Starting phenix.real_space_refine on Thu Sep 18 22:45:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1c_39722/09_2025/8z1c_39722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1c_39722/09_2025/8z1c_39722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1c_39722/09_2025/8z1c_39722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1c_39722/09_2025/8z1c_39722.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1c_39722/09_2025/8z1c_39722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1c_39722/09_2025/8z1c_39722.cif" } resolution = 3.15 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= 0.010 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 13128 2.51 5 N 3618 2.21 5 O 3978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20802 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "D" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "B" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Time building chain proxies: 5.19, per 1000 atoms: 0.25 Number of scatterers: 20802 At special positions: 0 Unit cell: (116.63, 119.84, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3978 8.00 N 3618 7.00 C 13128 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: 1.93 Conformation dependent library (CDL) restraints added in 948.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 17 sheets defined 51.6% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid 7 through 23 Processing helix chain 'E' and resid 24 through 30 removed outlier: 4.207A pdb=" N GLN E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 40 removed outlier: 4.080A pdb=" N LYS E 35 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.889A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 197 through 213 removed outlier: 4.148A pdb=" N VAL E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 removed outlier: 3.691A pdb=" N LEU E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS E 239 " --> pdb=" O TYR E 235 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.526A pdb=" N LEU E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 326 through 337 Processing helix chain 'E' and resid 350 through 364 removed outlier: 4.094A pdb=" N ALA E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN E 364 " --> pdb=" O HIS E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 379 Processing helix chain 'E' and resid 381 through 396 Processing helix chain 'E' and resid 400 through 422 removed outlier: 3.635A pdb=" N THR E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 456 removed outlier: 3.884A pdb=" N GLY E 440 " --> pdb=" O SER E 436 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 23 Processing helix chain 'F' and resid 24 through 30 removed outlier: 4.314A pdb=" N GLN F 28 " --> pdb=" O SER F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.226A pdb=" N LYS F 35 " --> pdb=" O PRO F 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.887A pdb=" N PHE F 101 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 106 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 142 Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 192 through 194 No H-bonds generated for 'chain 'F' and resid 192 through 194' Processing helix chain 'F' and resid 195 through 213 removed outlier: 3.672A pdb=" N VAL F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.743A pdb=" N LYS F 239 " --> pdb=" O TYR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 removed outlier: 3.534A pdb=" N LEU F 243 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 326 through 337 Processing helix chain 'F' and resid 350 through 363 Processing helix chain 'F' and resid 380 through 395 removed outlier: 3.509A pdb=" N ALA F 384 " --> pdb=" O ALA F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 408 Processing helix chain 'F' and resid 412 through 423 Processing helix chain 'F' and resid 436 through 457 removed outlier: 3.918A pdb=" N GLY F 440 " --> pdb=" O SER F 436 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 32 through 41 removed outlier: 4.212A pdb=" N ALA D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 removed outlier: 3.878A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 158 through 174 removed outlier: 3.576A pdb=" N LYS D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 213 removed outlier: 4.228A pdb=" N VAL D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 268 through 281 removed outlier: 3.632A pdb=" N ASP D 281 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 removed outlier: 4.219A pdb=" N LEU D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 305 through 309 removed outlier: 4.066A pdb=" N VAL D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 337 Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.784A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.626A pdb=" N ALA D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 395 Processing helix chain 'D' and resid 400 through 422 removed outlier: 3.524A pdb=" N THR D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 457 removed outlier: 4.098A pdb=" N LYS D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 32 through 42 removed outlier: 3.604A pdb=" N ALA A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.872A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.560A pdb=" N THR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 213 Processing helix chain 'A' and resid 229 through 241 removed outlier: 4.420A pdb=" N ALA A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.178A pdb=" N VAL A 310 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 removed outlier: 3.679A pdb=" N GLY A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 437 through 456 removed outlier: 4.602A pdb=" N ILE A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 23 removed outlier: 3.501A pdb=" N ASN B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.959A pdb=" N GLN B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 41 removed outlier: 3.652A pdb=" N ALA B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 removed outlier: 3.879A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 195 through 213 Processing helix chain 'B' and resid 231 through 242 removed outlier: 4.064A pdb=" N GLU B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 281 removed outlier: 3.619A pdb=" N ILE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 326 through 337 removed outlier: 3.617A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 400 through 408 Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.844A pdb=" N GLY B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.539A pdb=" N ASN C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.929A pdb=" N GLN C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.617A pdb=" N ALA C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 removed outlier: 3.878A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 142 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 195 through 214 Processing helix chain 'C' and resid 230 through 239 removed outlier: 4.000A pdb=" N ALA C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 326 through 337 removed outlier: 3.614A pdb=" N GLY C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.988A pdb=" N GLY C 440 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.259A pdb=" N ARG E 82 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLY B 115 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY B 80 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N SER B 117 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG B 82 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 77 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA B 152 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY B 79 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 77 through 79 removed outlier: 7.125A pdb=" N TYR E 77 " --> pdb=" O VAL E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 246 through 247 removed outlier: 3.991A pdb=" N VAL E 224 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG E 223 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU E 317 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 225 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA E 316 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 341 " --> pdb=" O ALA E 373 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 250 through 251 removed outlier: 3.614A pdb=" N LEU E 250 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E 257 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 149 through 153 removed outlier: 7.076A pdb=" N TYR F 77 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA F 152 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY F 79 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY F 115 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY F 80 " --> pdb=" O GLY F 115 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER F 117 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG F 82 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY C 115 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY C 80 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER C 117 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG C 82 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 77 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 152 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 79 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 223 through 224 Processing sheet with id=AA7, first strand: chain 'F' and resid 258 through 259 removed outlier: 3.576A pdb=" N ILE F 258 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 149 through 153 removed outlier: 6.981A pdb=" N TYR D 77 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA D 152 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY D 79 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY D 115 " --> pdb=" O LYS D 78 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY D 80 " --> pdb=" O GLY D 115 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N SER D 117 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG D 82 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY A 115 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY A 80 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER A 117 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR A 77 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA A 152 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 79 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.533A pdb=" N VAL D 224 " --> pdb=" O ARG D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.521A pdb=" N ILE D 258 " --> pdb=" O THR D 299 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 315 through 316 removed outlier: 5.926A pdb=" N ALA D 316 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AB4, first strand: chain 'A' and resid 257 through 258 removed outlier: 3.529A pdb=" N ILE A 258 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 246 through 247 removed outlier: 6.296A pdb=" N ARG B 223 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 317 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA B 225 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 255 through 259 removed outlier: 3.614A pdb=" N LEU B 301 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 258 removed outlier: 3.869A pdb=" N SER C 256 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 301 " --> pdb=" O SER C 256 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4637 1.33 - 1.47: 7444 1.47 - 1.61: 9015 1.61 - 1.75: 0 1.75 - 1.88: 126 Bond restraints: 21222 Sorted by residual: bond pdb=" CA SER A 117 " pdb=" CB SER A 117 " ideal model delta sigma weight residual 1.533 1.460 0.073 1.65e-02 3.67e+03 1.95e+01 bond pdb=" CA SER E 117 " pdb=" CB SER E 117 " ideal model delta sigma weight residual 1.532 1.458 0.074 1.68e-02 3.54e+03 1.94e+01 bond pdb=" C THR B 138 " pdb=" O THR B 138 " ideal model delta sigma weight residual 1.236 1.287 -0.050 1.15e-02 7.56e+03 1.92e+01 bond pdb=" CA SER C 117 " pdb=" CB SER C 117 " ideal model delta sigma weight residual 1.533 1.461 0.072 1.65e-02 3.67e+03 1.90e+01 bond pdb=" CA SER F 117 " pdb=" CB SER F 117 " ideal model delta sigma weight residual 1.533 1.463 0.070 1.65e-02 3.67e+03 1.80e+01 ... (remaining 21217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 28609 4.06 - 8.12: 99 8.12 - 12.18: 7 12.18 - 16.25: 0 16.25 - 20.31: 1 Bond angle restraints: 28716 Sorted by residual: angle pdb=" N PRO F 269 " pdb=" CD PRO F 269 " pdb=" CG PRO F 269 " ideal model delta sigma weight residual 103.20 82.89 20.31 1.50e+00 4.44e-01 1.83e+02 angle pdb=" N PRO A 374 " pdb=" CD PRO A 374 " pdb=" CG PRO A 374 " ideal model delta sigma weight residual 103.20 91.87 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" N PRO F 306 " pdb=" CD PRO F 306 " pdb=" CG PRO F 306 " ideal model delta sigma weight residual 103.20 93.15 10.05 1.50e+00 4.44e-01 4.49e+01 angle pdb=" CA PRO D 429 " pdb=" N PRO D 429 " pdb=" CD PRO D 429 " ideal model delta sigma weight residual 112.00 103.73 8.27 1.40e+00 5.10e-01 3.49e+01 angle pdb=" CB ARG D 170 " pdb=" CG ARG D 170 " pdb=" CD ARG D 170 " ideal model delta sigma weight residual 111.30 100.77 10.53 2.30e+00 1.89e-01 2.10e+01 ... (remaining 28711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10963 17.57 - 35.14: 1167 35.14 - 52.71: 269 52.71 - 70.28: 115 70.28 - 87.85: 14 Dihedral angle restraints: 12528 sinusoidal: 4782 harmonic: 7746 Sorted by residual: dihedral pdb=" CA ASP F 410 " pdb=" C ASP F 410 " pdb=" N ILE F 411 " pdb=" CA ILE F 411 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASP B 410 " pdb=" C ASP B 410 " pdb=" N ILE B 411 " pdb=" CA ILE B 411 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLU D 44 " pdb=" C GLU D 44 " pdb=" N ARG D 45 " pdb=" CA ARG D 45 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 12525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2105 0.066 - 0.131: 835 0.131 - 0.197: 147 0.197 - 0.262: 23 0.262 - 0.328: 10 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA LEU C 172 " pdb=" N LEU C 172 " pdb=" C LEU C 172 " pdb=" CB LEU C 172 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL E 52 " pdb=" CA VAL E 52 " pdb=" CG1 VAL E 52 " pdb=" CG2 VAL E 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 3117 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 170 " 0.374 9.50e-02 1.11e+02 1.68e-01 1.73e+01 pdb=" NE ARG F 170 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG F 170 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 170 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 170 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 170 " -0.345 9.50e-02 1.11e+02 1.55e-01 1.46e+01 pdb=" NE ARG C 170 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 170 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 170 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 170 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 170 " 0.322 9.50e-02 1.11e+02 1.45e-01 1.30e+01 pdb=" NE ARG D 170 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 170 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 170 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 170 " 0.008 2.00e-02 2.50e+03 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 562 2.69 - 3.24: 21712 3.24 - 3.79: 34863 3.79 - 4.35: 47019 4.35 - 4.90: 76097 Nonbonded interactions: 180253 Sorted by model distance: nonbonded pdb=" O GLY B 375 " pdb=" ND2 ASN B 379 " model vdw 2.137 3.120 nonbonded pdb=" OE1 GLN F 456 " pdb=" NH1 ARG D 170 " model vdw 2.154 3.120 nonbonded pdb=" O GLY A 375 " pdb=" ND2 ASN A 379 " model vdw 2.170 3.120 nonbonded pdb=" O VAL D 383 " pdb=" OG SER D 386 " model vdw 2.175 3.040 nonbonded pdb=" NH1 ARG E 170 " pdb=" OE1 GLN D 456 " model vdw 2.197 3.120 ... (remaining 180248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.030 Find NCS groups from input model: 0.380 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 0.009 0.082 21222 Z= 0.559 Angle : 1.007 20.307 28716 Z= 0.647 Chirality : 0.071 0.328 3120 Planarity : 0.011 0.168 3786 Dihedral : 16.339 87.846 7608 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.79 % Favored : 92.03 % Rotamer: Outliers : 1.14 % Allowed : 21.37 % Favored : 77.49 % 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 aren not related in a simple way. whole: -1.12 (0.16), residues: 2748 helix: 0.49 (0.14), residues: 1296 sheet: -1.49 (0.29), residues: 318 loop : -1.96 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG D 130 TYR 0.034 0.007 TYR B 14 PHE 0.043 0.007 PHE A 66 TRP 0.042 0.008 TRP E 176 HIS 0.019 0.004 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00892 (21222) covalent geometry : angle 1.00660 (28716) hydrogen bonds : bond 0.13593 ( 1010) hydrogen bonds : angle 5.89080 ( 2967) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.779 Fit side-chains REVERT: E 433 ILE cc_start: 0.6619 (mp) cc_final: 0.6282 (tp) REVERT: A 26 LEU cc_start: 0.5674 (tt) cc_final: 0.4894 (mm) REVERT: B 172 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8104 (pt) REVERT: C 208 MET cc_start: 0.4031 (ptp) cc_final: 0.3808 (mmt) REVERT: C 288 LEU cc_start: 0.3751 (OUTLIER) cc_final: 0.3515 (tp) outliers start: 24 outliers final: 9 residues processed: 207 average time/residue: 0.1715 time to fit residues: 53.9988 Evaluate side-chains 185 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 416 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 416 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 174 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN C 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.220789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.183515 restraints weight = 26516.623| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.39 r_work: 0.3753 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21222 Z= 0.130 Angle : 0.544 8.142 28716 Z= 0.286 Chirality : 0.041 0.173 3120 Planarity : 0.004 0.048 3786 Dihedral : 4.667 47.568 2971 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.51 % Favored : 93.30 % Rotamer: Outliers : 2.56 % Allowed : 21.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.16), residues: 2748 helix: 0.83 (0.14), residues: 1330 sheet: -1.39 (0.29), residues: 358 loop : -1.67 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 170 TYR 0.013 0.001 TYR B 77 PHE 0.021 0.002 PHE C 357 TRP 0.022 0.002 TRP E 371 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00276 (21222) covalent geometry : angle 0.54444 (28716) hydrogen bonds : bond 0.04798 ( 1010) hydrogen bonds : angle 4.88245 ( 2967) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: E 324 GLU cc_start: 0.5598 (pm20) cc_final: 0.5284 (pm20) REVERT: D 71 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8341 (t0) REVERT: A 160 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7743 (ptm160) REVERT: B 172 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8437 (pt) REVERT: C 35 LYS cc_start: 0.8280 (tptt) cc_final: 0.8025 (tptt) REVERT: C 208 MET cc_start: 0.4311 (ptp) cc_final: 0.4050 (mmt) REVERT: C 347 MET cc_start: 0.4336 (OUTLIER) cc_final: 0.3311 (ttm) outliers start: 54 outliers final: 23 residues processed: 247 average time/residue: 0.1605 time to fit residues: 60.7357 Evaluate side-chains 200 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 155 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 242 optimal weight: 0.0570 chunk 113 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.217949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168946 restraints weight = 26794.887| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.10 r_work: 0.3763 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21222 Z= 0.191 Angle : 0.576 8.777 28716 Z= 0.303 Chirality : 0.043 0.206 3120 Planarity : 0.004 0.053 3786 Dihedral : 4.379 40.956 2954 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.50 % Favored : 92.32 % Rotamer: Outliers : 3.94 % Allowed : 20.13 % Favored : 75.93 % 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 aren not related in a simple way. whole: -0.74 (0.16), residues: 2748 helix: 0.77 (0.14), residues: 1330 sheet: -1.66 (0.29), residues: 338 loop : -1.66 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 173 TYR 0.017 0.002 TYR E 204 PHE 0.024 0.002 PHE E 357 TRP 0.028 0.002 TRP E 371 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00433 (21222) covalent geometry : angle 0.57555 (28716) hydrogen bonds : bond 0.05174 ( 1010) hydrogen bonds : angle 4.93386 ( 2967) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 188 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: E 126 ASP cc_start: 0.6967 (m-30) cc_final: 0.6629 (m-30) REVERT: E 324 GLU cc_start: 0.5820 (pm20) cc_final: 0.5618 (pm20) REVERT: F 176 TRP cc_start: 0.8489 (OUTLIER) cc_final: 0.7421 (t60) REVERT: D 214 ASN cc_start: 0.5415 (m110) cc_final: 0.4976 (m-40) REVERT: D 324 GLU cc_start: 0.4734 (OUTLIER) cc_final: 0.4518 (pm20) REVERT: D 347 MET cc_start: 0.3984 (OUTLIER) cc_final: 0.3707 (ttm) REVERT: A 160 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7879 (ptm160) REVERT: B 172 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8524 (pt) REVERT: B 176 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.6597 (t60) REVERT: B 396 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6464 (mtt-85) REVERT: C 35 LYS cc_start: 0.8528 (tptt) cc_final: 0.8308 (tptt) REVERT: C 208 MET cc_start: 0.4468 (ptp) cc_final: 0.4055 (mmt) REVERT: C 347 MET cc_start: 0.4831 (OUTLIER) cc_final: 0.4117 (ttm) outliers start: 83 outliers final: 43 residues processed: 252 average time/residue: 0.1533 time to fit residues: 60.7432 Evaluate side-chains 225 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 415 CYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 87 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 163 optimal weight: 30.0000 chunk 149 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.221201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.186149 restraints weight = 26702.484| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 2.50 r_work: 0.3762 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21222 Z= 0.117 Angle : 0.510 7.015 28716 Z= 0.268 Chirality : 0.041 0.201 3120 Planarity : 0.003 0.050 3786 Dihedral : 4.087 39.980 2954 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.66 % Favored : 93.20 % Rotamer: Outliers : 2.85 % Allowed : 21.37 % Favored : 75.78 % 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 aren not related in a simple way. whole: -0.48 (0.16), residues: 2748 helix: 0.98 (0.14), residues: 1342 sheet: -1.35 (0.30), residues: 342 loop : -1.63 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 64 TYR 0.010 0.001 TYR A 204 PHE 0.020 0.001 PHE F 219 TRP 0.020 0.001 TRP E 371 HIS 0.005 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00246 (21222) covalent geometry : angle 0.51014 (28716) hydrogen bonds : bond 0.04162 ( 1010) hydrogen bonds : angle 4.63616 ( 2967) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 126 ASP cc_start: 0.6576 (m-30) cc_final: 0.6248 (m-30) REVERT: E 219 PHE cc_start: 0.2827 (OUTLIER) cc_final: 0.2422 (t80) REVERT: E 238 LEU cc_start: 0.5774 (mp) cc_final: 0.4518 (tt) REVERT: F 347 MET cc_start: 0.4198 (ttm) cc_final: 0.3530 (ttm) REVERT: D 347 MET cc_start: 0.4175 (OUTLIER) cc_final: 0.3905 (ttm) REVERT: A 208 MET cc_start: 0.1835 (OUTLIER) cc_final: 0.0303 (tpt) REVERT: B 305 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.2791 (mmp80) REVERT: B 396 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6590 (mtt-85) REVERT: C 208 MET cc_start: 0.4090 (ptp) cc_final: 0.3852 (mmt) REVERT: C 301 LEU cc_start: 0.2194 (OUTLIER) cc_final: 0.1660 (pt) REVERT: C 305 ARG cc_start: 0.4052 (OUTLIER) cc_final: 0.2718 (mmp80) REVERT: C 347 MET cc_start: 0.4276 (OUTLIER) cc_final: 0.3380 (ttm) outliers start: 60 outliers final: 28 residues processed: 247 average time/residue: 0.1586 time to fit residues: 60.6014 Evaluate side-chains 214 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 41 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 175 optimal weight: 0.0770 chunk 123 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 256 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.215971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170926 restraints weight = 26739.270| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.40 r_work: 0.3804 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 21222 Z= 0.254 Angle : 0.626 7.612 28716 Z= 0.329 Chirality : 0.045 0.243 3120 Planarity : 0.004 0.055 3786 Dihedral : 4.463 24.935 2952 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.11 % Favored : 91.70 % Rotamer: Outliers : 4.46 % Allowed : 20.94 % Favored : 74.60 % 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 aren not related in a simple way. whole: -0.85 (0.16), residues: 2748 helix: 0.69 (0.14), residues: 1330 sheet: -1.73 (0.29), residues: 338 loop : -1.73 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 142 TYR 0.019 0.002 TYR E 204 PHE 0.026 0.003 PHE E 357 TRP 0.023 0.002 TRP E 371 HIS 0.006 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00598 (21222) covalent geometry : angle 0.62591 (28716) hydrogen bonds : bond 0.05481 ( 1010) hydrogen bonds : angle 4.98557 ( 2967) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 183 time to evaluate : 0.806 Fit side-chains REVERT: F 176 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7750 (t60) REVERT: F 371 TRP cc_start: 0.3258 (OUTLIER) cc_final: 0.2780 (t60) REVERT: D 214 ASN cc_start: 0.5658 (m110) cc_final: 0.5114 (m-40) REVERT: D 409 LYS cc_start: 0.6216 (OUTLIER) cc_final: 0.5944 (mptp) REVERT: A 176 TRP cc_start: 0.8584 (OUTLIER) cc_final: 0.8163 (t60) REVERT: A 187 TRP cc_start: 0.5251 (OUTLIER) cc_final: 0.4876 (m-90) REVERT: A 390 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7475 (ptp) REVERT: B 176 TRP cc_start: 0.8423 (OUTLIER) cc_final: 0.7327 (t60) REVERT: B 250 LEU cc_start: 0.4172 (OUTLIER) cc_final: 0.3935 (mp) REVERT: B 251 SER cc_start: 0.5564 (p) cc_final: 0.5266 (t) REVERT: B 396 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6659 (mtt-85) REVERT: C 12 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: C 35 LYS cc_start: 0.8427 (tptt) cc_final: 0.8133 (tptt) REVERT: C 94 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8340 (t80) REVERT: C 305 ARG cc_start: 0.3973 (OUTLIER) cc_final: 0.2652 (mmp80) REVERT: C 347 MET cc_start: 0.4528 (OUTLIER) cc_final: 0.3967 (ttm) outliers start: 94 outliers final: 54 residues processed: 252 average time/residue: 0.1392 time to fit residues: 55.4541 Evaluate side-chains 241 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 132 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 393 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.220149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.183646 restraints weight = 26586.666| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.39 r_work: 0.3744 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21222 Z= 0.127 Angle : 0.526 7.749 28716 Z= 0.276 Chirality : 0.042 0.357 3120 Planarity : 0.003 0.054 3786 Dihedral : 4.106 21.869 2952 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.84 % Favored : 92.98 % Rotamer: Outliers : 3.28 % Allowed : 22.17 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 2748 helix: 0.93 (0.14), residues: 1340 sheet: -1.47 (0.30), residues: 342 loop : -1.60 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 246 TYR 0.010 0.001 TYR E 14 PHE 0.025 0.002 PHE A 219 TRP 0.020 0.001 TRP B 371 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00273 (21222) covalent geometry : angle 0.52629 (28716) hydrogen bonds : bond 0.04255 ( 1010) hydrogen bonds : angle 4.68721 ( 2967) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: E 219 PHE cc_start: 0.2877 (OUTLIER) cc_final: 0.2449 (t80) REVERT: E 238 LEU cc_start: 0.5785 (mp) cc_final: 0.4419 (tt) REVERT: E 412 MET cc_start: 0.4811 (OUTLIER) cc_final: 0.3602 (tmm) REVERT: F 176 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.7446 (t60) REVERT: F 235 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.3948 (t80) REVERT: F 306 PRO cc_start: 0.5207 (Cg_exo) cc_final: 0.4869 (Cg_endo) REVERT: B 176 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.6768 (t60) REVERT: B 240 VAL cc_start: 0.5446 (OUTLIER) cc_final: 0.5065 (m) REVERT: B 250 LEU cc_start: 0.3429 (OUTLIER) cc_final: 0.3226 (mp) REVERT: B 305 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.2752 (mmp80) REVERT: B 347 MET cc_start: 0.3774 (OUTLIER) cc_final: 0.2892 (ttm) REVERT: B 396 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6538 (mtt-85) REVERT: C 35 LYS cc_start: 0.8270 (tptt) cc_final: 0.8043 (tptt) REVERT: C 305 ARG cc_start: 0.3909 (OUTLIER) cc_final: 0.2580 (mmp80) REVERT: C 347 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.3645 (ttm) outliers start: 69 outliers final: 40 residues processed: 237 average time/residue: 0.1418 time to fit residues: 52.8922 Evaluate side-chains 224 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 127 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.212560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163962 restraints weight = 26700.333| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.75 r_work: 0.3721 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 21222 Z= 0.376 Angle : 0.750 8.773 28716 Z= 0.396 Chirality : 0.051 0.351 3120 Planarity : 0.006 0.057 3786 Dihedral : 5.010 28.579 2952 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.88 % Favored : 90.94 % Rotamer: Outliers : 4.61 % Allowed : 22.03 % Favored : 73.36 % 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 aren not related in a simple way. whole: -1.41 (0.16), residues: 2748 helix: 0.24 (0.14), residues: 1314 sheet: -2.02 (0.28), residues: 338 loop : -1.98 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 67 TYR 0.026 0.003 TYR D 204 PHE 0.029 0.003 PHE E 357 TRP 0.024 0.003 TRP F 371 HIS 0.009 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00885 (21222) covalent geometry : angle 0.75012 (28716) hydrogen bonds : bond 0.06499 ( 1010) hydrogen bonds : angle 5.33036 ( 2967) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 183 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 35 LYS cc_start: 0.8437 (tptt) cc_final: 0.8223 (tptt) REVERT: E 409 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.4880 (mptp) REVERT: E 412 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4229 (tmm) REVERT: F 176 TRP cc_start: 0.8554 (OUTLIER) cc_final: 0.8057 (t60) REVERT: F 235 TYR cc_start: 0.5290 (OUTLIER) cc_final: 0.4019 (t80) REVERT: F 412 MET cc_start: 0.7077 (tmm) cc_final: 0.6776 (tmm) REVERT: D 214 ASN cc_start: 0.5256 (m110) cc_final: 0.4996 (m110) REVERT: D 409 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5703 (mptp) REVERT: A 176 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8199 (t60) REVERT: A 187 TRP cc_start: 0.5533 (OUTLIER) cc_final: 0.5180 (m-90) REVERT: A 412 MET cc_start: 0.6996 (tmm) cc_final: 0.6722 (tmm) REVERT: B 176 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.7695 (t60) REVERT: B 251 SER cc_start: 0.5678 (p) cc_final: 0.5421 (t) REVERT: B 396 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6620 (mtt-85) REVERT: B 412 MET cc_start: 0.6912 (tmm) cc_final: 0.6530 (tmm) REVERT: C 35 LYS cc_start: 0.8600 (tptt) cc_final: 0.8356 (tptt) REVERT: C 94 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8348 (t80) REVERT: C 176 TRP cc_start: 0.8451 (OUTLIER) cc_final: 0.7768 (t60) REVERT: C 187 TRP cc_start: 0.5824 (OUTLIER) cc_final: 0.5468 (m-90) REVERT: C 305 ARG cc_start: 0.3895 (OUTLIER) cc_final: 0.2568 (mmp80) REVERT: C 347 MET cc_start: 0.4331 (OUTLIER) cc_final: 0.3393 (ttm) REVERT: C 371 TRP cc_start: 0.3582 (OUTLIER) cc_final: 0.3338 (t60) outliers start: 97 outliers final: 56 residues processed: 254 average time/residue: 0.1440 time to fit residues: 57.6102 Evaluate side-chains 239 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 409 LYS Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 409 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 176 TRP Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 94 PHE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 TRP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 371 TRP Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 393 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN C 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.218836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.179599 restraints weight = 26937.894| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.86 r_work: 0.3697 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21222 Z= 0.137 Angle : 0.554 11.471 28716 Z= 0.291 Chirality : 0.043 0.303 3120 Planarity : 0.004 0.063 3786 Dihedral : 4.345 23.506 2952 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.80 % Favored : 93.01 % Rotamer: Outliers : 3.32 % Allowed : 22.93 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.16), residues: 2748 helix: 0.67 (0.14), residues: 1330 sheet: -1.68 (0.29), residues: 342 loop : -1.74 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 246 TYR 0.014 0.001 TYR E 204 PHE 0.038 0.002 PHE B 219 TRP 0.031 0.002 TRP E 371 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00300 (21222) covalent geometry : angle 0.55370 (28716) hydrogen bonds : bond 0.04483 ( 1010) hydrogen bonds : angle 4.82232 ( 2967) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 412 MET cc_start: 0.4405 (OUTLIER) cc_final: 0.3614 (tmm) REVERT: F 176 TRP cc_start: 0.8309 (OUTLIER) cc_final: 0.7412 (t60) REVERT: F 306 PRO cc_start: 0.5106 (Cg_exo) cc_final: 0.4746 (Cg_endo) REVERT: D 324 GLU cc_start: 0.4510 (pm20) cc_final: 0.4218 (pm20) REVERT: D 412 MET cc_start: 0.4438 (tmm) cc_final: 0.4154 (tmm) REVERT: B 172 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8412 (pt) REVERT: B 176 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.6649 (t60) REVERT: B 305 ARG cc_start: 0.4851 (OUTLIER) cc_final: 0.2682 (mmp80) REVERT: B 347 MET cc_start: 0.3112 (OUTLIER) cc_final: 0.2570 (ttm) REVERT: B 396 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6365 (mtt-85) REVERT: C 305 ARG cc_start: 0.3742 (OUTLIER) cc_final: 0.2613 (mmp80) REVERT: C 347 MET cc_start: 0.4163 (OUTLIER) cc_final: 0.3213 (ttm) outliers start: 70 outliers final: 53 residues processed: 227 average time/residue: 0.1409 time to fit residues: 50.0104 Evaluate side-chains 233 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 ASN E 379 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.219301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.180244 restraints weight = 26929.293| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.86 r_work: 0.3703 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21222 Z= 0.134 Angle : 0.553 10.873 28716 Z= 0.287 Chirality : 0.042 0.292 3120 Planarity : 0.004 0.057 3786 Dihedral : 4.185 22.681 2952 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.10 % Favored : 92.72 % Rotamer: Outliers : 3.28 % Allowed : 23.27 % Favored : 73.46 % 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 aren not related in a simple way. whole: -0.73 (0.16), residues: 2748 helix: 0.80 (0.14), residues: 1326 sheet: -1.61 (0.30), residues: 342 loop : -1.69 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 246 TYR 0.029 0.001 TYR F 235 PHE 0.031 0.002 PHE B 219 TRP 0.034 0.002 TRP E 371 HIS 0.005 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00293 (21222) covalent geometry : angle 0.55252 (28716) hydrogen bonds : bond 0.04357 ( 1010) hydrogen bonds : angle 4.73944 ( 2967) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 181 time to evaluate : 0.794 Fit side-chains REVERT: E 35 LYS cc_start: 0.8034 (tptt) cc_final: 0.7804 (tptt) REVERT: E 238 LEU cc_start: 0.5726 (mp) cc_final: 0.4303 (tt) REVERT: E 412 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.3236 (tmm) REVERT: F 176 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7308 (t60) REVERT: F 235 TYR cc_start: 0.5273 (t80) cc_final: 0.4879 (t80) REVERT: F 306 PRO cc_start: 0.5096 (Cg_exo) cc_final: 0.4748 (Cg_endo) REVERT: F 412 MET cc_start: 0.6786 (tmm) cc_final: 0.6191 (tmm) REVERT: D 214 ASN cc_start: 0.5610 (m110) cc_final: 0.5318 (m110) REVERT: D 324 GLU cc_start: 0.4453 (pm20) cc_final: 0.4229 (pm20) REVERT: A 208 MET cc_start: 0.1888 (OUTLIER) cc_final: -0.0077 (tpt) REVERT: B 172 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8439 (pt) REVERT: B 176 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.6796 (t60) REVERT: B 305 ARG cc_start: 0.4554 (OUTLIER) cc_final: 0.2801 (mmp80) REVERT: B 347 MET cc_start: 0.3061 (OUTLIER) cc_final: 0.2478 (ttm) REVERT: B 396 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6264 (mtt-85) REVERT: C 35 LYS cc_start: 0.8366 (tptt) cc_final: 0.8093 (tptt) REVERT: C 305 ARG cc_start: 0.3649 (OUTLIER) cc_final: 0.2565 (mmp80) REVERT: C 347 MET cc_start: 0.4001 (OUTLIER) cc_final: 0.3103 (ttm) outliers start: 69 outliers final: 50 residues processed: 229 average time/residue: 0.1604 time to fit residues: 56.7915 Evaluate side-chains 236 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 237 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 GLN E 393 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.217887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163212 restraints weight = 26957.574| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.24 r_work: 0.3718 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21222 Z= 0.172 Angle : 0.578 10.615 28716 Z= 0.301 Chirality : 0.043 0.299 3120 Planarity : 0.004 0.056 3786 Dihedral : 4.270 23.650 2952 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.58 % Rotamer: Outliers : 3.32 % Allowed : 23.50 % Favored : 73.17 % 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 aren not related in a simple way. whole: -0.79 (0.16), residues: 2748 helix: 0.73 (0.14), residues: 1338 sheet: -1.66 (0.29), residues: 342 loop : -1.72 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 67 TYR 0.030 0.002 TYR F 235 PHE 0.029 0.002 PHE B 219 TRP 0.027 0.002 TRP E 371 HIS 0.006 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00393 (21222) covalent geometry : angle 0.57814 (28716) hydrogen bonds : bond 0.04706 ( 1010) hydrogen bonds : angle 4.80230 ( 2967) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: E 208 MET cc_start: 0.5094 (tpt) cc_final: 0.4639 (tpt) REVERT: E 412 MET cc_start: 0.4599 (OUTLIER) cc_final: 0.3786 (tmm) REVERT: F 176 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.7630 (t60) REVERT: F 405 ASP cc_start: 0.5418 (OUTLIER) cc_final: 0.5069 (p0) REVERT: F 412 MET cc_start: 0.6869 (tmm) cc_final: 0.6364 (tmm) REVERT: D 214 ASN cc_start: 0.5775 (m110) cc_final: 0.5467 (m110) REVERT: D 324 GLU cc_start: 0.4492 (pm20) cc_final: 0.4272 (pm20) REVERT: D 412 MET cc_start: 0.4571 (tmm) cc_final: 0.4282 (tmm) REVERT: B 172 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8447 (pt) REVERT: B 176 TRP cc_start: 0.8303 (OUTLIER) cc_final: 0.7134 (t60) REVERT: B 251 SER cc_start: 0.4983 (p) cc_final: 0.4760 (t) REVERT: B 305 ARG cc_start: 0.4741 (OUTLIER) cc_final: 0.2759 (mmp80) REVERT: B 347 MET cc_start: 0.3337 (OUTLIER) cc_final: 0.2661 (ttm) REVERT: B 396 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6265 (mtt-85) REVERT: C 305 ARG cc_start: 0.3654 (OUTLIER) cc_final: 0.2559 (mmp80) REVERT: C 347 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.3401 (ttm) outliers start: 70 outliers final: 55 residues processed: 225 average time/residue: 0.1565 time to fit residues: 55.1737 Evaluate side-chains 237 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 TRP Chi-restraints excluded: chain F residue 301 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 TRP Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 145 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 207 optimal weight: 0.0020 chunk 266 optimal weight: 0.0670 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.221399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.183361 restraints weight = 27054.798| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.85 r_work: 0.3746 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 21222 Z= 0.114 Angle : 0.531 10.356 28716 Z= 0.275 Chirality : 0.041 0.282 3120 Planarity : 0.003 0.056 3786 Dihedral : 4.009 20.875 2952 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.55 % Favored : 93.27 % Rotamer: Outliers : 2.85 % Allowed : 24.03 % Favored : 73.12 % 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 aren not related in a simple way. whole: -0.53 (0.16), residues: 2748 helix: 0.99 (0.14), residues: 1322 sheet: -1.44 (0.30), residues: 342 loop : -1.66 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 45 TYR 0.025 0.001 TYR F 235 PHE 0.024 0.001 PHE B 219 TRP 0.029 0.001 TRP E 371 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00240 (21222) covalent geometry : angle 0.53063 (28716) hydrogen bonds : bond 0.03882 ( 1010) hydrogen bonds : angle 4.56637 ( 2967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5590.44 seconds wall clock time: 96 minutes 29.21 seconds (5789.21 seconds total)