Starting phenix.real_space_refine on Sun Apr 5 08:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nsc_12564/04_2026/7nsc_12564.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsc_12564/04_2026/7nsc_12564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nsc_12564/04_2026/7nsc_12564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsc_12564/04_2026/7nsc_12564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nsc_12564/04_2026/7nsc_12564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsc_12564/04_2026/7nsc_12564.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 62 5.16 5 C 5955 2.51 5 N 1607 2.21 5 O 1703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2065 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 4631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4631 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 18, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 5, 'GLU:plan': 20, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "H" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1178 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 9, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "D" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1453 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 3 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.43, per 1000 atoms: 0.26 Number of scatterers: 9327 At special positions: 0 Unit cell: (83.3, 136.85, 118.15, 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 62 16.00 O 1703 8.00 N 1607 7.00 C 5955 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: 0.74 Conformation dependent library (CDL) restraints added in 385.3 milliseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 55.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.903A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 696 through 713 removed outlier: 3.668A pdb=" N ALA A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 No H-bonds generated for 'chain 'A' and resid 718 through 721' Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 37 through 43 Processing helix chain 'E' and resid 63 through 78 Processing helix chain 'E' and resid 81 through 90 removed outlier: 3.648A pdb=" N CYS E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 105 through 120 Processing helix chain 'E' and resid 127 through 131 removed outlier: 4.272A pdb=" N THR E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 127 through 131' Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 147 through 161 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.556A pdb=" N HIS E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 4.669A pdb=" N HIS E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 206 through 214 removed outlier: 3.817A pdb=" N THR E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASN E 214 " --> pdb=" O MET E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.815A pdb=" N VAL E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 262 through 274 removed outlier: 3.911A pdb=" N THR E 266 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU E 267 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Proline residue: E 268 - end of helix removed outlier: 3.965A pdb=" N CYS E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 293 removed outlier: 3.825A pdb=" N GLU E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 removed outlier: 3.766A pdb=" N ILE E 306 " --> pdb=" O ARG E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 334 through 338 Processing helix chain 'E' and resid 340 through 355 removed outlier: 4.102A pdb=" N ARG E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 367 Processing helix chain 'E' and resid 371 through 379 Processing helix chain 'E' and resid 384 through 398 removed outlier: 4.347A pdb=" N ALA E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 411 removed outlier: 4.608A pdb=" N PHE E 408 " --> pdb=" O LEU E 404 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLN E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.794A pdb=" N MET E 418 " --> pdb=" O TRP E 414 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 439 removed outlier: 4.066A pdb=" N VAL E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET E 435 " --> pdb=" O VAL E 431 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASN E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 452 removed outlier: 4.512A pdb=" N ILE E 450 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 464 removed outlier: 3.679A pdb=" N THR E 463 " --> pdb=" O LEU E 459 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN E 464 " --> pdb=" O CYS E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 482 removed outlier: 4.774A pdb=" N ASN E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU E 478 " --> pdb=" O GLY E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 496 removed outlier: 4.847A pdb=" N ASP E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 506 Processing helix chain 'E' and resid 511 through 525 removed outlier: 3.804A pdb=" N LEU E 525 " --> pdb=" O LEU E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 538 removed outlier: 3.604A pdb=" N ASP E 532 " --> pdb=" O ARG E 528 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 537 " --> pdb=" O LYS E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 551 removed outlier: 3.816A pdb=" N GLN E 544 " --> pdb=" O LYS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 571 Processing helix chain 'E' and resid 575 through 581 removed outlier: 3.767A pdb=" N ILE E 579 " --> pdb=" O ALA E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 592 Processing helix chain 'E' and resid 598 through 611 removed outlier: 3.763A pdb=" N CYS E 607 " --> pdb=" O ALA E 603 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE E 608 " --> pdb=" O ALA E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 629 removed outlier: 3.967A pdb=" N MET E 629 " --> pdb=" O LYS E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 639 Processing helix chain 'E' and resid 645 through 656 Processing helix chain 'H' and resid 27 through 38 Processing helix chain 'H' and resid 44 through 52 removed outlier: 3.871A pdb=" N LYS H 48 " --> pdb=" O GLU H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 No H-bonds generated for 'chain 'H' and resid 60 through 63' Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 92 through 96 removed outlier: 5.089A pdb=" N THR H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 92 through 96' Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 166 through 183 Processing helix chain 'H' and resid 191 through 209 removed outlier: 4.164A pdb=" N LYS H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 219 No H-bonds generated for 'chain 'H' and resid 216 through 219' Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.888A pdb=" N LYS D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 214 Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.935A pdb=" N ASN D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 5.760A pdb=" N ASP A 173 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER A 201 " --> pdb=" O PHE A 175 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 200 through 203 current: chain 'A' and resid 314 through 319 removed outlier: 6.714A pdb=" N TYR A 229 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N HIS A 250 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER A 251 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 181 removed outlier: 4.696A pdb=" N ARG A 186 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU A 323 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 279 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 280 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASN A 290 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 126 through 133 removed outlier: 3.801A pdb=" N SER D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS D 156 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR D 172 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU D 240 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE D 174 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG D 234 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ASP D 229 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU D 237 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY D 256 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 268 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA D 267 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN D 282 " --> pdb=" O TYR D 273 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1383 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: 1.51 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1519 1.30 - 1.43: 2422 1.43 - 1.56: 5480 1.56 - 1.68: 0 1.68 - 1.81: 97 Bond restraints: 9518 Sorted by residual: bond pdb=" C TYR A 254 " pdb=" O TYR A 254 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.14e-02 7.69e+03 2.82e+01 bond pdb=" N TYR A 727 " pdb=" CA TYR A 727 " ideal model delta sigma weight residual 1.457 1.389 0.068 1.29e-02 6.01e+03 2.81e+01 bond pdb=" CA TYR A 727 " pdb=" C TYR A 727 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.28e+00 bond pdb=" CG TYR A 254 " pdb=" CD1 TYR A 254 " ideal model delta sigma weight residual 1.389 1.338 0.051 2.10e-02 2.27e+03 5.96e+00 bond pdb=" CE2 TYR A 254 " pdb=" CZ TYR A 254 " ideal model delta sigma weight residual 1.378 1.321 0.057 2.40e-02 1.74e+03 5.72e+00 ... (remaining 9513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12545 1.76 - 3.51: 317 3.51 - 5.27: 52 5.27 - 7.03: 15 7.03 - 8.79: 4 Bond angle restraints: 12933 Sorted by residual: angle pdb=" N HIS E 181 " pdb=" CA HIS E 181 " pdb=" C HIS E 181 " ideal model delta sigma weight residual 114.56 106.20 8.36 1.27e+00 6.20e-01 4.33e+01 angle pdb=" CA ASP A 726 " pdb=" C ASP A 726 " pdb=" N TYR A 727 " ideal model delta sigma weight residual 118.08 112.46 5.62 1.30e+00 5.92e-01 1.87e+01 angle pdb=" O GLY A 253 " pdb=" C GLY A 253 " pdb=" N TYR A 254 " ideal model delta sigma weight residual 123.54 126.90 -3.36 9.20e-01 1.18e+00 1.33e+01 angle pdb=" CA HIS E 181 " pdb=" C HIS E 181 " pdb=" N LEU E 182 " ideal model delta sigma weight residual 119.26 115.12 4.14 1.14e+00 7.69e-01 1.32e+01 angle pdb=" O ASP A 726 " pdb=" C ASP A 726 " pdb=" N TYR A 727 " ideal model delta sigma weight residual 122.39 127.03 -4.64 1.30e+00 5.92e-01 1.27e+01 ... (remaining 12928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5079 17.59 - 35.17: 495 35.17 - 52.76: 102 52.76 - 70.34: 15 70.34 - 87.93: 4 Dihedral angle restraints: 5695 sinusoidal: 2107 harmonic: 3588 Sorted by residual: dihedral pdb=" CA ASP E 316 " pdb=" C ASP E 316 " pdb=" N TYR E 317 " pdb=" CA TYR E 317 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA MET H 73 " pdb=" C MET H 73 " pdb=" N ILE H 74 " pdb=" CA ILE H 74 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU H 89 " pdb=" C LEU H 89 " pdb=" N HIS H 90 " pdb=" CA HIS H 90 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 984 0.038 - 0.076: 411 0.076 - 0.113: 91 0.113 - 0.151: 19 0.151 - 0.189: 1 Chirality restraints: 1506 Sorted by residual: chirality pdb=" CG LEU H 164 " pdb=" CB LEU H 164 " pdb=" CD1 LEU H 164 " pdb=" CD2 LEU H 164 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CG LEU A 318 " pdb=" CB LEU A 318 " pdb=" CD1 LEU A 318 " pdb=" CD2 LEU A 318 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CB ILE A 232 " pdb=" CA ILE A 232 " pdb=" CG1 ILE A 232 " pdb=" CG2 ILE A 232 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1503 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 317 " 0.023 2.00e-02 2.50e+03 1.71e-02 5.82e+00 pdb=" CG TYR E 317 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 317 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR E 317 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 317 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 317 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 695 " 0.037 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 696 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 696 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 696 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 726 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP A 726 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP A 726 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 727 " -0.013 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 22 2.37 - 3.00: 5071 3.00 - 3.63: 13713 3.63 - 4.27: 20345 4.27 - 4.90: 34848 Nonbonded interactions: 73999 Sorted by model distance: nonbonded pdb=" NE2 GLN A 350 " pdb=" OH TYR A 727 " model vdw 1.732 3.120 nonbonded pdb=" OE1 GLU A 344 " pdb=" NH1 ARG E 232 " model vdw 2.212 3.120 nonbonded pdb=" O SER E 526 " pdb=" OG1 THR E 527 " model vdw 2.228 3.040 nonbonded pdb=" O ALA E 352 " pdb=" OG SER E 396 " model vdw 2.231 3.040 nonbonded pdb=" O HIS E 595 " pdb=" NE2 GLN E 601 " model vdw 2.231 3.120 ... (remaining 73994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.005 0.068 9518 Z= 0.217 Angle : 0.705 8.786 12933 Z= 0.383 Chirality : 0.042 0.189 1506 Planarity : 0.004 0.057 1648 Dihedral : 14.497 87.927 3371 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1206 helix: 0.05 (0.20), residues: 677 sheet: -0.78 (0.46), residues: 140 loop : -2.83 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 399 TYR 0.041 0.002 TYR E 317 PHE 0.017 0.002 PHE D 186 TRP 0.016 0.002 TRP A 345 HIS 0.012 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9518) covalent geometry : angle 0.70547 (12933) hydrogen bonds : bond 0.05032 ( 464) hydrogen bonds : angle 4.87291 ( 1383) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.368 Fit side-chains REVERT: A 727 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.5149 (m-10) REVERT: D 149 ASP cc_start: 0.6918 (p0) cc_final: 0.6211 (p0) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.0816 time to fit residues: 17.3947 Evaluate side-chains 122 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 350 GLN A 380 HIS E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.117057 restraints weight = 14201.741| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.81 r_work: 0.3343 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9518 Z= 0.141 Angle : 0.596 7.689 12933 Z= 0.306 Chirality : 0.040 0.137 1506 Planarity : 0.004 0.054 1648 Dihedral : 4.811 27.501 1311 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.04 % Allowed : 8.94 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1206 helix: 0.36 (0.21), residues: 677 sheet: -0.65 (0.46), residues: 140 loop : -2.75 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 362 TYR 0.023 0.001 TYR E 317 PHE 0.012 0.002 PHE E 318 TRP 0.015 0.001 TRP A 345 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9518) covalent geometry : angle 0.59562 (12933) hydrogen bonds : bond 0.03745 ( 464) hydrogen bonds : angle 4.63617 ( 1383) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.296 Fit side-chains REVERT: A 376 TYR cc_start: 0.8134 (t80) cc_final: 0.7176 (t80) REVERT: H 92 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8106 (tm-30) REVERT: H 111 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 149 ASP cc_start: 0.7388 (p0) cc_final: 0.6992 (p0) outliers start: 10 outliers final: 7 residues processed: 134 average time/residue: 0.0828 time to fit residues: 16.5880 Evaluate side-chains 132 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 240 ASN A 380 HIS E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 203 GLN D 244 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111496 restraints weight = 14419.116| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.80 r_work: 0.3265 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9518 Z= 0.300 Angle : 0.729 7.728 12933 Z= 0.375 Chirality : 0.045 0.168 1506 Planarity : 0.005 0.056 1648 Dihedral : 5.155 21.838 1309 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.18 % Allowed : 14.14 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.24), residues: 1206 helix: 0.06 (0.20), residues: 675 sheet: -0.89 (0.45), residues: 140 loop : -2.83 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 272 TYR 0.029 0.002 TYR A 376 PHE 0.023 0.002 PHE E 318 TRP 0.015 0.002 TRP A 345 HIS 0.007 0.002 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00736 ( 9518) covalent geometry : angle 0.72882 (12933) hydrogen bonds : bond 0.05394 ( 464) hydrogen bonds : angle 4.99853 ( 1383) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.383 Fit side-chains REVERT: E 548 LEU cc_start: 0.8044 (mt) cc_final: 0.7639 (mp) REVERT: H 73 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8194 (ptp) REVERT: H 92 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8102 (tm-30) REVERT: H 185 ASN cc_start: 0.7809 (t0) cc_final: 0.7551 (t0) REVERT: D 149 ASP cc_start: 0.7543 (p0) cc_final: 0.7072 (p0) REVERT: D 152 ASN cc_start: 0.8324 (m110) cc_final: 0.8090 (m110) outliers start: 21 outliers final: 15 residues processed: 140 average time/residue: 0.0846 time to fit residues: 17.5044 Evaluate side-chains 134 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 181 HIS Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 571 ASP Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115484 restraints weight = 14334.517| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.82 r_work: 0.3323 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9518 Z= 0.140 Angle : 0.589 12.061 12933 Z= 0.302 Chirality : 0.040 0.148 1506 Planarity : 0.004 0.054 1648 Dihedral : 4.765 22.228 1309 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.49 % Allowed : 16.53 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.24), residues: 1206 helix: 0.43 (0.21), residues: 676 sheet: -0.68 (0.45), residues: 140 loop : -2.71 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 362 TYR 0.017 0.001 TYR D 230 PHE 0.013 0.001 PHE E 318 TRP 0.015 0.001 TRP A 345 HIS 0.008 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9518) covalent geometry : angle 0.58915 (12933) hydrogen bonds : bond 0.03758 ( 464) hydrogen bonds : angle 4.60252 ( 1383) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.371 Fit side-chains REVERT: E 89 ASP cc_start: 0.8533 (m-30) cc_final: 0.8244 (m-30) REVERT: E 548 LEU cc_start: 0.7948 (mt) cc_final: 0.7534 (mp) REVERT: H 73 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8130 (ptp) REVERT: H 105 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8383 (mm110) REVERT: H 111 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7045 (mm-30) REVERT: D 149 ASP cc_start: 0.7412 (p0) cc_final: 0.6968 (p0) REVERT: D 152 ASN cc_start: 0.8201 (m110) cc_final: 0.7927 (m110) outliers start: 24 outliers final: 13 residues processed: 143 average time/residue: 0.0792 time to fit residues: 17.0386 Evaluate side-chains 132 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.2980 chunk 6 optimal weight: 0.2980 chunk 50 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 27 optimal weight: 0.0670 chunk 98 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.120799 restraints weight = 14010.422| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.66 r_work: 0.3406 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9518 Z= 0.102 Angle : 0.538 9.034 12933 Z= 0.274 Chirality : 0.038 0.165 1506 Planarity : 0.003 0.049 1648 Dihedral : 4.420 28.662 1309 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.60 % Allowed : 16.74 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.25), residues: 1206 helix: 0.72 (0.21), residues: 680 sheet: -0.35 (0.46), residues: 140 loop : -2.62 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 362 TYR 0.017 0.001 TYR D 230 PHE 0.011 0.001 PHE A 217 TRP 0.012 0.001 TRP A 365 HIS 0.003 0.000 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9518) covalent geometry : angle 0.53762 (12933) hydrogen bonds : bond 0.02991 ( 464) hydrogen bonds : angle 4.32341 ( 1383) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.351 Fit side-chains REVERT: E 78 MET cc_start: 0.7664 (ppp) cc_final: 0.7459 (ptm) REVERT: E 89 ASP cc_start: 0.8532 (m-30) cc_final: 0.8275 (m-30) REVERT: E 470 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7889 (tp) REVERT: E 548 LEU cc_start: 0.7984 (mt) cc_final: 0.7607 (mp) REVERT: H 73 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8123 (ptp) REVERT: H 111 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7060 (mm-30) REVERT: D 149 ASP cc_start: 0.7316 (p0) cc_final: 0.6863 (p0) REVERT: D 152 ASN cc_start: 0.8012 (m110) cc_final: 0.7735 (m110) outliers start: 25 outliers final: 13 residues processed: 151 average time/residue: 0.0812 time to fit residues: 18.2185 Evaluate side-chains 138 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 ASN H 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117350 restraints weight = 14221.866| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.81 r_work: 0.3351 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9518 Z= 0.130 Angle : 0.557 9.153 12933 Z= 0.282 Chirality : 0.039 0.180 1506 Planarity : 0.004 0.046 1648 Dihedral : 4.356 25.128 1309 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.49 % Allowed : 17.88 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1206 helix: 0.76 (0.21), residues: 683 sheet: -0.31 (0.46), residues: 140 loop : -2.59 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 362 TYR 0.017 0.001 TYR D 230 PHE 0.014 0.001 PHE E 318 TRP 0.012 0.001 TRP A 345 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9518) covalent geometry : angle 0.55679 (12933) hydrogen bonds : bond 0.03395 ( 464) hydrogen bonds : angle 4.31648 ( 1383) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.369 Fit side-chains REVERT: E 89 ASP cc_start: 0.8582 (m-30) cc_final: 0.8295 (m-30) REVERT: E 371 MET cc_start: 0.7869 (tpp) cc_final: 0.7586 (tpp) REVERT: E 548 LEU cc_start: 0.7906 (mt) cc_final: 0.7528 (mp) REVERT: H 73 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8153 (ptp) REVERT: H 111 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 149 ASP cc_start: 0.7317 (p0) cc_final: 0.6856 (p0) REVERT: D 152 ASN cc_start: 0.8039 (m110) cc_final: 0.7798 (m110) outliers start: 24 outliers final: 20 residues processed: 142 average time/residue: 0.0799 time to fit residues: 17.1343 Evaluate side-chains 141 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 597 HIS Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** E 345 GLN ** 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 = 0.3657 r_free = 0.3657 target = 0.133432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115643 restraints weight = 14344.693| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.75 r_work: 0.3329 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9518 Z= 0.194 Angle : 0.621 10.445 12933 Z= 0.316 Chirality : 0.041 0.193 1506 Planarity : 0.004 0.046 1648 Dihedral : 4.590 25.786 1309 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.33 % Allowed : 17.88 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1206 helix: 0.59 (0.21), residues: 683 sheet: -0.42 (0.46), residues: 140 loop : -2.62 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 272 TYR 0.018 0.002 TYR D 230 PHE 0.019 0.002 PHE E 318 TRP 0.012 0.002 TRP A 345 HIS 0.004 0.001 HIS D 244 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9518) covalent geometry : angle 0.62119 (12933) hydrogen bonds : bond 0.04125 ( 464) hydrogen bonds : angle 4.52398 ( 1383) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.353 Fit side-chains REVERT: A 337 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7462 (p0) REVERT: E 89 ASP cc_start: 0.8590 (m-30) cc_final: 0.8296 (m-30) REVERT: E 548 LEU cc_start: 0.7978 (mt) cc_final: 0.7575 (mp) REVERT: H 73 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8183 (ttp) REVERT: H 111 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7118 (mm-30) REVERT: D 149 ASP cc_start: 0.7394 (p0) cc_final: 0.6906 (p0) REVERT: D 152 ASN cc_start: 0.8135 (m110) cc_final: 0.7817 (m110) outliers start: 32 outliers final: 21 residues processed: 146 average time/residue: 0.0747 time to fit residues: 16.6540 Evaluate side-chains 139 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 120 optimal weight: 0.7980 chunk 23 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** E 345 GLN ** 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 = 0.3675 r_free = 0.3675 target = 0.134950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117051 restraints weight = 14127.225| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.80 r_work: 0.3348 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9518 Z= 0.128 Angle : 0.559 9.850 12933 Z= 0.285 Chirality : 0.040 0.227 1506 Planarity : 0.004 0.044 1648 Dihedral : 4.424 25.144 1309 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.81 % Allowed : 17.88 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1206 helix: 0.75 (0.21), residues: 682 sheet: -0.29 (0.46), residues: 140 loop : -2.59 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 362 TYR 0.018 0.001 TYR D 230 PHE 0.013 0.001 PHE E 318 TRP 0.013 0.001 TRP A 345 HIS 0.003 0.001 HIS E 181 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9518) covalent geometry : angle 0.55862 (12933) hydrogen bonds : bond 0.03349 ( 464) hydrogen bonds : angle 4.41814 ( 1383) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.250 Fit side-chains REVERT: A 198 ASP cc_start: 0.7558 (p0) cc_final: 0.7358 (p0) REVERT: A 337 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7314 (p0) REVERT: E 78 MET cc_start: 0.7643 (ppp) cc_final: 0.7257 (ttp) REVERT: E 89 ASP cc_start: 0.8559 (m-30) cc_final: 0.8274 (m-30) REVERT: H 73 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8287 (ptp) REVERT: H 111 GLU cc_start: 0.7214 (mm-30) cc_final: 0.7000 (mm-30) REVERT: D 149 ASP cc_start: 0.7361 (p0) cc_final: 0.6904 (p0) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.0799 time to fit residues: 17.5025 Evaluate side-chains 145 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.0980 chunk 23 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS D 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117472 restraints weight = 14105.046| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.79 r_work: 0.3355 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9518 Z= 0.126 Angle : 0.557 11.742 12933 Z= 0.283 Chirality : 0.039 0.186 1506 Planarity : 0.003 0.044 1648 Dihedral : 4.352 25.180 1309 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.70 % Allowed : 18.30 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.25), residues: 1206 helix: 0.78 (0.21), residues: 684 sheet: -0.24 (0.46), residues: 140 loop : -2.58 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 272 TYR 0.018 0.001 TYR D 230 PHE 0.013 0.001 PHE E 318 TRP 0.012 0.001 TRP A 345 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9518) covalent geometry : angle 0.55710 (12933) hydrogen bonds : bond 0.03343 ( 464) hydrogen bonds : angle 4.36003 ( 1383) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.371 Fit side-chains REVERT: A 337 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7340 (p0) REVERT: E 78 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7201 (ttt) REVERT: E 89 ASP cc_start: 0.8584 (m-30) cc_final: 0.8334 (m-30) REVERT: H 73 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8272 (ptp) REVERT: H 105 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8400 (mm-40) outliers start: 26 outliers final: 21 residues processed: 140 average time/residue: 0.0763 time to fit residues: 16.2933 Evaluate side-chains 145 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 0.0020 chunk 86 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.117753 restraints weight = 14222.029| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.78 r_work: 0.3358 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9518 Z= 0.127 Angle : 0.560 12.017 12933 Z= 0.285 Chirality : 0.039 0.167 1506 Planarity : 0.003 0.043 1648 Dihedral : 4.337 25.785 1309 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.70 % Allowed : 18.19 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1206 helix: 0.82 (0.21), residues: 685 sheet: -0.27 (0.46), residues: 140 loop : -2.56 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 272 TYR 0.021 0.001 TYR D 230 PHE 0.013 0.001 PHE E 318 TRP 0.012 0.001 TRP A 345 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9518) covalent geometry : angle 0.56024 (12933) hydrogen bonds : bond 0.03302 ( 464) hydrogen bonds : angle 4.34511 ( 1383) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.378 Fit side-chains REVERT: A 198 ASP cc_start: 0.7540 (p0) cc_final: 0.7336 (p0) REVERT: A 337 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7327 (p0) REVERT: E 89 ASP cc_start: 0.8576 (m-30) cc_final: 0.8320 (m-30) REVERT: H 73 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8286 (ptp) REVERT: H 105 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8381 (mm-40) outliers start: 26 outliers final: 22 residues processed: 139 average time/residue: 0.0755 time to fit residues: 15.9496 Evaluate side-chains 142 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 511 LEU Chi-restraints excluded: chain E residue 626 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 73 MET Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 233 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 28 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118903 restraints weight = 13974.313| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.79 r_work: 0.3373 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9518 Z= 0.115 Angle : 0.556 12.348 12933 Z= 0.284 Chirality : 0.039 0.169 1506 Planarity : 0.003 0.041 1648 Dihedral : 4.259 25.404 1309 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.70 % Allowed : 18.71 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1206 helix: 0.89 (0.21), residues: 684 sheet: -0.19 (0.46), residues: 140 loop : -2.56 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 362 TYR 0.022 0.001 TYR D 230 PHE 0.011 0.001 PHE E 318 TRP 0.013 0.001 TRP A 365 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9518) covalent geometry : angle 0.55616 (12933) hydrogen bonds : bond 0.03101 ( 464) hydrogen bonds : angle 4.29948 ( 1383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.08 seconds wall clock time: 42 minutes 24.95 seconds (2544.95 seconds total)