D 253 " --> pdb=" O MET D 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 249 " --> pdb=" O ALA D 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 287 through 288 removed outlier: 4.260A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.523A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL E 158 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP E 177 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 160 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG E 175 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.533A pdb=" N ILE E 255 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 44 through 52 removed outlier: 4.619A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.837A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 334 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 19 through 20 removed outlier: 4.449A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG F 172 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 20 removed outlier: 5.066A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 252 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 44 through 51 Processing sheet with id=AC5, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC6, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.525A pdb=" N LYS F 293 " --> pdb=" O VAL F 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AC8, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.424A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL G 160 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG G 175 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 162 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA G 173 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS G 164 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 19 through 20 removed outlier: 4.791A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.790A pdb=" N ASN G 75 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD3, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AD4, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.538A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU H 12 " --> pdb=" O PHE H 336 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.933A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL H 158 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP H 177 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.527A pdb=" N ILE H 255 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA H 253 " --> pdb=" O MET H 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 45 through 52 removed outlier: 4.429A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 266 through 268 Processing sheet with id=AD9, first strand: chain 'H' and resid 287 through 288 removed outlier: 3.528A pdb=" N LYS H 293 " --> pdb=" O VAL H 288 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.190A pdb=" N TYR L 4 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.543A pdb=" N HIS L 61 " --> pdb=" O GLY L 41 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6685 1.33 - 1.46: 5321 1.46 - 1.58: 11067 1.58 - 1.70: 225 1.70 - 1.82: 27 Bond restraints: 23325 Sorted by residual: bond pdb=" C1' DC N 9 " pdb=" N1 DC N 9 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C5' DG N 39 " pdb=" C4' DG N 39 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.09e+01 bond pdb=" C3' DT O 13 " pdb=" C2' DT O 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC N 11 " pdb=" O3' DC N 11 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.40e+00 bond pdb=" C3' DG N 4 " pdb=" O3' DG N 4 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.23e+00 ... (remaining 23320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 31478 3.43 - 6.85: 439 6.85 - 10.28: 32 10.28 - 13.71: 6 13.71 - 17.14: 2 Bond angle restraints: 31957 Sorted by residual: angle pdb=" C ARG D 250 " pdb=" N ASP D 251 " pdb=" CA ASP D 251 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 angle pdb=" N ILE E 267 " pdb=" CA ILE E 267 " pdb=" C ILE E 267 " ideal model delta sigma weight residual 112.96 107.51 5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" O4' DT N 38 " pdb=" C1' DT N 38 " pdb=" N1 DT N 38 " ideal model delta sigma weight residual 108.00 111.60 -3.60 7.00e-01 2.04e+00 2.64e+01 angle pdb=" C ARG F 250 " pdb=" N ASP F 251 " pdb=" CA ASP F 251 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 ... (remaining 31952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 11605 16.74 - 33.49: 876 33.49 - 50.23: 288 50.23 - 66.97: 184 66.97 - 83.71: 32 Dihedral angle restraints: 12985 sinusoidal: 5671 harmonic: 7314 Sorted by residual: dihedral pdb=" C4' C M 44 " pdb=" C3' C M 44 " pdb=" C2' C M 44 " pdb=" C1' C M 44 " ideal model delta sinusoidal sigma weight residual 36.34 -38.29 74.64 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' U M 21 " pdb=" C3' U M 21 " pdb=" C2' U M 21 " pdb=" C1' U M 21 " ideal model delta sinusoidal sigma weight residual 36.34 -37.88 74.22 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' G M 19 " pdb=" C3' G M 19 " pdb=" C2' G M 19 " pdb=" C1' G M 19 " ideal model delta sinusoidal sigma weight residual 36.34 -37.75 74.10 1 3.10e+00 1.04e-01 7.25e+02 ... (remaining 12982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2587 0.073 - 0.146: 584 0.146 - 0.219: 83 0.219 - 0.292: 66 0.292 - 0.365: 11 Chirality restraints: 3331 Sorted by residual: chirality pdb=" P C M 1 " pdb=" OP1 C M 1 " pdb=" OP2 C M 1 " pdb=" O5' C M 1 " both_signs ideal model delta sigma weight residual True 2.17 2.54 -0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3' C M 44 " pdb=" C4' C M 44 " pdb=" O3' C M 44 " pdb=" C2' C M 44 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" P A M 55 " pdb=" OP1 A M 55 " pdb=" OP2 A M 55 " pdb=" O5' A M 55 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3328 not shown) Planarity restraints: 3954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 311 " 0.031 2.00e-02 2.50e+03 2.48e-02 1.53e+01 pdb=" CG TRP D 311 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 311 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 311 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 311 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 311 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 311 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 311 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 311 " 0.027 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP E 311 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP E 311 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP E 311 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 311 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 311 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 311 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 311 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP E 311 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 311 " 0.030 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP F 311 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 311 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP F 311 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 311 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 311 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP F 311 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 311 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 311 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 311 " 0.005 2.00e-02 2.50e+03 ... (remaining 3951 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4130 2.77 - 3.30: 19156 3.30 - 3.83: 37114 3.83 - 4.37: 43862 4.37 - 4.90: 72597 Nonbonded interactions: 176859 Sorted by model distance: nonbonded pdb=" OD1 ASN B 269 " pdb=" OG SER H 10 " model vdw 2.237 3.040 nonbonded pdb=" O GLY L 152 " pdb=" O2' G M 40 " model vdw 2.284 3.040 nonbonded pdb=" O ALA B 270 " pdb=" ND2 ASN H 110 " model vdw 2.285 3.120 nonbonded pdb=" O GLU H 283 " pdb=" OH TYR H 325 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLN D 229 " pdb=" O2' U M 33 " model vdw 2.291 3.040 ... (remaining 176854 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' and (resid 6 through 272 or (resid 273 through 275 and (name N or nam \ e CA or name C or name O or name CB )) or resid 276 through 338)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 231 or resid 244 through \ 338)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 23325 Z= 0.357 Angle : 1.042 17.136 31957 Z= 0.580 Chirality : 0.072 0.365 3331 Planarity : 0.007 0.071 3954 Dihedral : 15.606 83.713 8599 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.43 % Allowed : 3.24 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.12), residues: 2855 helix: -3.30 (0.12), residues: 772 sheet: -1.45 (0.25), residues: 401 loop : -3.33 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 137 TYR 0.031 0.003 TYR G 138 PHE 0.039 0.004 PHE H 336 TRP 0.065 0.005 TRP D 311 HIS 0.013 0.003 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.36 (23325) covalent geometry : angle 1.04215 / 0.58 (31957) hydrogen bonds : bond 0.19627 / 15.05 ( 768) hydrogen bonds : angle 7.97597 / 5.75 ( 2135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 264 time to evaluate : 0.708 Fit side-chains REVERT: A 242 LYS cc_start: 0.8078 (mptp) cc_final: 0.7866 (mmmt) REVERT: B 159 LEU cc_start: 0.5757 (pt) cc_final: 0.5413 (mt) REVERT: B 263 LEU cc_start: 0.7051 (mm) cc_final: 0.6710 (tp) REVERT: C 172 ARG cc_start: 0.4562 (tpt170) cc_final: 0.2757 (mtt90) REVERT: C 271 TYR cc_start: 0.3148 (p90) cc_final: 0.1680 (p90) REVERT: D 30 TRP cc_start: 0.6210 (m100) cc_final: 0.5980 (m100) REVERT: D 293 LYS cc_start: 0.7366 (tmmm) cc_final: 0.7099 (tppp) REVERT: H 175 ARG cc_start: 0.7026 (mtp85) cc_final: 0.6822 (ttm-80) REVERT: L -1 MET cc_start: 0.1241 (mmm) cc_final: -0.0394 (mmm) outliers start: 8 outliers final: 2 residues processed: 272 average time/residue: 0.7249 time to fit residues: 219.9667 Evaluate side-chains 135 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 82 ASN B 104 HIS B 114 HIS B 124 GLN B 194 GLN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 144 ASN D 83 ASN D 223 GLN D 229 GLN D 324 HIS E 127 ASN E 164 HIS E 167 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 120 GLN G 129 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.173351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.145857 restraints weight = 43390.258| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.04 r_work: 0.3783 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23325 Z= 0.196 Angle : 1.089 25.314 31957 Z= 0.479 Chirality : 0.096 1.217 3331 Planarity : 0.006 0.077 3954 Dihedral : 15.947 129.227 4421 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.27 % Allowed : 9.62 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.14), residues: 2855 helix: -1.95 (0.16), residues: 766 sheet: -1.04 (0.26), residues: 393 loop : -2.93 (0.13), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 184 TYR 0.016 0.002 TYR F 285 PHE 0.019 0.002 PHE H 336 TRP 0.025 0.002 TRP E 311 HIS 0.010 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (23325) covalent geometry : angle 1.08946 / 0.48 (31957) hydrogen bonds : bond 0.05387 / 3.65 ( 768) hydrogen bonds : angle 5.55472 / 4.02 ( 2135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.659 Fit side-chains REVERT: A 207 ARG cc_start: 0.6791 (ttm110) cc_final: 0.6521 (tpt90) REVERT: A 234 GLU cc_start: 0.6499 (tp30) cc_final: 0.6145 (tp30) REVERT: A 242 LYS cc_start: 0.8148 (mptp) cc_final: 0.7805 (mmmt) REVERT: B 118 LEU cc_start: 0.6030 (tp) cc_final: 0.5587 (mt) REVERT: B 159 LEU cc_start: 0.5771 (pt) cc_final: 0.5306 (mt) REVERT: B 161 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.3456 (ptp) REVERT: B 239 TRP cc_start: 0.4282 (OUTLIER) cc_final: 0.3814 (p90) REVERT: B 263 LEU cc_start: 0.6919 (mm) cc_final: 0.6605 (tp) REVERT: C 133 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4539 (mm-30) REVERT: C 172 ARG cc_start: 0.4031 (tpt170) cc_final: 0.3324 (tpt90) REVERT: C 203 LEU cc_start: 0.5256 (OUTLIER) cc_final: 0.5006 (pt) REVERT: D 25 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5454 (mmt) REVERT: D 241 GLN cc_start: 0.5724 (OUTLIER) cc_final: 0.5107 (mm-40) REVERT: D 267 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7657 (mm) REVERT: F 38 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: H 175 ARG cc_start: 0.7359 (mtp85) cc_final: 0.7078 (ttm-80) REVERT: H 321 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6679 (pt0) REVERT: L -1 MET cc_start: 0.1587 (mmm) cc_final: 0.0844 (mmm) outliers start: 42 outliers final: 17 residues processed: 185 average time/residue: 0.6996 time to fit residues: 146.5463 Evaluate side-chains 147 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 222 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 60.0000 chunk 239 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 283 optimal weight: 40.0000 chunk 192 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS B 293 HIS B 305 HIS C 151 ASN D 140 HIS E 167 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS G 120 GLN H 223 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.173032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.145918 restraints weight = 43594.513| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.95 r_work: 0.3795 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23325 Z= 0.180 Angle : 0.889 17.281 31957 Z= 0.410 Chirality : 0.073 0.905 3331 Planarity : 0.005 0.055 3954 Dihedral : 15.812 144.050 4418 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.35 % Allowed : 9.62 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.14), residues: 2855 helix: -1.20 (0.17), residues: 770 sheet: -0.76 (0.25), residues: 410 loop : -2.68 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 175 TYR 0.018 0.002 TYR F 305 PHE 0.018 0.002 PHE H 336 TRP 0.020 0.002 TRP F 311 HIS 0.008 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (23325) covalent geometry : angle 0.88912 / 0.41 (31957) hydrogen bonds : bond 0.05070 / 3.45 ( 768) hydrogen bonds : angle 5.02192 / 3.63 ( 2135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 133 time to evaluate : 0.886 Fit side-chains REVERT: A 207 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6532 (tpt90) REVERT: A 234 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6123 (tp30) REVERT: A 242 LYS cc_start: 0.8133 (mptp) cc_final: 0.7641 (mmmt) REVERT: A 258 ARG cc_start: 0.5147 (OUTLIER) cc_final: 0.4687 (mtp180) REVERT: B 118 LEU cc_start: 0.6055 (tp) cc_final: 0.5608 (mt) REVERT: B 156 ASN cc_start: 0.7158 (m110) cc_final: 0.6947 (m-40) REVERT: B 159 LEU cc_start: 0.5862 (pt) cc_final: 0.5207 (mt) REVERT: B 161 MET cc_start: 0.4164 (OUTLIER) cc_final: 0.3389 (ptp) REVERT: C 121 THR cc_start: 0.1940 (OUTLIER) cc_final: 0.1411 (p) REVERT: C 133 GLU cc_start: 0.5140 (OUTLIER) cc_final: 0.4561 (mm-30) REVERT: C 172 ARG cc_start: 0.3791 (tpt170) cc_final: 0.3032 (tpt90) REVERT: C 203 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4800 (pt) REVERT: C 231 LEU cc_start: 0.1865 (OUTLIER) cc_final: -0.0536 (pt) REVERT: D 116 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: D 191 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: E 231 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7697 (mp) REVERT: F 38 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: F 197 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: H 18 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8243 (mt) REVERT: H 175 ARG cc_start: 0.7367 (mtp85) cc_final: 0.7087 (mtt90) REVERT: H 321 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6653 (pt0) REVERT: L -1 MET cc_start: 0.1379 (mmm) cc_final: 0.0509 (mmm) outliers start: 62 outliers final: 24 residues processed: 182 average time/residue: 0.6472 time to fit residues: 134.4583 Evaluate side-chains 154 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 290 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 249 optimal weight: 0.0070 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 50.0000 chunk 74 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 293 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.172142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143169 restraints weight = 43670.216| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.62 r_work: 0.3733 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23325 Z= 0.164 Angle : 0.813 16.465 31957 Z= 0.381 Chirality : 0.065 0.702 3331 Planarity : 0.004 0.045 3954 Dihedral : 15.701 140.033 4418 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.13 % Allowed : 10.97 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.15), residues: 2855 helix: -0.78 (0.18), residues: 772 sheet: -0.51 (0.27), residues: 391 loop : -2.54 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 137 TYR 0.016 0.002 TYR F 305 PHE 0.014 0.002 PHE H 336 TRP 0.015 0.002 TRP C 311 HIS 0.015 0.002 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (23325) covalent geometry : angle 0.81350 / 0.38 (31957) hydrogen bonds : bond 0.04620 / 3.06 ( 768) hydrogen bonds : angle 4.78682 / 3.45 ( 2135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 131 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6688 (ttm110) cc_final: 0.6427 (tpt90) REVERT: A 216 LYS cc_start: 0.4063 (mmtp) cc_final: 0.3459 (mmmt) REVERT: A 234 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6058 (tp30) REVERT: A 242 LYS cc_start: 0.8099 (mptp) cc_final: 0.7706 (mmmt) REVERT: B 118 LEU cc_start: 0.6028 (tp) cc_final: 0.5549 (mt) REVERT: B 161 MET cc_start: 0.4036 (OUTLIER) cc_final: 0.3261 (ptp) REVERT: C 133 GLU cc_start: 0.4858 (OUTLIER) cc_final: 0.4264 (mm-30) REVERT: C 172 ARG cc_start: 0.3457 (tpt170) cc_final: 0.1970 (mtt90) REVERT: C 203 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4623 (pt) REVERT: C 231 LEU cc_start: 0.1760 (OUTLIER) cc_final: -0.0611 (pt) REVERT: D 25 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.5384 (mmt) REVERT: D 26 SER cc_start: 0.7544 (p) cc_final: 0.7310 (m) REVERT: D 191 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: D 250 ARG cc_start: 0.5461 (mpp-170) cc_final: 0.5242 (mtm110) REVERT: D 267 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7791 (mm) REVERT: E 231 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7759 (mp) REVERT: F 38 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: F 166 ARG cc_start: 0.7765 (ptm160) cc_final: 0.7555 (ttp-170) REVERT: H 175 ARG cc_start: 0.7443 (mtp85) cc_final: 0.7080 (ttm-80) REVERT: H 321 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6598 (pt0) REVERT: L -1 MET cc_start: 0.1314 (mmm) cc_final: 0.0536 (mmm) outliers start: 58 outliers final: 22 residues processed: 173 average time/residue: 0.6800 time to fit residues: 134.1280 Evaluate side-chains 146 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 167 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 293 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 282 optimal weight: 0.0000 chunk 69 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 185 optimal weight: 0.2980 chunk 171 optimal weight: 7.9990 overall best weight: 4.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 293 HIS D 140 HIS E 127 ASN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS G 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.171746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.143367 restraints weight = 43296.727| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.40 r_work: 0.3727 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23325 Z= 0.167 Angle : 0.787 15.559 31957 Z= 0.371 Chirality : 0.063 0.666 3331 Planarity : 0.004 0.049 3954 Dihedral : 15.750 149.215 4418 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.84 % Allowed : 11.62 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.15), residues: 2855 helix: -0.49 (0.19), residues: 764 sheet: -0.42 (0.26), residues: 406 loop : -2.45 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 47 TYR 0.016 0.002 TYR F 305 PHE 0.013 0.002 PHE D 216 TRP 0.018 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (23325) covalent geometry : angle 0.78670 / 0.37 (31957) hydrogen bonds : bond 0.04617 / 3.06 ( 768) hydrogen bonds : angle 4.68257 / 3.37 ( 2135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 126 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6690 (ttm110) cc_final: 0.6452 (tpt90) REVERT: A 216 LYS cc_start: 0.4140 (mmtp) cc_final: 0.3339 (mmmt) REVERT: A 242 LYS cc_start: 0.8071 (mptp) cc_final: 0.7685 (mmmt) REVERT: A 258 ARG cc_start: 0.5322 (OUTLIER) cc_final: 0.4786 (mtp180) REVERT: B 97 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7886 (mp) REVERT: B 118 LEU cc_start: 0.6043 (tp) cc_final: 0.5572 (mt) REVERT: B 161 MET cc_start: 0.4082 (OUTLIER) cc_final: 0.3292 (ptp) REVERT: C 121 THR cc_start: 0.1676 (OUTLIER) cc_final: 0.1172 (p) REVERT: C 172 ARG cc_start: 0.3432 (tpt170) cc_final: 0.2003 (mtt90) REVERT: C 203 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4689 (pt) REVERT: C 231 LEU cc_start: 0.1728 (OUTLIER) cc_final: -0.0707 (pt) REVERT: D 25 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.5347 (mmt) REVERT: D 26 SER cc_start: 0.7540 (p) cc_final: 0.7305 (m) REVERT: D 116 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: D 191 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: E 231 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7899 (mp) REVERT: F 38 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7571 (pp20) REVERT: H 175 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7116 (ttm-80) REVERT: H 321 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6676 (pt0) REVERT: L -1 MET cc_start: 0.1269 (mmm) cc_final: 0.0566 (mmm) outliers start: 71 outliers final: 27 residues processed: 181 average time/residue: 0.6091 time to fit residues: 126.8368 Evaluate side-chains 151 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 86 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 152 optimal weight: 0.6980 chunk 28 optimal weight: 50.0000 chunk 48 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 242 optimal weight: 2.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.171506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.142241 restraints weight = 43463.386| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.41 r_work: 0.3733 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23325 Z= 0.171 Angle : 0.781 15.901 31957 Z= 0.368 Chirality : 0.062 0.641 3331 Planarity : 0.004 0.048 3954 Dihedral : 15.771 176.275 4418 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.62 % Allowed : 12.32 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.15), residues: 2855 helix: -0.45 (0.19), residues: 777 sheet: -0.38 (0.26), residues: 399 loop : -2.42 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 137 TYR 0.028 0.002 TYR C 271 PHE 0.013 0.002 PHE D 216 TRP 0.017 0.002 TRP C 311 HIS 0.009 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (23325) covalent geometry : angle 0.78134 / 0.37 (31957) hydrogen bonds : bond 0.04547 / 2.99 ( 768) hydrogen bonds : angle 4.64875 / 3.34 ( 2135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 116 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6685 (ttm110) cc_final: 0.6456 (tpt90) REVERT: A 216 LYS cc_start: 0.4118 (mmtp) cc_final: 0.3333 (mmmt) REVERT: A 242 LYS cc_start: 0.8059 (mptp) cc_final: 0.7516 (mmmt) REVERT: A 258 ARG cc_start: 0.5292 (OUTLIER) cc_final: 0.4751 (mtp180) REVERT: B 97 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 118 LEU cc_start: 0.6086 (tp) cc_final: 0.5591 (mt) REVERT: B 161 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.3342 (ptp) REVERT: C 121 THR cc_start: 0.1545 (OUTLIER) cc_final: 0.1063 (p) REVERT: C 133 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.3915 (mm-30) REVERT: C 203 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.4708 (pt) REVERT: C 231 LEU cc_start: 0.1793 (OUTLIER) cc_final: -0.0592 (pt) REVERT: C 295 TYR cc_start: 0.5960 (m-80) cc_final: 0.4804 (m-10) REVERT: D 25 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.5195 (mmt) REVERT: D 26 SER cc_start: 0.7543 (p) cc_final: 0.7311 (m) REVERT: D 116 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: D 191 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: D 267 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7870 (mm) REVERT: E 24 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8467 (mp) REVERT: E 231 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7886 (mp) REVERT: F 38 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7530 (pp20) REVERT: H 175 ARG cc_start: 0.7446 (mtp85) cc_final: 0.7087 (ttm-80) REVERT: H 321 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6695 (pt0) REVERT: L -1 MET cc_start: 0.1135 (mmm) cc_final: 0.0378 (mmm) outliers start: 67 outliers final: 32 residues processed: 173 average time/residue: 0.6097 time to fit residues: 120.9679 Evaluate side-chains 152 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 62 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 258 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.172419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142387 restraints weight = 43280.215| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.74 r_work: 0.3761 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23325 Z= 0.140 Angle : 0.750 15.508 31957 Z= 0.353 Chirality : 0.059 0.590 3331 Planarity : 0.004 0.050 3954 Dihedral : 15.710 175.763 4418 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.19 % Allowed : 13.24 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.15), residues: 2855 helix: -0.26 (0.19), residues: 775 sheet: -0.33 (0.27), residues: 385 loop : -2.33 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 218 TYR 0.031 0.002 TYR C 271 PHE 0.016 0.001 PHE A 243 TRP 0.016 0.001 TRP C 311 HIS 0.008 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (23325) covalent geometry : angle 0.74986 / 0.35 (31957) hydrogen bonds : bond 0.04311 / 2.77 ( 768) hydrogen bonds : angle 4.53776 / 3.27 ( 2135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6680 (ttm110) cc_final: 0.6475 (tpt170) REVERT: A 216 LYS cc_start: 0.4138 (mmtp) cc_final: 0.3361 (mmmt) REVERT: A 242 LYS cc_start: 0.7885 (mptp) cc_final: 0.7604 (mmmt) REVERT: B 97 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7765 (mp) REVERT: B 118 LEU cc_start: 0.6051 (tp) cc_final: 0.5574 (mt) REVERT: B 161 MET cc_start: 0.4171 (OUTLIER) cc_final: 0.3315 (ptp) REVERT: C 133 GLU cc_start: 0.4875 (OUTLIER) cc_final: 0.3946 (mm-30) REVERT: C 203 LEU cc_start: 0.4871 (OUTLIER) cc_final: 0.4622 (pt) REVERT: C 231 LEU cc_start: 0.1775 (OUTLIER) cc_final: -0.0578 (pt) REVERT: C 274 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.4766 (mt-10) REVERT: C 295 TYR cc_start: 0.6029 (m-80) cc_final: 0.4887 (m-10) REVERT: D 26 SER cc_start: 0.7499 (p) cc_final: 0.7269 (m) REVERT: D 116 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: D 191 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: D 232 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5828 (mt) REVERT: D 267 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7921 (mm) REVERT: E 24 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8331 (mp) REVERT: E 231 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7762 (mp) REVERT: F 38 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: H 175 ARG cc_start: 0.7436 (mtp85) cc_final: 0.7133 (ttm-80) REVERT: H 321 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6673 (pt0) REVERT: L -1 MET cc_start: 0.0942 (mmm) cc_final: 0.0211 (mmm) outliers start: 59 outliers final: 28 residues processed: 170 average time/residue: 0.6446 time to fit residues: 125.4661 Evaluate side-chains 147 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 176 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 209 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 225 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 277 optimal weight: 50.0000 chunk 200 optimal weight: 9.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS B 293 HIS ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.172977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143348 restraints weight = 43423.715| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.53 r_work: 0.3753 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23325 Z= 0.136 Angle : 0.731 15.387 31957 Z= 0.346 Chirality : 0.058 0.549 3331 Planarity : 0.004 0.061 3954 Dihedral : 15.648 172.079 4418 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.19 % Allowed : 13.40 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.15), residues: 2855 helix: -0.10 (0.19), residues: 771 sheet: -0.31 (0.26), residues: 406 loop : -2.30 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG D 218 TYR 0.025 0.001 TYR C 271 PHE 0.014 0.001 PHE D 216 TRP 0.016 0.001 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (23325) covalent geometry : angle 0.73138 / 0.35 (31957) hydrogen bonds : bond 0.04259 / 2.72 ( 768) hydrogen bonds : angle 4.47958 / 3.22 ( 2135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6687 (ttm110) cc_final: 0.6469 (tpt170) REVERT: A 216 LYS cc_start: 0.4098 (mmtp) cc_final: 0.3299 (mmmt) REVERT: A 242 LYS cc_start: 0.7963 (mptp) cc_final: 0.7517 (mmmt) REVERT: B 97 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7772 (mp) REVERT: B 118 LEU cc_start: 0.5854 (tp) cc_final: 0.5540 (mt) REVERT: B 161 MET cc_start: 0.4236 (OUTLIER) cc_final: 0.3961 (ptp) REVERT: C 121 THR cc_start: 0.1540 (OUTLIER) cc_final: 0.1039 (p) REVERT: C 133 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.4013 (mm-30) REVERT: C 203 LEU cc_start: 0.4867 (OUTLIER) cc_final: 0.4617 (pt) REVERT: C 231 LEU cc_start: 0.1892 (OUTLIER) cc_final: -0.0471 (pt) REVERT: C 295 TYR cc_start: 0.6019 (m-80) cc_final: 0.4932 (m-10) REVERT: D 25 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.5084 (mmt) REVERT: D 26 SER cc_start: 0.7584 (p) cc_final: 0.7374 (m) REVERT: D 116 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: D 191 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: D 232 ILE cc_start: 0.6197 (OUTLIER) cc_final: 0.5820 (mt) REVERT: D 267 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7912 (mm) REVERT: E 24 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8271 (mp) REVERT: E 45 ARG cc_start: 0.6910 (ttm170) cc_final: 0.6357 (mtm180) REVERT: E 231 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7864 (mp) REVERT: F 38 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: G 238 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5759 (tmmt) REVERT: H 175 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7134 (ttm-80) REVERT: H 321 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6676 (pt0) REVERT: L -1 MET cc_start: 0.0840 (mmm) cc_final: 0.0121 (mmm) outliers start: 59 outliers final: 34 residues processed: 164 average time/residue: 0.5995 time to fit residues: 113.0604 Evaluate side-chains 159 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 266 optimal weight: 40.0000 chunk 156 optimal weight: 7.9990 chunk 292 optimal weight: 40.0000 chunk 192 optimal weight: 3.9990 chunk 12 optimal weight: 50.0000 chunk 277 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 290 optimal weight: 50.0000 chunk 75 optimal weight: 0.1980 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 140 HIS ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.171226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.141999 restraints weight = 43643.994| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.71 r_work: 0.3710 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23325 Z= 0.190 Angle : 0.783 15.245 31957 Z= 0.371 Chirality : 0.061 0.599 3331 Planarity : 0.005 0.052 3954 Dihedral : 15.663 168.162 4418 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 3.08 % Allowed : 13.72 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.15), residues: 2855 helix: -0.22 (0.19), residues: 771 sheet: -0.27 (0.26), residues: 414 loop : -2.34 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 218 TYR 0.031 0.002 TYR C 271 PHE 0.015 0.002 PHE D 216 TRP 0.019 0.002 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (23325) covalent geometry : angle 0.78320 / 0.37 (31957) hydrogen bonds : bond 0.04649 / 3.06 ( 768) hydrogen bonds : angle 4.58365 / 3.30 ( 2135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.6543 (ttm110) cc_final: 0.6342 (tpt170) REVERT: A 216 LYS cc_start: 0.4189 (mmtp) cc_final: 0.3333 (mmmt) REVERT: A 242 LYS cc_start: 0.7927 (mptp) cc_final: 0.7428 (mmmt) REVERT: B 97 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7818 (mp) REVERT: B 118 LEU cc_start: 0.5826 (tp) cc_final: 0.5505 (mt) REVERT: C 121 THR cc_start: 0.1403 (OUTLIER) cc_final: 0.0977 (p) REVERT: C 133 GLU cc_start: 0.4801 (OUTLIER) cc_final: 0.3909 (mm-30) REVERT: C 203 LEU cc_start: 0.4855 (OUTLIER) cc_final: 0.4609 (pt) REVERT: C 231 LEU cc_start: 0.1757 (OUTLIER) cc_final: -0.0489 (pt) REVERT: C 295 TYR cc_start: 0.6074 (m-80) cc_final: 0.4724 (m-10) REVERT: D 25 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.4809 (mmt) REVERT: D 116 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: D 191 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: D 232 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5675 (mt) REVERT: D 267 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7770 (mm) REVERT: D 283 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: E 24 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8403 (mp) REVERT: E 45 ARG cc_start: 0.6769 (ttm170) cc_final: 0.6231 (mtm180) REVERT: E 231 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7840 (mp) REVERT: F 38 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7374 (pp20) REVERT: H 175 ARG cc_start: 0.7366 (mtp85) cc_final: 0.7060 (ttm-80) REVERT: H 321 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6703 (pt0) REVERT: L -1 MET cc_start: 0.0819 (mmm) cc_final: 0.0102 (mmm) outliers start: 57 outliers final: 37 residues processed: 158 average time/residue: 0.6108 time to fit residues: 111.3692 Evaluate side-chains 158 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 204 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 7 optimal weight: 0.0770 chunk 207 optimal weight: 7.9990 chunk 249 optimal weight: 0.0870 chunk 154 optimal weight: 0.0470 chunk 218 optimal weight: 20.0000 chunk 49 optimal weight: 0.4980 overall best weight: 1.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN G 241 GLN H 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.173694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143815 restraints weight = 43517.133| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.65 r_work: 0.3773 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23325 Z= 0.119 Angle : 0.720 15.176 31957 Z= 0.341 Chirality : 0.056 0.522 3331 Planarity : 0.004 0.053 3954 Dihedral : 15.560 168.459 4418 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.70 % Allowed : 14.15 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.15), residues: 2855 helix: 0.05 (0.19), residues: 762 sheet: -0.32 (0.27), residues: 382 loop : -2.21 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 218 TYR 0.026 0.001 TYR C 271 PHE 0.013 0.001 PHE A 232 TRP 0.015 0.001 TRP E 174 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (23325) covalent geometry : angle 0.71969 / 0.34 (31957) hydrogen bonds : bond 0.04160 / 2.62 ( 768) hydrogen bonds : angle 4.41961 / 3.19 ( 2135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.816 Fit side-chains REVERT: A 216 LYS cc_start: 0.4114 (mmtp) cc_final: 0.3241 (mmmt) REVERT: A 242 LYS cc_start: 0.7929 (mptp) cc_final: 0.7502 (mmmt) REVERT: B 97 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7734 (mp) REVERT: B 118 LEU cc_start: 0.5827 (tp) cc_final: 0.5520 (mt) REVERT: C 121 THR cc_start: 0.1437 (OUTLIER) cc_final: 0.0962 (p) REVERT: C 133 GLU cc_start: 0.5017 (OUTLIER) cc_final: 0.4031 (mm-30) REVERT: C 203 LEU cc_start: 0.4846 (OUTLIER) cc_final: 0.4600 (pt) REVERT: C 218 ARG cc_start: 0.1005 (mtt90) cc_final: -0.0297 (pmm150) REVERT: C 231 LEU cc_start: 0.1867 (OUTLIER) cc_final: -0.0569 (pt) REVERT: C 295 TYR cc_start: 0.6085 (m-80) cc_final: 0.4943 (m-10) REVERT: D 25 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5007 (mmt) REVERT: D 26 SER cc_start: 0.7597 (p) cc_final: 0.7388 (m) REVERT: D 116 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: D 191 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: D 232 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5738 (mt) REVERT: D 267 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 302 LEU cc_start: 0.6393 (OUTLIER) cc_final: 0.6036 (mm) REVERT: E 24 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8290 (mp) REVERT: E 45 ARG cc_start: 0.6797 (ttm170) cc_final: 0.6307 (mtm180) REVERT: E 231 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7839 (mp) REVERT: F 38 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7394 (pp20) REVERT: G 238 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5713 (tmmt) REVERT: H 175 ARG cc_start: 0.7423 (mtp85) cc_final: 0.7120 (ttm-80) REVERT: H 321 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6653 (pt0) REVERT: L -1 MET cc_start: 0.0790 (mmm) cc_final: 0.0112 (mmm) outliers start: 50 outliers final: 28 residues processed: 160 average time/residue: 0.6195 time to fit residues: 114.3755 Evaluate side-chains 150 residues out of total 2327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 39 TRP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 TRP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 184 ARG Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 288 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 133 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 8 optimal weight: 40.0000 chunk 232 optimal weight: 9.9990 chunk 55 optimal weight: 0.3980 chunk 172 optimal weight: 20.0000 chunk 5 optimal weight: 50.0000 chunk 119 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN B 293 HIS ** C 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN H 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.172441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142169 restraints weight = 43272.102| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.54 r_work: 0.3770 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23325 Z= 0.143 Angle : 0.725 15.051 31957 Z= 0.344 Chirality : 0.057 0.523 3331 Planarity : 0.004 0.050 3954 Dihedral : 15.534 166.350 4418 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.76 % Allowed : 14.37 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.15), residues: 2855 helix: -0.00 (0.19), residues: 772 sheet: -0.13 (0.26), residues: 407 loop : -2.20 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 218 TYR 0.029 0.002 TYR C 271 PHE 0.012 0.001 PHE D 216 TRP 0.017 0.001 TRP C 311 HIS 0.007 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (23325) covalent geometry : angle 0.72523 / 0.34 (31957) hydrogen bonds : bond 0.04230 / 2.70 ( 768) hydrogen bonds : angle 4.40953 / 3.18 ( 2135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7941.40 seconds wall clock time: 135 minutes 59.75 seconds (8159.75 seconds total)