Starting phenix.real_space_refine on Wed May 21 03:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1c_39722/05_2025/8z1c_39722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1c_39722/05_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_39722/05_2025/8z1c_39722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1c_39722/05_2025/8z1c_39722.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1c_39722/05_2025/8z1c_39722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1c_39722/05_2025/8z1c_39722.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.61, per 1000 atoms: 0.56 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: 4.88 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.15 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: 6.11 Time building geometry restraints manager: 5.71 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: 0.04 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: 1.110 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.220 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- 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 : 14.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.042 0.008 TRP E 176 HIS 0.019 0.004 HIS D 143 PHE 0.043 0.007 PHE A 66 TYR 0.034 0.007 TYR B 14 ARG 0.028 0.004 ARG D 130 Details of bonding type rmsd hydrogen bonds : bond 0.13593 ( 1010) hydrogen bonds : angle 5.89080 ( 2967) covalent geometry : bond 0.00892 (21222) covalent geometry : angle 1.00660 (28716) *********************** 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 : 2.080 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: 0.3514 (tp) outliers start: 24 outliers final: 9 residues processed: 207 average time/residue: 0.3651 time to fit residues: 115.4268 Evaluate side-chains 184 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 233 optimal weight: 0.8980 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 0.0980 chunk 216 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.221063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.184184 restraints weight = 26532.387| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.46 r_work: 0.3742 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 21222 Z= 0.129 Angle : 0.543 8.195 28716 Z= 0.285 Chirality : 0.041 0.176 3120 Planarity : 0.003 0.048 3786 Dihedral : 4.651 47.359 2971 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.44 % Favored : 93.38 % Rotamer: Outliers : 2.66 % Allowed : 20.99 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2748 helix: 0.85 (0.14), residues: 1330 sheet: -1.37 (0.29), residues: 358 loop : -1.67 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 371 HIS 0.004 0.001 HIS B 309 PHE 0.021 0.002 PHE C 357 TYR 0.014 0.001 TYR B 77 ARG 0.005 0.001 ARG D 170 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 1010) hydrogen bonds : angle 4.85267 ( 2967) covalent geometry : bond 0.00272 (21222) covalent geometry : angle 0.54321 (28716) *********************** 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 265 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: E 324 GLU cc_start: 0.5626 (pm20) cc_final: 0.5331 (pm20) REVERT: D 71 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8397 (t0) REVERT: B 172 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8369 (pt) REVERT: C 35 LYS cc_start: 0.8277 (tptt) cc_final: 0.8043 (tptt) REVERT: C 208 MET cc_start: 0.4299 (ptp) cc_final: 0.4051 (mmt) REVERT: C 347 MET cc_start: 0.4410 (OUTLIER) cc_final: 0.3388 (ttm) outliers start: 56 outliers final: 23 residues processed: 253 average time/residue: 0.3350 time to fit residues: 130.2536 Evaluate side-chains 201 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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 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 199 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 230 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.222186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.186652 restraints weight = 26466.450| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.22 r_work: 0.3779 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 21222 Z= 0.116 Angle : 0.506 8.932 28716 Z= 0.266 Chirality : 0.041 0.201 3120 Planarity : 0.003 0.047 3786 Dihedral : 4.041 39.229 2954 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.62 % Favored : 93.23 % Rotamer: Outliers : 2.85 % Allowed : 20.80 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2748 helix: 1.02 (0.14), residues: 1342 sheet: -1.38 (0.30), residues: 338 loop : -1.59 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 371 HIS 0.003 0.001 HIS F 309 PHE 0.023 0.001 PHE E 357 TYR 0.011 0.001 TYR E 204 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 1010) hydrogen bonds : angle 4.63925 ( 2967) covalent geometry : bond 0.00238 (21222) covalent geometry : angle 0.50637 (28716) *********************** 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 254 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 126 ASP cc_start: 0.6522 (m-30) cc_final: 0.6191 (m-30) REVERT: E 219 PHE cc_start: 0.2960 (OUTLIER) cc_final: 0.2537 (t80) REVERT: D 334 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5880 (mp) REVERT: D 347 MET cc_start: 0.4221 (OUTLIER) cc_final: 0.3980 (ttm) REVERT: B 172 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8344 (pt) REVERT: B 396 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6627 (mtt-85) REVERT: C 347 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4487 (ttm) outliers start: 60 outliers final: 30 residues processed: 241 average time/residue: 0.3148 time to fit residues: 117.9234 Evaluate side-chains 215 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 F residue 27 PHE Chi-restraints excluded: chain F residue 317 LEU 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 70 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 334 ILE 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 317 LEU Chi-restraints excluded: chain A residue 371 TRP Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 172 LEU 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 26 LEU Chi-restraints excluded: chain C residue 250 LEU 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 183 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 141 optimal weight: 0.3980 chunk 251 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.217403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167454 restraints weight = 26846.572| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.91 r_work: 0.3774 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21222 Z= 0.208 Angle : 0.585 7.951 28716 Z= 0.308 Chirality : 0.044 0.274 3120 Planarity : 0.004 0.049 3786 Dihedral : 4.371 41.647 2954 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.53 % Favored : 92.29 % Rotamer: Outliers : 4.04 % Allowed : 19.99 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 2748 helix: 0.82 (0.14), residues: 1330 sheet: -1.61 (0.30), residues: 338 loop : -1.66 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 371 HIS 0.006 0.001 HIS D 143 PHE 0.024 0.002 PHE E 357 TYR 0.016 0.002 TYR E 204 ARG 0.004 0.001 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.05181 ( 1010) hydrogen bonds : angle 4.86158 ( 2967) covalent geometry : bond 0.00475 (21222) covalent geometry : angle 0.58529 (28716) *********************** 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 275 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 190 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 176 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.7599 (t60) REVERT: F 235 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4260 (t80) REVERT: D 214 ASN cc_start: 0.5693 (m110) cc_final: 0.5216 (m-40) REVERT: A 176 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.7957 (t60) REVERT: B 172 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8556 (pt) REVERT: B 176 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7050 (t60) REVERT: B 396 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6499 (mtt-85) REVERT: C 305 ARG cc_start: 0.4095 (OUTLIER) cc_final: 0.2704 (mmp80) REVERT: C 347 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.3425 (ttm) outliers start: 85 outliers final: 49 residues processed: 253 average time/residue: 0.3097 time to fit residues: 123.7668 Evaluate side-chains 235 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 2.185 ------------------------------------------------------------------------------- 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 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 235 TYR 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 393 ASN 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 A residue 26 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 176 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 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 247 VAL 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 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 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 379 ASN 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 19 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 227 optimal weight: 0.0870 chunk 275 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.220831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.184676 restraints weight = 26640.949| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.60 r_work: 0.3732 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21222 Z= 0.117 Angle : 0.512 7.173 28716 Z= 0.268 Chirality : 0.041 0.293 3120 Planarity : 0.003 0.051 3786 Dihedral : 4.091 40.016 2954 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.84 % Favored : 93.01 % Rotamer: Outliers : 3.28 % Allowed : 21.37 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2748 helix: 1.05 (0.14), residues: 1338 sheet: -1.39 (0.30), residues: 342 loop : -1.54 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 371 HIS 0.007 0.001 HIS B 309 PHE 0.025 0.001 PHE F 219 TYR 0.010 0.001 TYR E 204 ARG 0.003 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 1010) hydrogen bonds : angle 4.60334 ( 2967) covalent geometry : bond 0.00246 (21222) covalent geometry : angle 0.51213 (28716) *********************** 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 270 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 201 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 PHE cc_start: 0.2960 (OUTLIER) cc_final: 0.2531 (t80) REVERT: E 238 LEU cc_start: 0.5694 (mp) cc_final: 0.4376 (tt) REVERT: F 176 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7439 (t60) REVERT: F 306 PRO cc_start: 0.5669 (Cg_exo) cc_final: 0.5351 (Cg_endo) REVERT: F 371 TRP cc_start: 0.3172 (OUTLIER) cc_final: 0.2720 (t60) REVERT: D 347 MET cc_start: 0.4398 (OUTLIER) cc_final: 0.4078 (ttm) REVERT: D 390 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7326 (ttm) REVERT: A 408 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6227 (tt) REVERT: B 172 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8455 (pt) REVERT: B 250 LEU cc_start: 0.3287 (OUTLIER) cc_final: 0.3048 (mp) REVERT: B 305 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.2788 (mmp80) REVERT: B 396 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6584 (mtt-85) REVERT: C 305 ARG cc_start: 0.4030 (OUTLIER) cc_final: 0.2673 (mmp80) REVERT: C 347 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.3620 (ttm) outliers start: 69 outliers final: 37 residues processed: 251 average time/residue: 0.2997 time to fit residues: 118.6854 Evaluate side-chains 228 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 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 317 LEU 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 27 PHE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 390 MET 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 208 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 408 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 139 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 GLU 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 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 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 379 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 222 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 235 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 273 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.220366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.184396 restraints weight = 26680.236| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.55 r_work: 0.3733 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21222 Z= 0.130 Angle : 0.514 7.110 28716 Z= 0.270 Chirality : 0.042 0.319 3120 Planarity : 0.003 0.046 3786 Dihedral : 4.049 40.850 2954 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.10 % Favored : 92.76 % Rotamer: Outliers : 3.89 % Allowed : 21.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2748 helix: 1.03 (0.14), residues: 1342 sheet: -1.42 (0.30), residues: 342 loop : -1.54 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 371 HIS 0.004 0.001 HIS F 309 PHE 0.023 0.002 PHE A 219 TYR 0.011 0.001 TYR E 204 ARG 0.002 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1010) hydrogen bonds : angle 4.58162 ( 2967) covalent geometry : bond 0.00284 (21222) covalent geometry : angle 0.51416 (28716) *********************** 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 271 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 189 time to evaluate : 2.014 Fit side-chains revert: symmetry clash REVERT: E 219 PHE cc_start: 0.2959 (OUTLIER) cc_final: 0.2529 (t80) REVERT: E 238 LEU cc_start: 0.5629 (mp) cc_final: 0.4350 (tt) REVERT: F 176 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7486 (t60) REVERT: F 235 TYR cc_start: 0.4883 (OUTLIER) cc_final: 0.3915 (t80) REVERT: F 306 PRO cc_start: 0.5581 (Cg_exo) cc_final: 0.5244 (Cg_endo) REVERT: F 371 TRP cc_start: 0.3249 (OUTLIER) cc_final: 0.2790 (t60) REVERT: D 347 MET cc_start: 0.4314 (OUTLIER) cc_final: 0.4080 (ttm) REVERT: D 390 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7576 (ttt) REVERT: A 390 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7173 (ptp) REVERT: A 408 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6205 (tt) REVERT: B 176 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.6903 (t60) REVERT: B 305 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.2767 (mmp80) REVERT: B 347 MET cc_start: 0.4174 (OUTLIER) cc_final: 0.2923 (ttm) REVERT: B 371 TRP cc_start: 0.2991 (OUTLIER) cc_final: 0.2441 (m-90) REVERT: B 396 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6546 (mtt-85) REVERT: C 305 ARG cc_start: 0.3941 (OUTLIER) cc_final: 0.2608 (mmp80) REVERT: C 347 MET cc_start: 0.4471 (OUTLIER) cc_final: 0.3680 (ttm) outliers start: 82 outliers final: 48 residues processed: 248 average time/residue: 0.3084 time to fit residues: 119.9324 Evaluate side-chains 244 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 181 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain E residue 289 VAL 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 110 MET Chi-restraints excluded: chain F residue 175 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 371 TRP 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 347 MET Chi-restraints excluded: chain D residue 390 MET 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 390 MET Chi-restraints excluded: chain A residue 408 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 90 SER 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 247 VAL 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 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 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 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 379 ASN 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 61 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 168 optimal weight: 0.2980 chunk 32 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 418 ASN F 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.221698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.185715 restraints weight = 26674.641| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.42 r_work: 0.3761 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21222 Z= 0.115 Angle : 0.500 6.931 28716 Z= 0.262 Chirality : 0.041 0.265 3120 Planarity : 0.003 0.048 3786 Dihedral : 3.861 20.580 2952 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.62 % Favored : 93.20 % Rotamer: Outliers : 3.89 % Allowed : 21.60 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2748 helix: 1.13 (0.14), residues: 1340 sheet: -1.35 (0.31), residues: 342 loop : -1.61 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 371 HIS 0.006 0.001 HIS B 309 PHE 0.023 0.002 PHE C 219 TYR 0.011 0.001 TYR E 14 ARG 0.002 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 1010) hydrogen bonds : angle 4.48541 ( 2967) covalent geometry : bond 0.00244 (21222) covalent geometry : angle 0.50039 (28716) *********************** 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 277 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 195 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 PHE cc_start: 0.3027 (OUTLIER) cc_final: 0.2578 (t80) REVERT: E 238 LEU cc_start: 0.5661 (mp) cc_final: 0.4306 (tt) REVERT: E 412 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4754 (ttp) REVERT: F 176 TRP cc_start: 0.8380 (OUTLIER) cc_final: 0.7486 (t60) REVERT: F 235 TYR cc_start: 0.4799 (OUTLIER) cc_final: 0.3819 (t80) REVERT: F 306 PRO cc_start: 0.5587 (Cg_exo) cc_final: 0.5257 (Cg_endo) REVERT: F 371 TRP cc_start: 0.3139 (OUTLIER) cc_final: 0.2888 (t60) REVERT: F 405 ASP cc_start: 0.5504 (OUTLIER) cc_final: 0.5197 (p0) REVERT: D 347 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.4160 (ttm) REVERT: D 390 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7448 (ttm) REVERT: A 390 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7176 (ptp) REVERT: A 408 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6175 (tt) REVERT: B 176 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.6994 (t60) REVERT: B 305 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.2901 (mmp80) REVERT: B 347 MET cc_start: 0.3784 (OUTLIER) cc_final: 0.2949 (ttm) REVERT: B 371 TRP cc_start: 0.2894 (OUTLIER) cc_final: 0.2410 (m-90) REVERT: B 396 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6522 (mtt-85) REVERT: C 305 ARG cc_start: 0.4091 (OUTLIER) cc_final: 0.2723 (mmp80) REVERT: C 347 MET cc_start: 0.4554 (OUTLIER) cc_final: 0.4142 (ttm) outliers start: 82 outliers final: 50 residues processed: 256 average time/residue: 0.3120 time to fit residues: 125.3538 Evaluate side-chains 252 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 90 SER 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 289 VAL Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 418 ASN 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 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 340 PHE Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain F residue 405 ASP 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 180 LEU Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 390 MET 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 390 MET Chi-restraints excluded: chain A residue 408 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 90 SER 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 247 VAL 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 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 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 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 379 ASN Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 416 PHE 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 31 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 253 optimal weight: 0.0040 chunk 230 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 chunk 18 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 379 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 = 0.4516 r_free = 0.4516 target = 0.220642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.183362 restraints weight = 26802.535| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.45 r_work: 0.3747 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21222 Z= 0.139 Angle : 0.525 7.780 28716 Z= 0.274 Chirality : 0.042 0.332 3120 Planarity : 0.003 0.047 3786 Dihedral : 3.921 21.333 2952 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.88 % Favored : 92.98 % Rotamer: Outliers : 4.13 % Allowed : 21.65 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2748 helix: 1.08 (0.14), residues: 1336 sheet: -1.40 (0.30), residues: 342 loop : -1.56 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 371 HIS 0.004 0.001 HIS B 309 PHE 0.022 0.002 PHE E 357 TYR 0.011 0.001 TYR E 204 ARG 0.002 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 1010) hydrogen bonds : angle 4.52814 ( 2967) covalent geometry : bond 0.00310 (21222) covalent geometry : angle 0.52501 (28716) *********************** 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 276 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 189 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 PHE cc_start: 0.2826 (OUTLIER) cc_final: 0.2400 (t80) REVERT: E 238 LEU cc_start: 0.5724 (mp) cc_final: 0.4384 (tt) REVERT: E 412 MET cc_start: 0.4875 (OUTLIER) cc_final: 0.4494 (ttp) REVERT: F 143 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7395 (m90) REVERT: F 176 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.7563 (t60) REVERT: F 235 TYR cc_start: 0.4852 (OUTLIER) cc_final: 0.3665 (t80) REVERT: F 306 PRO cc_start: 0.5575 (Cg_exo) cc_final: 0.5243 (Cg_endo) REVERT: F 371 TRP cc_start: 0.3192 (OUTLIER) cc_final: 0.2962 (t60) REVERT: F 405 ASP cc_start: 0.5413 (OUTLIER) cc_final: 0.5121 (p0) REVERT: D 347 MET cc_start: 0.4242 (OUTLIER) cc_final: 0.4016 (ttm) REVERT: D 390 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (ttt) REVERT: D 409 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5913 (mptp) REVERT: A 390 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7128 (ptp) REVERT: A 408 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6104 (tt) REVERT: B 176 TRP cc_start: 0.8317 (OUTLIER) cc_final: 0.7163 (t60) REVERT: B 251 SER cc_start: 0.5376 (p) cc_final: 0.5102 (t) REVERT: B 305 ARG cc_start: 0.4844 (OUTLIER) cc_final: 0.2817 (mmp80) REVERT: B 347 MET cc_start: 0.3697 (OUTLIER) cc_final: 0.2912 (ttm) REVERT: B 371 TRP cc_start: 0.2919 (OUTLIER) cc_final: 0.2387 (m-90) REVERT: B 396 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6489 (mtt-85) REVERT: C 94 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8375 (t80) REVERT: C 305 ARG cc_start: 0.3910 (OUTLIER) cc_final: 0.2684 (mmp80) REVERT: C 347 MET cc_start: 0.4309 (OUTLIER) cc_final: 0.3315 (ttm) outliers start: 87 outliers final: 54 residues processed: 250 average time/residue: 0.3077 time to fit residues: 120.9150 Evaluate side-chains 257 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 90 SER 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 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 26 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 143 HIS 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 340 PHE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 418 ASN Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 1 MET 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 347 MET Chi-restraints excluded: chain D residue 390 MET Chi-restraints excluded: chain D residue 409 LYS 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 86 SER Chi-restraints excluded: chain A residue 137 MET 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 408 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 90 SER 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 247 VAL 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 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 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 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 347 MET Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 416 PHE 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 250 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 260 optimal weight: 30.0000 chunk 224 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 163 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 0.0370 chunk 230 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- 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 C 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.218476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167568 restraints weight = 26591.113| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.15 r_work: 0.3788 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21222 Z= 0.176 Angle : 0.560 7.756 28716 Z= 0.294 Chirality : 0.043 0.302 3120 Planarity : 0.004 0.051 3786 Dihedral : 4.143 23.322 2952 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % Rotamer: Outliers : 3.89 % Allowed : 22.22 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2748 helix: 0.91 (0.14), residues: 1342 sheet: -1.48 (0.30), residues: 342 loop : -1.58 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 371 HIS 0.006 0.001 HIS B 143 PHE 0.022 0.002 PHE C 357 TYR 0.015 0.002 TYR F 199 ARG 0.003 0.000 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 1010) hydrogen bonds : angle 4.67662 ( 2967) covalent geometry : bond 0.00402 (21222) covalent geometry : angle 0.56044 (28716) *********************** 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 265 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 183 time to evaluate : 2.070 Fit side-chains revert: symmetry clash REVERT: E 35 LYS cc_start: 0.7962 (tptt) cc_final: 0.7745 (tptt) REVERT: E 238 LEU cc_start: 0.5812 (mp) cc_final: 0.4392 (tt) REVERT: E 412 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4459 (ttp) REVERT: F 176 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7641 (t60) REVERT: F 235 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4425 (t80) REVERT: F 371 TRP cc_start: 0.3424 (OUTLIER) cc_final: 0.3161 (t60) REVERT: D 214 ASN cc_start: 0.5697 (m110) cc_final: 0.5162 (m-40) REVERT: D 347 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.3871 (ttm) REVERT: D 409 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5688 (mptp) REVERT: A 176 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.7908 (t60) REVERT: A 390 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7217 (ptp) REVERT: A 408 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6224 (tt) REVERT: B 176 TRP cc_start: 0.8355 (OUTLIER) cc_final: 0.7332 (t60) REVERT: B 251 SER cc_start: 0.5266 (p) cc_final: 0.5001 (t) REVERT: B 305 ARG cc_start: 0.4804 (OUTLIER) cc_final: 0.2825 (mmp80) REVERT: B 347 MET cc_start: 0.3845 (OUTLIER) cc_final: 0.2944 (ttm) REVERT: B 396 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6461 (mtt-85) REVERT: C 94 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8380 (t80) REVERT: C 305 ARG cc_start: 0.3895 (OUTLIER) cc_final: 0.2635 (mmp80) REVERT: C 347 MET cc_start: 0.4337 (OUTLIER) cc_final: 0.3365 (ttm) outliers start: 82 outliers final: 55 residues processed: 238 average time/residue: 0.3137 time to fit residues: 116.7807 Evaluate side-chains 250 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 179 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 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 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 340 PHE 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 437 LEU Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 27 PHE 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 347 MET Chi-restraints excluded: chain D residue 409 LYS 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 86 SER Chi-restraints excluded: chain A residue 176 TRP 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 408 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 90 SER 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 285 ILE Chi-restraints excluded: chain B residue 301 LEU 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 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 94 PHE 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 438 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 94 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 252 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4524 r_free = 0.4524 target = 0.221493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.186095 restraints weight = 26767.020| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 2.41 r_work: 0.3759 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1981 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= 0.118 Angle : 0.517 7.175 28716 Z= 0.269 Chirality : 0.041 0.290 3120 Planarity : 0.003 0.053 3786 Dihedral : 3.913 21.007 2952 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.73 % Favored : 93.09 % Rotamer: Outliers : 3.13 % Allowed : 22.93 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2748 helix: 1.12 (0.14), residues: 1328 sheet: -1.38 (0.30), residues: 342 loop : -1.54 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 371 HIS 0.007 0.001 HIS A 309 PHE 0.020 0.001 PHE C 357 TYR 0.012 0.001 TYR F 199 ARG 0.003 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 1010) hydrogen bonds : angle 4.50875 ( 2967) covalent geometry : bond 0.00253 (21222) covalent geometry : angle 0.51687 (28716) ********************** 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 246 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: E 35 LYS cc_start: 0.7734 (tptt) cc_final: 0.7526 (tptt) REVERT: E 238 LEU cc_start: 0.5658 (mp) cc_final: 0.4257 (tt) REVERT: E 347 MET cc_start: 0.4106 (ttm) cc_final: 0.3244 (ttm) REVERT: E 412 MET cc_start: 0.5121 (OUTLIER) cc_final: 0.4685 (ttp) REVERT: F 176 TRP cc_start: 0.8362 (OUTLIER) cc_final: 0.7617 (t60) REVERT: F 235 TYR cc_start: 0.5009 (OUTLIER) cc_final: 0.4111 (t80) REVERT: F 306 PRO cc_start: 0.5536 (Cg_exo) cc_final: 0.5222 (Cg_endo) REVERT: F 371 TRP cc_start: 0.3380 (OUTLIER) cc_final: 0.3111 (t60) REVERT: F 405 ASP cc_start: 0.5489 (OUTLIER) cc_final: 0.5210 (p0) REVERT: F 412 MET cc_start: 0.6825 (tmm) cc_final: 0.6176 (tmm) REVERT: D 214 ASN cc_start: 0.5689 (m110) cc_final: 0.5078 (m-40) REVERT: D 347 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.4157 (ttm) REVERT: D 409 LYS cc_start: 0.6432 (OUTLIER) cc_final: 0.6066 (mptp) REVERT: A 390 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7133 (ptp) REVERT: A 408 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6241 (tt) REVERT: B 176 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.7057 (t60) REVERT: B 251 SER cc_start: 0.5495 (p) cc_final: 0.5205 (t) REVERT: B 305 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.2805 (mmp80) REVERT: B 347 MET cc_start: 0.3669 (OUTLIER) cc_final: 0.3128 (ttm) REVERT: B 396 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6501 (mtt-85) REVERT: C 94 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8383 (t80) REVERT: C 305 ARG cc_start: 0.3888 (OUTLIER) cc_final: 0.2610 (mmp80) REVERT: C 347 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3527 (ttm) outliers start: 66 outliers final: 48 residues processed: 228 average time/residue: 0.3094 time to fit residues: 110.7245 Evaluate side-chains 237 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 173 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU 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 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 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 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 340 PHE Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 405 ASP 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 347 MET Chi-restraints excluded: chain D residue 409 LYS 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 208 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 408 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 90 SER 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 285 ILE Chi-restraints excluded: chain B residue 301 LEU 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 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 94 PHE 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 418 ASN 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 34 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 188 optimal weight: 0.1980 chunk 155 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.219038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167699 restraints weight = 26539.006| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.16 r_work: 0.3779 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21222 Z= 0.165 Angle : 0.557 7.782 28716 Z= 0.291 Chirality : 0.043 0.270 3120 Planarity : 0.004 0.052 3786 Dihedral : 4.067 22.616 2952 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.39 % Favored : 92.43 % Rotamer: Outliers : 3.61 % Allowed : 22.60 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2748 helix: 1.01 (0.14), residues: 1328 sheet: -1.49 (0.30), residues: 342 loop : -1.57 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 371 HIS 0.005 0.001 HIS B 143 PHE 0.021 0.002 PHE C 357 TYR 0.017 0.001 TYR F 199 ARG 0.003 0.000 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 1010) hydrogen bonds : angle 4.63389 ( 2967) covalent geometry : bond 0.00373 (21222) covalent geometry : angle 0.55665 (28716) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10479.32 seconds wall clock time: 181 minutes 59.27 seconds (10919.27 seconds total)