Starting phenix.real_space_refine on Sun Sep 13 11:22:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.map" model { file = "/net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ecw_31059/09_2026/7ecw_31059.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 69 5.49 5 S 27 5.16 5 C 14163 2.51 5 N 4253 2.21 5 O 4577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s 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: 23089 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'GLU:plan': 24, 'ARG:plan': 29, 'PHE:plan': 10, 'ASP:plan': 21, 'HIS:plan': 6, 'TRP:plan': 8, 'ASN:plan1': 9, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 670 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2364 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2264 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 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': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2534 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 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: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2569 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: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2556 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} 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: "H" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 928 Classifications: {'RNAv2': 44} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 25} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 4.86, per 1000 atoms: 0.21 Number of scatterers: 23089 At special positions: 0 Unit cell: (135.3, 134.2, 171.6, 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 27 16.00 P 69 15.00 O 4577 8.00 N 4253 7.00 C 14163 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: 1.66 Conformation dependent library (CDL) restraints added in 950.9 milliseconds 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 38 sheets defined 32.1% alpha, 19.4% beta 10 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.559A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.534A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.624A pdb=" N ASN A 132 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.793A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.736A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 314 through 341 removed outlier: 3.806A pdb=" N ILE A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.932A 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 385 through 399 removed outlier: 4.295A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 3.862A 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 409 through 423 removed outlier: 4.080A pdb=" N GLN A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'B' and resid 33 through 53 removed outlier: 4.000A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.569A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 181 removed outlier: 4.057A pdb=" N LEU B 181 " --> pdb=" O ARG B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.847A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 212' Processing helix chain 'B' and resid 291 through 295 removed outlier: 4.009A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.757A pdb=" N ASP B 300 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.873A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.611A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.787A pdb=" N GLY C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.776A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.768A pdb=" N TYR C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.837A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.929A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.649A pdb=" N ARG D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.742A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.821A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 332 removed outlier: 4.343A pdb=" N VAL D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 327 " --> pdb=" O GLN D 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.875A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 4.169A pdb=" N ILE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.977A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.971A pdb=" N ARG E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.937A pdb=" N ALA E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.693A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.550A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.792A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.732A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 70 removed outlier: 3.562A pdb=" N ASP F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.250A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.843A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.583A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 313 Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.868A pdb=" N HIS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 4.042A pdb=" N ASP G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.850A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.705A pdb=" N ASN G 141 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.893A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 263 removed outlier: 3.502A pdb=" N ALA G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.508A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 313 " --> pdb=" O ASP G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.845A pdb=" N HIS G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL G 326 " --> pdb=" O GLN G 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 327 " --> pdb=" O GLN G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.607A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 72 removed outlier: 3.748A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 removed outlier: 3.591A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 191 through 204 removed outlier: 3.936A pdb=" N LEU H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.722A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 removed outlier: 3.722A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 333 removed outlier: 3.991A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE H 327 " --> pdb=" O GLN H 323 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY H 333 " --> pdb=" O ASN H 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 42 through 56 removed outlier: 3.969A pdb=" N ILE I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 75 Processing helix chain 'I' and resid 109 through 121 Processing helix chain 'J' and resid 3 through 12 Processing helix chain 'J' and resid 21 through 30 Processing helix chain 'J' and resid 42 through 56 removed outlier: 3.969A pdb=" N ILE J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 75 Processing helix chain 'J' and resid 109 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.539A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 14.042A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 21 removed outlier: 5.323A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 14.042A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.695A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.688A pdb=" N ALA C 157 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.593A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.564A pdb=" N ARG C 45 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 81 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.609A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.603A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 172 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.603A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 28 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 49 removed outlier: 4.744A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.753A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 266 through 268 removed outlier: 3.800A pdb=" N ASP D 268 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.526A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.957A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 172 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.547A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 49 removed outlier: 7.737A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC5, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.689A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.844A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.501A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 44 through 51 removed outlier: 4.110A pdb=" N PHE I 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR F 78 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 11.528A pdb=" N CYS I 106 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 14.996A pdb=" N ASP F 80 " --> pdb=" O CYS I 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR I 102 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER I 96 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE I 104 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS I 94 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD1, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AD2, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.167A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.573A pdb=" N LEU G 24 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 51 removed outlier: 4.068A pdb=" N ASN G 75 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU G 76 " --> pdb=" O GLN G 241 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD6, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.648A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.524A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.594A pdb=" N ASP H 19 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL H 158 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP H 177 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE H 162 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.594A pdb=" N ASP H 19 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY H 28 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.637A pdb=" N PHE J 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR H 78 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N CYS J 106 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP H 80 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR J 102 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER J 96 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE J 104 " --> pdb=" O LYS J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS J 94 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 266 through 268 removed outlier: 3.637A pdb=" N ASP H 268 " --> pdb=" O ILE H 280 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4386 1.32 - 1.45: 6167 1.45 - 1.57: 12936 1.57 - 1.69: 136 1.69 - 1.81: 39 Bond restraints: 23664 Sorted by residual: bond pdb=" C1' DC O 3 " pdb=" N1 DC O 3 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.54e+01 bond pdb=" C1' DT O 7 " pdb=" N1 DT O 7 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C3' DC O 6 " pdb=" C2' DC O 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA O 4 " pdb=" C2' DA O 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" C3' DA O 1 " pdb=" C2' DA O 1 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 ... (remaining 23659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 31209 2.30 - 4.60: 941 4.60 - 6.89: 126 6.89 - 9.19: 16 9.19 - 11.49: 7 Bond angle restraints: 32299 Sorted by residual: angle pdb=" N GLY G 240 " pdb=" CA GLY G 240 " pdb=" C GLY G 240 " ideal model delta sigma weight residual 115.32 123.37 -8.05 1.38e+00 5.25e-01 3.40e+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 97.85 11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N LEU G 233 " pdb=" CA LEU G 233 " pdb=" C LEU G 233 " ideal model delta sigma weight residual 111.36 117.29 -5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N VAL G 249 " pdb=" CA VAL G 249 " pdb=" C VAL G 249 " ideal model delta sigma weight residual 109.34 98.26 11.08 2.08e+00 2.31e-01 2.84e+01 angle pdb=" N GLU A 261 " pdb=" CA GLU A 261 " pdb=" C GLU A 261 " ideal model delta sigma weight residual 108.96 116.81 -7.85 1.49e+00 4.50e-01 2.78e+01 ... (remaining 32294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.61: 11917 18.61 - 37.22: 1181 37.22 - 55.83: 380 55.83 - 74.44: 136 74.44 - 93.06: 21 Dihedral angle restraints: 13635 sinusoidal: 5709 harmonic: 7926 Sorted by residual: dihedral pdb=" C4' A M 3 " pdb=" C3' A M 3 " pdb=" C2' A M 3 " pdb=" C1' A M 3 " ideal model delta sinusoidal sigma weight residual 36.34 -38.06 74.41 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' A M 7 " pdb=" C3' A M 7 " pdb=" C2' A M 7 " pdb=" C1' A M 7 " ideal model delta sinusoidal sigma weight residual 36.34 -37.49 73.84 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' C M 31 " pdb=" C3' C M 31 " pdb=" C2' C M 31 " pdb=" C1' C M 31 " ideal model delta sinusoidal sigma weight residual 36.34 -36.63 72.97 1 3.10e+00 1.04e-01 7.06e+02 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2897 0.075 - 0.151: 442 0.151 - 0.226: 92 0.226 - 0.301: 49 0.301 - 0.377: 4 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CA HIS B 305 " pdb=" N HIS B 305 " pdb=" C HIS B 305 " pdb=" CB HIS B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ALA G 319 " pdb=" N ALA G 319 " pdb=" C ALA G 319 " pdb=" CB ALA G 319 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C2' A M 8 " pdb=" C3' A M 8 " pdb=" O2' A M 8 " pdb=" C1' A M 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3481 not shown) Planarity restraints: 4078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 232 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ILE G 232 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE G 232 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU G 233 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 127 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ASN C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU C 128 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 228 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO A 229 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.038 5.00e-02 4.00e+02 ... (remaining 4075 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 111 2.54 - 3.13: 15611 3.13 - 3.72: 33173 3.72 - 4.31: 47071 4.31 - 4.90: 79839 Nonbonded interactions: 175805 Sorted by model distance: nonbonded pdb=" O ASN G 75 " pdb=" OD1 ASN G 75 " model vdw 1.950 3.040 nonbonded pdb=" OD1 ASP H 111 " pdb=" N ALA H 112 " model vdw 2.174 3.120 nonbonded pdb=" O LEU B 139 " pdb=" O2 U M 2 " model vdw 2.202 3.040 nonbonded pdb=" CG1 VAL A 199 " pdb=" NH1 ARG A 258 " model vdw 2.218 3.540 nonbonded pdb=" O VAL I 36 " pdb=" OD1 ASP I 37 " model vdw 2.270 3.040 ... (remaining 175800 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 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 272 or (resid 273 through 275 an \ d (name N or name CA or name C or name O or name CB )) or resid 276 through 337 \ or (resid 338 and (name N or name CA or name C or name O )))) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 231 or re \ sid 244 through 323 or (resid 324 and (name N or name CA or name C or name O or \ name CB )) or resid 325 through 337 or (resid 338 and (name N or name CA or name \ C or name O )))) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 338)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 124)) } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 22.910 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 0.083 23664 Z= 0.332 Angle : 0.928 11.489 32299 Z= 0.532 Chirality : 0.067 0.377 3484 Planarity : 0.006 0.068 4078 Dihedral : 17.608 93.056 8703 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.81 % Rotamer: Outliers : 1.10 % Allowed : 14.77 % Favored : 84.13 % Cbeta Deviations : 0.04 % 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: -3.73 (0.12), residues: 2906 helix: -3.20 (0.11), residues: 880 sheet: -0.28 (0.25), residues: 445 loop : -2.77 (0.12), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 152 TYR 0.021 0.002 TYR H 285 PHE 0.019 0.002 PHE B 66 TRP 0.026 0.002 TRP G 30 HIS 0.009 0.002 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.33 (23664) covalent geometry : angle 0.92784 / 0.53 (32299) hydrogen bonds : bond 0.17065 / 12.73 ( 857) hydrogen bonds : angle 6.86904 / 5.03 ( 2409) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 PHE cc_start: 0.7192 (p90) cc_final: 0.6719 (p90) REVERT: A 225 GLN cc_start: 0.6663 (mm-40) cc_final: 0.6309 (tp-100) REVERT: A 237 ASN cc_start: 0.8555 (p0) cc_final: 0.8272 (p0) REVERT: B 110 LEU cc_start: 0.8178 (pp) cc_final: 0.7817 (mt) REVERT: B 218 ARG cc_start: 0.5786 (ptm160) cc_final: 0.4799 (ttt-90) REVERT: C 150 ARG cc_start: 0.6423 (mtp-110) cc_final: 0.5804 (mmp80) REVERT: C 161 ARG cc_start: 0.6574 (ttm110) cc_final: 0.5948 (tpt-90) REVERT: D 16 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8246 (ptp90) REVERT: D 208 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.5693 (p90) REVERT: D 291 GLN cc_start: 0.7900 (tt0) cc_final: 0.7659 (tt0) REVERT: E 241 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6773 (tp40) REVERT: G 159 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: G 260 ILE cc_start: 0.8681 (pt) cc_final: 0.8222 (mt) REVERT: G 285 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7502 (m-80) outliers start: 23 outliers final: 10 residues processed: 332 average time/residue: 0.2022 time to fit residues: 96.3302 Evaluate side-chains 247 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 19 ASN B 45 GLN B 82 ASN B 269 ASN B 293 HIS C 83 ASN C 163 ASN C 167 GLN C 256 HIS D 163 ASN ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 163 ASN E 310 ASN F 110 ASN F 129 GLN F 163 ASN F 223 GLN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN G 163 ASN G 310 ASN H 110 ASN H 223 GLN H 241 GLN I 14 GLN I 114 ASN J 21 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142487 restraints weight = 27046.381| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.78 r_work: 0.3100 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23664 Z= 0.164 Angle : 0.948 19.758 32299 Z= 0.422 Chirality : 0.082 1.021 3484 Planarity : 0.005 0.056 4078 Dihedral : 13.063 130.514 4011 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.58 % Allowed : 16.92 % Favored : 80.50 % 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: -2.46 (0.14), residues: 2906 helix: -1.45 (0.15), residues: 896 sheet: 0.16 (0.24), residues: 466 loop : -2.39 (0.13), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 175 TYR 0.016 0.002 TYR H 285 PHE 0.022 0.001 PHE A 232 TRP 0.013 0.001 TRP E 174 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (23664) covalent geometry : angle 0.94849 / 0.42 (32299) hydrogen bonds : bond 0.04645 / 3.45 ( 857) hydrogen bonds : angle 4.93829 / 3.59 ( 2409) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 211 PHE cc_start: 0.7301 (p90) cc_final: 0.6861 (p90) REVERT: A 225 GLN cc_start: 0.6539 (mm-40) cc_final: 0.5851 (tp-100) REVERT: B 218 ARG cc_start: 0.5634 (ptm160) cc_final: 0.4500 (ttt-90) REVERT: C 150 ARG cc_start: 0.6630 (mtp-110) cc_final: 0.6163 (ttt90) REVERT: C 161 ARG cc_start: 0.6399 (ttm110) cc_final: 0.5428 (tpt-90) REVERT: D 16 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8476 (ptp90) REVERT: D 208 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.5742 (p90) REVERT: D 291 GLN cc_start: 0.8099 (tt0) cc_final: 0.7543 (tt0) REVERT: E 184 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.7838 (mmt180) REVERT: E 241 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6439 (tp40) REVERT: F 175 ARG cc_start: 0.8578 (ttt180) cc_final: 0.8312 (ttt180) REVERT: F 297 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8637 (mt0) REVERT: G 129 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7054 (pt0) REVERT: G 241 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7719 (mm-40) REVERT: G 285 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7369 (m-80) outliers start: 54 outliers final: 33 residues processed: 286 average time/residue: 0.2008 time to fit residues: 82.8056 Evaluate side-chains 264 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 140 HIS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 262 optimal weight: 0.0980 chunk 8 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 3 optimal weight: 40.0000 chunk 83 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 HIS ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 129 GLN F 241 GLN G 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.138384 restraints weight = 27661.564| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.26 r_work: 0.3087 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 23664 Z= 0.147 Angle : 0.733 15.841 32299 Z= 0.353 Chirality : 0.059 0.637 3484 Planarity : 0.004 0.049 4078 Dihedral : 13.246 156.893 3993 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.37 % Favored : 94.60 % Rotamer: Outliers : 2.92 % Allowed : 18.02 % Favored : 79.06 % 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: -1.77 (0.15), residues: 2906 helix: -0.50 (0.17), residues: 889 sheet: 0.44 (0.24), residues: 465 loop : -2.18 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 222 TYR 0.014 0.002 TYR C 271 PHE 0.027 0.001 PHE A 232 TRP 0.019 0.001 TRP B 239 HIS 0.005 0.001 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (23664) covalent geometry : angle 0.73263 / 0.35 (32299) hydrogen bonds : bond 0.04050 / 3.02 ( 857) hydrogen bonds : angle 4.52958 / 3.28 ( 2409) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 59 ARG cc_start: 0.6866 (mtp180) cc_final: 0.6652 (mtp-110) REVERT: A 225 GLN cc_start: 0.6571 (mm-40) cc_final: 0.5877 (tp-100) REVERT: A 247 LYS cc_start: 0.8338 (mmmm) cc_final: 0.8033 (mmmm) REVERT: B 175 ARG cc_start: 0.8324 (tmm-80) cc_final: 0.8025 (tmm-80) REVERT: B 218 ARG cc_start: 0.5614 (ptm160) cc_final: 0.4531 (ttp-170) REVERT: C 161 ARG cc_start: 0.6210 (ttm110) cc_final: 0.5328 (ttt-90) REVERT: D 16 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8381 (ptp90) REVERT: D 208 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.5646 (p90) REVERT: D 291 GLN cc_start: 0.7976 (tt0) cc_final: 0.7398 (tt0) REVERT: E 184 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7668 (mmt180) REVERT: E 241 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6304 (tp40) REVERT: F 297 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: G 16 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8792 (ptt90) REVERT: G 129 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: G 241 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7640 (mm-40) REVERT: G 285 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: H 148 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8417 (pp) REVERT: I 12 ASN cc_start: 0.6250 (p0) cc_final: 0.5923 (p0) outliers start: 61 outliers final: 37 residues processed: 274 average time/residue: 0.2015 time to fit residues: 80.3866 Evaluate side-chains 261 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 293 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 80 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 235 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 51 optimal weight: 0.0370 chunk 4 optimal weight: 9.9990 chunk 289 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS B 305 HIS D 322 GLN E 167 GLN F 129 GLN H 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.147950 restraints weight = 26964.080| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.69 r_work: 0.3228 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23664 Z= 0.109 Angle : 0.651 11.602 32299 Z= 0.316 Chirality : 0.051 0.430 3484 Planarity : 0.004 0.047 4078 Dihedral : 13.245 152.815 3993 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 3.11 % Allowed : 18.69 % Favored : 78.20 % 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: -1.31 (0.15), residues: 2906 helix: 0.03 (0.18), residues: 905 sheet: 0.83 (0.25), residues: 449 loop : -2.04 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 184 TYR 0.011 0.001 TYR C 271 PHE 0.025 0.001 PHE A 232 TRP 0.010 0.001 TRP G 174 HIS 0.004 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (23664) covalent geometry : angle 0.65070 / 0.32 (32299) hydrogen bonds : bond 0.03495 / 2.61 ( 857) hydrogen bonds : angle 4.27068 / 3.10 ( 2409) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 220 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.6660 (mm-40) cc_final: 0.6023 (tp-100) REVERT: B 175 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.8198 (tmm-80) REVERT: B 218 ARG cc_start: 0.5686 (ptm160) cc_final: 0.4804 (ttm-80) REVERT: C 150 ARG cc_start: 0.6743 (mtp-110) cc_final: 0.5693 (mmp80) REVERT: C 151 ASN cc_start: 0.6451 (m-40) cc_final: 0.6001 (m110) REVERT: C 161 ARG cc_start: 0.6337 (ttm110) cc_final: 0.5539 (ttt-90) REVERT: D 208 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.5663 (p90) REVERT: D 291 GLN cc_start: 0.8073 (tt0) cc_final: 0.7560 (tt0) REVERT: E 184 ARG cc_start: 0.7937 (mmt-90) cc_final: 0.7668 (mmt180) REVERT: E 241 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6493 (tp40) REVERT: F 297 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8445 (mt0) REVERT: G 241 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7673 (mm-40) REVERT: G 285 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: H 148 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8428 (pp) REVERT: I 6 MET cc_start: 0.6182 (mtt) cc_final: 0.5973 (mtp) REVERT: I 12 ASN cc_start: 0.6318 (p0) cc_final: 0.5935 (p0) outliers start: 65 outliers final: 44 residues processed: 269 average time/residue: 0.1966 time to fit residues: 77.7240 Evaluate side-chains 263 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 80 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 237 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 31 optimal weight: 40.0000 chunk 2 optimal weight: 0.0020 chunk 261 optimal weight: 0.0870 chunk 257 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 167 GLN F 129 GLN G 129 GLN J 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144167 restraints weight = 26835.275| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.61 r_work: 0.3230 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23664 Z= 0.174 Angle : 0.707 11.129 32299 Z= 0.345 Chirality : 0.054 0.437 3484 Planarity : 0.004 0.046 4078 Dihedral : 13.368 150.688 3989 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.87 % Allowed : 18.83 % Favored : 77.29 % 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: -1.24 (0.15), residues: 2906 helix: 0.15 (0.18), residues: 905 sheet: 0.76 (0.25), residues: 445 loop : -1.99 (0.14), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 184 TYR 0.018 0.002 TYR C 271 PHE 0.027 0.002 PHE A 232 TRP 0.020 0.001 TRP G 30 HIS 0.006 0.001 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (23664) covalent geometry : angle 0.70698 / 0.35 (32299) hydrogen bonds : bond 0.04021 / 2.97 ( 857) hydrogen bonds : angle 4.32403 / 3.13 ( 2409) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 211 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.6752 (mm-40) cc_final: 0.6050 (tp-100) REVERT: B 218 ARG cc_start: 0.5665 (ptm160) cc_final: 0.4689 (ttp-170) REVERT: C 150 ARG cc_start: 0.6749 (mtp-110) cc_final: 0.5735 (mmp80) REVERT: C 151 ASN cc_start: 0.6490 (m-40) cc_final: 0.6021 (m110) REVERT: C 161 ARG cc_start: 0.6530 (ttm110) cc_final: 0.5549 (ttt-90) REVERT: C 250 ARG cc_start: 0.3455 (OUTLIER) cc_final: 0.2326 (ptt180) REVERT: D 16 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (ptp90) REVERT: D 208 HIS cc_start: 0.7640 (OUTLIER) cc_final: 0.5841 (p90) REVERT: D 297 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: E 184 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.7669 (mmt180) REVERT: E 241 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6581 (tp40) REVERT: F 221 ASP cc_start: 0.8408 (t0) cc_final: 0.8164 (t70) REVERT: F 297 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: G 16 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8618 (ptt90) REVERT: G 80 ASP cc_start: 0.8455 (m-30) cc_final: 0.8216 (m-30) REVERT: G 241 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7668 (mm-40) REVERT: G 285 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: H 148 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8531 (pp) REVERT: I 12 ASN cc_start: 0.6517 (p0) cc_final: 0.6091 (p0) outliers start: 81 outliers final: 54 residues processed: 274 average time/residue: 0.2023 time to fit residues: 80.6999 Evaluate side-chains 267 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 229 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 238 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145591 restraints weight = 27019.140| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.80 r_work: 0.3120 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23664 Z= 0.118 Angle : 0.633 11.053 32299 Z= 0.312 Chirality : 0.050 0.404 3484 Planarity : 0.004 0.048 4078 Dihedral : 13.354 148.789 3987 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.49 % Allowed : 19.60 % Favored : 76.91 % 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: -1.01 (0.15), residues: 2906 helix: 0.42 (0.18), residues: 905 sheet: 0.84 (0.25), residues: 447 loop : -1.89 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 222 TYR 0.013 0.001 TYR H 285 PHE 0.029 0.001 PHE A 232 TRP 0.012 0.001 TRP B 147 HIS 0.004 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (23664) covalent geometry : angle 0.63277 / 0.31 (32299) hydrogen bonds : bond 0.03447 / 2.56 ( 857) hydrogen bonds : angle 4.15534 / 3.01 ( 2409) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.6693 (mm-40) cc_final: 0.5996 (tp-100) REVERT: B 147 TRP cc_start: 0.6506 (t60) cc_final: 0.6167 (t60) REVERT: B 218 ARG cc_start: 0.5391 (ptm160) cc_final: 0.4579 (ttp-170) REVERT: C 151 ASN cc_start: 0.6481 (m-40) cc_final: 0.6003 (m110) REVERT: C 161 ARG cc_start: 0.6186 (ttm110) cc_final: 0.5438 (ttt-90) REVERT: C 250 ARG cc_start: 0.3297 (OUTLIER) cc_final: 0.2232 (ptt180) REVERT: C 255 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6921 (mt) REVERT: D 16 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8333 (ptp90) REVERT: D 208 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.5743 (p90) REVERT: D 291 GLN cc_start: 0.8082 (tt0) cc_final: 0.7523 (tt0) REVERT: D 297 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: E 166 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6967 (ptp-110) REVERT: E 184 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7616 (mmt180) REVERT: E 241 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6495 (tp40) REVERT: F 297 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: G 16 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8586 (ptt90) REVERT: G 80 ASP cc_start: 0.8402 (m-30) cc_final: 0.8138 (m-30) REVERT: G 241 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7647 (mm-40) REVERT: G 285 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: H 148 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8487 (pp) REVERT: H 219 ILE cc_start: 0.8782 (tt) cc_final: 0.8343 (pt) outliers start: 73 outliers final: 52 residues processed: 271 average time/residue: 0.1974 time to fit residues: 78.0558 Evaluate side-chains 271 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 140 HIS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 62 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 129 GLN F 262 ASN I 14 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.177074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135916 restraints weight = 27254.328| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.18 r_work: 0.3045 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23664 Z= 0.208 Angle : 0.737 11.104 32299 Z= 0.363 Chirality : 0.055 0.475 3484 Planarity : 0.005 0.048 4078 Dihedral : 13.474 144.345 3987 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.92 % Allowed : 19.89 % Favored : 76.20 % 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: -1.10 (0.15), residues: 2906 helix: 0.36 (0.18), residues: 896 sheet: 0.78 (0.25), residues: 441 loop : -1.93 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 45 TYR 0.020 0.002 TYR C 271 PHE 0.027 0.002 PHE A 232 TRP 0.022 0.002 TRP G 30 HIS 0.007 0.001 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (23664) covalent geometry : angle 0.73694 / 0.36 (32299) hydrogen bonds : bond 0.04240 / 3.13 ( 857) hydrogen bonds : angle 4.33632 / 3.14 ( 2409) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 211 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.6565 (mm-40) cc_final: 0.5997 (tp-100) REVERT: B 218 ARG cc_start: 0.5577 (ptm160) cc_final: 0.4649 (ttp-170) REVERT: C 151 ASN cc_start: 0.6513 (m-40) cc_final: 0.6215 (m-40) REVERT: C 161 ARG cc_start: 0.6278 (ttm110) cc_final: 0.5440 (ttt-90) REVERT: C 250 ARG cc_start: 0.3247 (OUTLIER) cc_final: 0.2234 (ptt180) REVERT: D 16 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8439 (ptp90) REVERT: D 208 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.5669 (p90) REVERT: D 297 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: E 184 ARG cc_start: 0.8016 (mmt-90) cc_final: 0.7685 (mmt180) REVERT: E 241 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6532 (tp40) REVERT: E 264 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8601 (mp) REVERT: F 297 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: G 16 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8649 (ptt90) REVERT: G 241 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7647 (mm-40) REVERT: G 285 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: H 148 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8566 (pp) REVERT: H 219 ILE cc_start: 0.8950 (tt) cc_final: 0.8693 (tt) REVERT: I 12 ASN cc_start: 0.6504 (p0) cc_final: 0.6123 (p0) outliers start: 82 outliers final: 55 residues processed: 273 average time/residue: 0.1917 time to fit residues: 76.1147 Evaluate side-chains 271 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 253 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 290 optimal weight: 3.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.178658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.137927 restraints weight = 27217.038| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.15 r_work: 0.3087 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23664 Z= 0.125 Angle : 0.640 10.848 32299 Z= 0.317 Chirality : 0.050 0.428 3484 Planarity : 0.004 0.050 4078 Dihedral : 13.463 144.379 3987 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.25 % Allowed : 20.51 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2906 helix: 0.53 (0.18), residues: 902 sheet: 0.96 (0.25), residues: 438 loop : -1.87 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 222 TYR 0.013 0.001 TYR G 325 PHE 0.027 0.001 PHE A 232 TRP 0.012 0.001 TRP G 30 HIS 0.004 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (23664) covalent geometry : angle 0.63989 / 0.32 (32299) hydrogen bonds : bond 0.03530 / 2.61 ( 857) hydrogen bonds : angle 4.16599 / 3.02 ( 2409) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 211 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.6738 (mm-40) cc_final: 0.5950 (tp-100) REVERT: B 69 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.6990 (mt0) REVERT: B 147 TRP cc_start: 0.6439 (t60) cc_final: 0.6182 (t60) REVERT: B 218 ARG cc_start: 0.5533 (ptm160) cc_final: 0.4826 (ttm-80) REVERT: C 150 ARG cc_start: 0.6489 (mtp-110) cc_final: 0.6053 (ttt90) REVERT: C 151 ASN cc_start: 0.6517 (m-40) cc_final: 0.6177 (m-40) REVERT: C 161 ARG cc_start: 0.6194 (ttm110) cc_final: 0.5507 (ttt-90) REVERT: C 250 ARG cc_start: 0.3284 (OUTLIER) cc_final: 0.2178 (ptt180) REVERT: D 16 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (ptp90) REVERT: D 208 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.5521 (p90) REVERT: D 291 GLN cc_start: 0.8041 (tt0) cc_final: 0.7469 (tt0) REVERT: D 297 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: E 184 ARG cc_start: 0.8071 (mmt-90) cc_final: 0.7737 (mmt180) REVERT: E 241 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6466 (tp40) REVERT: F 297 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: G 16 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8601 (ptt90) REVERT: G 159 GLU cc_start: 0.8137 (tt0) cc_final: 0.7930 (tt0) REVERT: G 241 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7649 (mm-40) REVERT: G 285 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: H 148 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8499 (pp) REVERT: H 219 ILE cc_start: 0.8826 (tt) cc_final: 0.8595 (tt) outliers start: 68 outliers final: 52 residues processed: 264 average time/residue: 0.1981 time to fit residues: 76.1584 Evaluate side-chains 267 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 286 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 40.0000 chunk 109 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS D 322 GLN F 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.174835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134103 restraints weight = 27320.627| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.42 r_work: 0.3013 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 23664 Z= 0.293 Angle : 0.820 13.471 32299 Z= 0.403 Chirality : 0.060 0.533 3484 Planarity : 0.005 0.053 4078 Dihedral : 13.639 143.786 3987 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.59 % Allowed : 20.55 % Favored : 75.86 % 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: -1.21 (0.15), residues: 2906 helix: 0.26 (0.18), residues: 890 sheet: 0.75 (0.25), residues: 437 loop : -1.99 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 222 TYR 0.021 0.003 TYR C 271 PHE 0.027 0.002 PHE A 232 TRP 0.026 0.002 TRP G 30 HIS 0.008 0.002 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.29 (23664) covalent geometry : angle 0.82012 / 0.40 (32299) hydrogen bonds : bond 0.04789 / 3.53 ( 857) hydrogen bonds : angle 4.49894 / 3.26 ( 2409) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.6726 (mm-40) cc_final: 0.5962 (tp40) REVERT: B 69 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: B 218 ARG cc_start: 0.5670 (ptm160) cc_final: 0.4919 (ttm-80) REVERT: C 151 ASN cc_start: 0.6560 (m-40) cc_final: 0.6250 (m-40) REVERT: C 161 ARG cc_start: 0.6250 (ttm110) cc_final: 0.5532 (ttt-90) REVERT: C 250 ARG cc_start: 0.3279 (OUTLIER) cc_final: 0.2172 (ptt180) REVERT: D 16 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8412 (ptp90) REVERT: D 50 ARG cc_start: 0.6206 (ptm160) cc_final: 0.5925 (ptm160) REVERT: D 297 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: D 322 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7973 (pp30) REVERT: E 184 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7718 (mmt180) REVERT: E 241 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6488 (tp40) REVERT: F 297 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: G 16 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8705 (ptt90) REVERT: G 128 GLU cc_start: 0.8397 (tp30) cc_final: 0.8131 (mm-30) REVERT: G 241 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7715 (mm-40) REVERT: G 260 ILE cc_start: 0.8588 (pt) cc_final: 0.8375 (mt) REVERT: H 148 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8640 (pp) REVERT: H 219 ILE cc_start: 0.9031 (tt) cc_final: 0.8767 (tt) REVERT: I 12 ASN cc_start: 0.6875 (p0) cc_final: 0.6521 (p0) outliers start: 75 outliers final: 60 residues processed: 260 average time/residue: 0.1916 time to fit residues: 71.9633 Evaluate side-chains 267 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 322 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 140 HIS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 30 optimal weight: 50.0000 chunk 235 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 0 optimal weight: 60.0000 chunk 14 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 51 optimal weight: 0.0670 chunk 200 optimal weight: 8.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.175340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134061 restraints weight = 27723.813| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.36 r_work: 0.3067 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23664 Z= 0.135 Angle : 0.665 10.825 32299 Z= 0.330 Chirality : 0.052 0.446 3484 Planarity : 0.004 0.049 4078 Dihedral : 13.590 145.697 3987 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 21.22 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2906 helix: 0.49 (0.18), residues: 896 sheet: 0.91 (0.25), residues: 431 loop : -1.89 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 184 TYR 0.015 0.001 TYR H 285 PHE 0.028 0.001 PHE A 232 TRP 0.015 0.001 TRP G 30 HIS 0.005 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (23664) covalent geometry : angle 0.66527 / 0.33 (32299) hydrogen bonds : bond 0.03679 / 2.73 ( 857) hydrogen bonds : angle 4.23921 / 3.08 ( 2409) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 0.809 Fit side-chains REVERT: A 225 GLN cc_start: 0.6735 (mm-40) cc_final: 0.5907 (tp-100) REVERT: B 69 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: B 218 ARG cc_start: 0.5552 (ptm160) cc_final: 0.4871 (ttm-80) REVERT: C 150 ARG cc_start: 0.6571 (mtp-110) cc_final: 0.5602 (mmp80) REVERT: C 151 ASN cc_start: 0.6497 (m-40) cc_final: 0.6204 (m-40) REVERT: C 161 ARG cc_start: 0.6181 (ttm110) cc_final: 0.5493 (ttt-90) REVERT: C 250 ARG cc_start: 0.3244 (OUTLIER) cc_final: 0.2140 (ptt180) REVERT: D 16 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8387 (ptp90) REVERT: D 50 ARG cc_start: 0.6024 (ptm160) cc_final: 0.5800 (ptm160) REVERT: D 297 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: E 184 ARG cc_start: 0.8058 (mmt-90) cc_final: 0.7701 (mmt180) REVERT: E 241 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6378 (tp40) REVERT: F 297 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: G 16 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8621 (ptt90) REVERT: G 159 GLU cc_start: 0.8138 (tt0) cc_final: 0.7926 (tt0) REVERT: G 241 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7747 (mm-40) REVERT: G 285 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: H 148 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8533 (pp) REVERT: H 219 ILE cc_start: 0.8822 (tt) cc_final: 0.8581 (tt) outliers start: 61 outliers final: 51 residues processed: 255 average time/residue: 0.1911 time to fit residues: 71.1463 Evaluate side-chains 264 residues out of total 2385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 140 HIS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 188 optimal weight: 5.9990 chunk 36 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 226 optimal weight: 0.6980 chunk 187 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 305 HIS D 322 GLN F 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142929 restraints weight = 27195.774| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.93 r_work: 0.3149 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23664 Z= 0.105 Angle : 0.603 10.981 32299 Z= 0.299 Chirality : 0.048 0.383 3484 Planarity : 0.004 0.051 4078 Dihedral : 13.425 142.234 3987 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.77 % Allowed : 21.61 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.16), residues: 2906 helix: 0.76 (0.18), residues: 905 sheet: 0.90 (0.25), residues: 440 loop : -1.71 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 222 TYR 0.013 0.001 TYR C 271 PHE 0.015 0.001 PHE A 232 TRP 0.021 0.001 TRP B 147 HIS 0.004 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (23664) covalent geometry : angle 0.60258 / 0.30 (32299) hydrogen bonds : bond 0.03132 / 2.32 ( 857) hydrogen bonds : angle 4.00593 / 2.91 ( 2409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5601.14 seconds wall clock time: 96 minutes 23.35 seconds (5783.35 seconds total)