Starting phenix.real_space_refine on Sun Sep 13 15:57:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mca_23755/09_2026/7mca_23755.cif" } resolution = 3.6 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= 0.003 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: 6 Type Number sf(0) Gaussians P 112 5.49 5 Mg 4 5.21 5 S 104 5.16 5 C 15509 2.51 5 N 4145 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24692 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 483} Chain breaks: 3 Chain: "B" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2096 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain breaks: 1 Chain: "C" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4830 Classifications: {'peptide': 584} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3572 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "E" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3702 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1369 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1018 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "H" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1032 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "I" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2999 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.26, per 1000 atoms: 0.21 Number of scatterers: 24692 At special positions: 0 Unit cell: (117.576, 138.276, 182.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 112 15.00 Mg 4 11.99 O 4818 8.00 N 4145 7.00 C 15509 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5354 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 17 sheets defined 49.5% alpha, 4.8% beta 21 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.505A pdb=" N LYS A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 378 " --> pdb=" O PHE A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.702A pdb=" N ILE A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.900A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 397 " --> pdb=" O PHE A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.771A pdb=" N LYS A 409 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 410 " --> pdb=" O GLU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 455 through 468 removed outlier: 4.400A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Processing helix chain 'A' and resid 522 through 534 removed outlier: 4.325A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.668A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 699 removed outlier: 4.186A pdb=" N LYS A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 726 removed outlier: 3.653A pdb=" N ALA A 714 " --> pdb=" O CYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 5.476A pdb=" N LYS A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 781 " --> pdb=" O HIS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 798 through 816 removed outlier: 3.600A pdb=" N MET A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 836 removed outlier: 3.625A pdb=" N ILE A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 4.229A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 removed outlier: 3.746A pdb=" N LEU A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 905 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.732A pdb=" N MET B 265 " --> pdb=" O THR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.703A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.564A pdb=" N GLN B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 removed outlier: 3.679A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.532A pdb=" N SER B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.641A pdb=" N TRP B 465 " --> pdb=" O PRO B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 removed outlier: 3.554A pdb=" N ASN B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 91 removed outlier: 3.954A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 156 removed outlier: 3.708A pdb=" N MET C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.628A pdb=" N ASN C 218 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.564A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 230' Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.563A pdb=" N ILE C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 279 through 286 removed outlier: 3.547A pdb=" N LEU C 285 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 Processing helix chain 'C' and resid 313 through 330 removed outlier: 3.989A pdb=" N THR C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 removed outlier: 4.039A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 4.437A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 345 " --> pdb=" O ASN C 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 345' Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.522A pdb=" N LEU C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 370 Processing helix chain 'C' and resid 373 through 382 removed outlier: 4.117A pdb=" N ILE C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.262A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 397 removed outlier: 3.906A pdb=" N LEU C 396 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 397 " --> pdb=" O GLU C 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 393 through 397' Processing helix chain 'C' and resid 405 through 415 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 removed outlier: 3.749A pdb=" N TYR C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 4.040A pdb=" N LYS C 450 " --> pdb=" O LYS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 512 through 517 removed outlier: 3.844A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.704A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 removed outlier: 3.637A pdb=" N PHE C 544 " --> pdb=" O PHE C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 564 through 569 removed outlier: 3.929A pdb=" N GLU C 568 " --> pdb=" O THR C 564 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 564 through 569' Processing helix chain 'C' and resid 574 through 592 removed outlier: 4.221A pdb=" N ILE C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 4.032A pdb=" N LEU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.364A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 228 through 240 removed outlier: 4.190A pdb=" N VAL D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.826A pdb=" N SER D 266 " --> pdb=" O LYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.870A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 4.366A pdb=" N GLU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 removed outlier: 3.501A pdb=" N GLU D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 348 removed outlier: 3.744A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 343 - end of helix removed outlier: 3.679A pdb=" N SER D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.665A pdb=" N GLU D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.786A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.562A pdb=" N ALA D 487 " --> pdb=" O ALA D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.526A pdb=" N THR D 495 " --> pdb=" O PHE D 492 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D 496 " --> pdb=" O GLN D 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 492 through 496' Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.526A pdb=" N LEU D 501 " --> pdb=" O PRO D 498 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 498 through 502' Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.556A pdb=" N ARG D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.626A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.703A pdb=" N THR E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 69 through 87 removed outlier: 3.689A pdb=" N LEU E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 146 through 151 removed outlier: 3.553A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 Processing helix chain 'E' and resid 193 through 206 removed outlier: 4.069A pdb=" N THR E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.698A pdb=" N ARG E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 229 through 247 removed outlier: 4.496A pdb=" N VAL E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.537A pdb=" N LEU E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 288 through 292 Processing helix chain 'E' and resid 325 through 339 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 removed outlier: 3.509A pdb=" N LEU E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.673A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.590A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 292 removed outlier: 3.583A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 306 removed outlier: 4.097A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR F 306 " --> pdb=" O ILE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 327 removed outlier: 4.260A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS F 321 " --> pdb=" O TRP F 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 325 " --> pdb=" O CYS F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 removed outlier: 3.517A pdb=" N ARG F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 337 " --> pdb=" O ASN F 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 332 through 337' Processing helix chain 'F' and resid 340 through 354 removed outlier: 3.569A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 371 removed outlier: 3.752A pdb=" N CYS F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS F 367 " --> pdb=" O ILE F 363 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 384 removed outlier: 3.901A pdb=" N ILE F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 402 removed outlier: 4.510A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 402 " --> pdb=" O ILE F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 424 removed outlier: 4.270A pdb=" N ASN F 419 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG F 424 " --> pdb=" O ILE F 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.578A pdb=" N MET I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 207 Processing helix chain 'I' and resid 238 through 245 Processing helix chain 'I' and resid 292 through 303 removed outlier: 3.778A pdb=" N MET I 296 " --> pdb=" O THR I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 323 Processing helix chain 'I' and resid 330 through 346 removed outlier: 3.717A pdb=" N LEU I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP I 336 " --> pdb=" O ARG I 332 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 338 " --> pdb=" O LEU I 334 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG I 339 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY I 340 " --> pdb=" O ASP I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 349 No H-bonds generated for 'chain 'I' and resid 347 through 349' Processing helix chain 'I' and resid 389 through 399 removed outlier: 3.811A pdb=" N SER I 395 " --> pdb=" O ALA I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 410 removed outlier: 3.646A pdb=" N ARG I 406 " --> pdb=" O SER I 402 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 407 " --> pdb=" O THR I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 411 through 414 Processing helix chain 'I' and resid 415 through 423 removed outlier: 3.962A pdb=" N CYS I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 439 Processing helix chain 'I' and resid 454 through 468 removed outlier: 3.811A pdb=" N PHE I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR I 463 " --> pdb=" O LEU I 459 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE I 464 " --> pdb=" O GLU I 460 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 465 " --> pdb=" O ILE I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 502 removed outlier: 3.501A pdb=" N MET I 502 " --> pdb=" O PHE I 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 477 through 478 Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 514 removed outlier: 3.643A pdb=" N VAL A 562 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 651 Processing sheet with id=AA4, first strand: chain 'A' and resid 682 through 684 Processing sheet with id=AA5, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA6, first strand: chain 'B' and resid 475 through 477 removed outlier: 6.328A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 240 removed outlier: 6.299A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 127 through 131 Processing sheet with id=AA9, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.471A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.907A pdb=" N SER D 97 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.770A pdb=" N HIS E 58 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE E 131 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB6, first strand: chain 'I' and resid 105 through 106 removed outlier: 3.557A pdb=" N ILE I 106 " --> pdb=" O GLY I 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 170 through 171 removed outlier: 7.524A pdb=" N ILE I 170 " --> pdb=" O ASP I 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 475 through 476 removed outlier: 3.604A pdb=" N THR I 476 " --> pdb=" O VAL I 486 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL I 486 " --> pdb=" O THR I 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 764 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 9510 1.38 - 1.55: 15478 1.55 - 1.73: 218 1.73 - 1.90: 165 1.90 - 2.08: 4 Bond restraints: 25375 Sorted by residual: bond pdb=" C4 AGS D2001 " pdb=" C5 AGS D2001 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.85e+01 bond pdb=" C5 AGS D2001 " pdb=" C6 AGS D2001 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" PG AGS D2001 " pdb=" S1G AGS D2001 " ideal model delta sigma weight residual 1.949 2.076 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C8 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 1.311 1.357 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.94e+01 ... (remaining 25370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 34189 3.12 - 6.24: 477 6.24 - 9.36: 53 9.36 - 12.48: 6 12.48 - 15.60: 2 Bond angle restraints: 34727 Sorted by residual: angle pdb=" C5 AGS D2001 " pdb=" C4 AGS D2001 " pdb=" N3 AGS D2001 " ideal model delta sigma weight residual 126.80 118.79 8.01 7.41e-01 1.82e+00 1.17e+02 angle pdb=" C4 AGS D2001 " pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " ideal model delta sigma weight residual 110.73 106.70 4.03 4.52e-01 4.89e+00 7.95e+01 angle pdb=" C5 AGS D2001 " pdb=" N7 AGS D2001 " pdb=" C8 AGS D2001 " ideal model delta sigma weight residual 103.67 107.42 -3.75 4.26e-01 5.51e+00 7.74e+01 angle pdb=" N3 AGS D2001 " pdb=" C4 AGS D2001 " pdb=" N9 AGS D2001 " ideal model delta sigma weight residual 127.16 134.97 -7.81 1.06e+00 8.92e-01 5.44e+01 angle pdb=" C4 AGS D2001 " pdb=" N9 AGS D2001 " pdb=" C8 AGS D2001 " ideal model delta sigma weight residual 105.70 108.58 -2.88 4.55e-01 4.83e+00 4.01e+01 ... (remaining 34722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 14232 33.57 - 67.14: 880 67.14 - 100.72: 43 100.72 - 134.29: 1 134.29 - 167.86: 1 Dihedral angle restraints: 15157 sinusoidal: 6956 harmonic: 8201 Sorted by residual: dihedral pdb=" CA GLU I 235 " pdb=" C GLU I 235 " pdb=" N THR I 236 " pdb=" CA THR I 236 " ideal model delta harmonic sigma weight residual -180.00 -137.59 -42.41 0 5.00e+00 4.00e-02 7.19e+01 dihedral pdb=" CA PHE I 126 " pdb=" C PHE I 126 " pdb=" N GLN I 127 " pdb=" CA GLN I 127 " ideal model delta harmonic sigma weight residual 180.00 -143.87 -36.13 0 5.00e+00 4.00e-02 5.22e+01 dihedral pdb=" CA LEU I 282 " pdb=" C LEU I 282 " pdb=" N PRO I 283 " pdb=" CA PRO I 283 " ideal model delta harmonic sigma weight residual -180.00 -146.71 -33.29 0 5.00e+00 4.00e-02 4.43e+01 ... (remaining 15154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3288 0.078 - 0.155: 612 0.155 - 0.233: 49 0.233 - 0.310: 8 0.310 - 0.388: 3 Chirality restraints: 3960 Sorted by residual: chirality pdb=" CB ILE D 508 " pdb=" CA ILE D 508 " pdb=" CG1 ILE D 508 " pdb=" CG2 ILE D 508 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB ILE A 622 " pdb=" CA ILE A 622 " pdb=" CG1 ILE A 622 " pdb=" CG2 ILE A 622 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB ILE B 432 " pdb=" CA ILE B 432 " pdb=" CG1 ILE B 432 " pdb=" CG2 ILE B 432 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3957 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 214 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS I 214 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS I 214 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS I 215 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 454 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO E 455 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 455 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 455 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER I 395 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C SER I 395 " -0.051 2.00e-02 2.50e+03 pdb=" O SER I 395 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS I 396 " 0.017 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 13 1.82 - 2.59: 268 2.59 - 3.36: 29999 3.36 - 4.13: 59776 4.13 - 4.90: 108925 Nonbonded interactions: 198981 Sorted by model distance: nonbonded pdb=" O4 DT G 7 " pdb=" N1 DA H 79 " model vdw 1.053 2.496 nonbonded pdb=" N3 DT G 5 " pdb=" N1 DA H 81 " model vdw 1.099 3.200 nonbonded pdb=" O4 DT G 5 " pdb=" N6 DA H 81 " model vdw 1.161 3.120 nonbonded pdb=" O4 DT G 6 " pdb=" N1 DA H 80 " model vdw 1.375 2.496 nonbonded pdb=" O2 DT G 5 " pdb=" C2 DA H 81 " model vdw 1.508 3.340 ... (remaining 198976 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 group one per residue 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: 2.160 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.008 0.417 25379 Z= 0.541 Angle : 0.999 15.601 34727 Z= 0.620 Chirality : 0.059 0.388 3960 Planarity : 0.006 0.076 4013 Dihedral : 19.349 167.859 9803 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.24 % Favored : 91.69 % Rotamer: Outliers : 0.75 % Allowed : 10.87 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.08 % 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: -5.13 (0.12), residues: 2718 helix: -3.47 (0.09), residues: 1379 sheet: -2.53 (0.33), residues: 197 loop : -3.33 (0.15), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 267 TYR 0.031 0.003 TYR C 483 PHE 0.051 0.002 PHE I 126 TRP 0.014 0.002 TRP B 305 HIS 0.011 0.002 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.42 (25375) covalent geometry : angle 0.99942 / 0.62 (34727) hydrogen bonds : bond 0.17497 / 10.92 ( 813) hydrogen bonds : angle 8.09610 / 5.30 ( 2309) Misc. bond : bond 0.27355 / 15.43 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 495 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9136 (tp) cc_final: 0.8843 (tt) REVERT: B 262 THR cc_start: 0.8177 (m) cc_final: 0.7775 (t) REVERT: B 380 THR cc_start: 0.7608 (p) cc_final: 0.7289 (t) REVERT: C 37 LYS cc_start: 0.6776 (tptt) cc_final: 0.6492 (tptt) REVERT: C 100 ARG cc_start: 0.6778 (mmt180) cc_final: 0.6422 (mpt180) REVERT: C 186 SER cc_start: 0.7665 (p) cc_final: 0.7143 (t) REVERT: C 421 ASN cc_start: 0.7769 (t0) cc_final: 0.7510 (t0) REVERT: C 469 ASP cc_start: 0.7527 (t0) cc_final: 0.5899 (t0) REVERT: D 284 MET cc_start: 0.8296 (mtp) cc_final: 0.8044 (mtp) REVERT: D 454 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7937 (mttt) REVERT: E 297 ASP cc_start: 0.6726 (m-30) cc_final: 0.6084 (p0) REVERT: F 273 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8484 (pp) REVERT: I 87 GLN cc_start: 0.3942 (tm-30) cc_final: 0.3586 (mt0) REVERT: I 226 ASP cc_start: 0.5007 (m-30) cc_final: 0.4745 (m-30) REVERT: I 268 LYS cc_start: 0.3708 (tppt) cc_final: 0.3222 (tttt) REVERT: I 334 LEU cc_start: 0.8162 (tp) cc_final: 0.7708 (tp) REVERT: I 484 ARG cc_start: 0.5035 (mtt90) cc_final: 0.4754 (mtm110) outliers start: 19 outliers final: 5 residues processed: 512 average time/residue: 0.1893 time to fit residues: 145.5836 Evaluate side-chains 281 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 275 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 409 LYS Chi-restraints excluded: chain I residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN A 600 ASN A 771 GLN A 820 GLN B 256 ASN B 284 ASN B 291 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN B 425 HIS B 478 HIS B 493 GLN C 67 HIS C 178 ASN C 241 ASN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN C 523 GLN C 536 ASN D 137 HIS D 255 ASN D 306 ASN D 370 ASN D 371 GLN D 409 ASN D 458 ASN E 32 ASN E 52 ASN E 82 GLN E 113 HIS E 139 GLN E 193 ASN E 223 GLN E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN I 99 HIS I 193 ASN I 198 GLN I 213 HIS I 313 GLN I 439 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.162433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127802 restraints weight = 35737.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.127272 restraints weight = 33017.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128586 restraints weight = 31192.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128771 restraints weight = 21245.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129155 restraints weight = 19281.991| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25379 Z= 0.213 Angle : 0.718 12.232 34727 Z= 0.381 Chirality : 0.048 0.246 3960 Planarity : 0.005 0.064 4013 Dihedral : 19.609 165.965 4167 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.56 % Allowed : 15.87 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.14), residues: 2718 helix: -2.23 (0.12), residues: 1380 sheet: -2.43 (0.35), residues: 185 loop : -3.07 (0.16), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 471 TYR 0.031 0.002 TYR I 291 PHE 0.051 0.002 PHE I 126 TRP 0.012 0.001 TRP F 378 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (25375) covalent geometry : angle 0.71832 / 0.38 (34727) hydrogen bonds : bond 0.05699 / 3.41 ( 813) hydrogen bonds : angle 5.04603 / 3.46 ( 2309) Misc. bond : bond 0.00065 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 315 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9267 (tp) cc_final: 0.8979 (tt) REVERT: A 566 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: B 262 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7704 (t) REVERT: B 380 THR cc_start: 0.7967 (p) cc_final: 0.7654 (t) REVERT: C 37 LYS cc_start: 0.6835 (tptt) cc_final: 0.6613 (tptt) REVERT: C 98 LYS cc_start: 0.6511 (tptp) cc_final: 0.5981 (mtmm) REVERT: C 100 ARG cc_start: 0.7172 (mmt180) cc_final: 0.6671 (ptp-170) REVERT: C 186 SER cc_start: 0.7680 (p) cc_final: 0.7477 (t) REVERT: C 241 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6951 (t0) REVERT: C 421 ASN cc_start: 0.7908 (t0) cc_final: 0.7656 (t0) REVERT: D 454 LYS cc_start: 0.8540 (ttpt) cc_final: 0.7923 (mttt) REVERT: D 471 GLU cc_start: 0.7494 (mp0) cc_final: 0.7001 (mp0) REVERT: D 512 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7252 (mt-10) REVERT: E 297 ASP cc_start: 0.6936 (m-30) cc_final: 0.6168 (p0) REVERT: E 320 GLN cc_start: 0.4475 (OUTLIER) cc_final: 0.4150 (pt0) REVERT: F 273 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8505 (pp) REVERT: I 268 LYS cc_start: 0.3455 (tppt) cc_final: 0.2966 (tptm) REVERT: I 334 LEU cc_start: 0.8061 (tp) cc_final: 0.7753 (tp) REVERT: I 418 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7273 (tt) REVERT: I 477 LYS cc_start: 0.8563 (mmtt) cc_final: 0.7956 (mtpt) outliers start: 65 outliers final: 32 residues processed: 360 average time/residue: 0.1599 time to fit residues: 91.9931 Evaluate side-chains 298 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 165 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN B 493 GLN C 126 ASN C 178 ASN C 342 ASN C 430 ASN ** C 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN E 36 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS E 223 GLN E 248 HIS ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122239 restraints weight = 36399.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121187 restraints weight = 32658.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.122495 restraints weight = 33587.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122811 restraints weight = 21548.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123153 restraints weight = 19770.165| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 25379 Z= 0.305 Angle : 0.763 15.037 34727 Z= 0.398 Chirality : 0.050 0.241 3960 Planarity : 0.005 0.050 4013 Dihedral : 19.716 164.895 4161 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.86 % Allowed : 18.07 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.14), residues: 2718 helix: -1.85 (0.13), residues: 1371 sheet: -2.80 (0.34), residues: 186 loop : -3.04 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 888 TYR 0.025 0.002 TYR D 524 PHE 0.033 0.002 PHE C 102 TRP 0.014 0.002 TRP C 58 HIS 0.019 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.31 (25375) covalent geometry : angle 0.76310 / 0.40 (34727) hydrogen bonds : bond 0.05168 / 3.24 ( 813) hydrogen bonds : angle 4.96819 / 3.40 ( 2309) Misc. bond : bond 0.00071 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 287 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9339 (tp) cc_final: 0.9096 (tt) REVERT: A 566 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 262 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7673 (t) REVERT: B 468 MET cc_start: 0.8886 (tpp) cc_final: 0.8661 (tpt) REVERT: C 98 LYS cc_start: 0.6673 (tptp) cc_final: 0.6340 (ttmt) REVERT: C 100 ARG cc_start: 0.7413 (mmt180) cc_final: 0.6813 (ptp-170) REVERT: C 186 SER cc_start: 0.7971 (p) cc_final: 0.7686 (t) REVERT: C 421 ASN cc_start: 0.8007 (t0) cc_final: 0.7791 (t0) REVERT: D 113 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6942 (t0) REVERT: D 255 ASN cc_start: 0.7224 (p0) cc_final: 0.6930 (p0) REVERT: D 454 LYS cc_start: 0.8587 (ttpt) cc_final: 0.7935 (mttt) REVERT: D 471 GLU cc_start: 0.7697 (mp0) cc_final: 0.7287 (mp0) REVERT: D 493 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7765 (tm-30) REVERT: D 512 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: D 514 ARG cc_start: 0.7711 (tpt170) cc_final: 0.7309 (ttt90) REVERT: E 171 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8695 (tt) REVERT: E 297 ASP cc_start: 0.6994 (m-30) cc_final: 0.6137 (p0) REVERT: F 273 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (pp) REVERT: I 89 MET cc_start: 0.3504 (mmm) cc_final: 0.3244 (mmm) REVERT: I 268 LYS cc_start: 0.3222 (tppt) cc_final: 0.2752 (tptm) REVERT: I 318 LYS cc_start: 0.7035 (mmtt) cc_final: 0.6479 (pptt) REVERT: I 418 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7159 (tt) REVERT: I 477 LYS cc_start: 0.8522 (mmtt) cc_final: 0.7897 (mtpt) outliers start: 98 outliers final: 60 residues processed: 362 average time/residue: 0.1625 time to fit residues: 94.2871 Evaluate side-chains 327 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 356 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 476 THR Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 16 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 112 optimal weight: 0.0010 chunk 13 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 281 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 120 optimal weight: 30.0000 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN E 36 GLN E 139 GLN E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 232 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.160913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126399 restraints weight = 35788.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125744 restraints weight = 31265.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127155 restraints weight = 30098.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127505 restraints weight = 19329.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127964 restraints weight = 18004.785| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25379 Z= 0.129 Angle : 0.619 13.668 34727 Z= 0.327 Chirality : 0.044 0.186 3960 Planarity : 0.004 0.048 4013 Dihedral : 19.413 169.569 4161 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.25 % Favored : 92.72 % Rotamer: Outliers : 3.31 % Allowed : 19.41 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.15), residues: 2718 helix: -1.33 (0.13), residues: 1374 sheet: -2.77 (0.34), residues: 183 loop : -2.81 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 250 TYR 0.027 0.002 TYR C 61 PHE 0.033 0.001 PHE I 126 TRP 0.013 0.001 TRP F 378 HIS 0.007 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (25375) covalent geometry : angle 0.61933 / 0.33 (34727) hydrogen bonds : bond 0.04123 / 2.53 ( 813) hydrogen bonds : angle 4.53718 / 3.11 ( 2309) Misc. bond : bond 0.00028 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 308 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9322 (tp) cc_final: 0.9073 (tt) REVERT: B 262 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7643 (t) REVERT: B 380 THR cc_start: 0.7969 (p) cc_final: 0.7604 (t) REVERT: C 98 LYS cc_start: 0.6538 (tptp) cc_final: 0.6336 (ttmt) REVERT: C 100 ARG cc_start: 0.7259 (mmt180) cc_final: 0.6738 (ptp-170) REVERT: C 141 MET cc_start: 0.8423 (mmm) cc_final: 0.8034 (mmt) REVERT: C 412 PHE cc_start: 0.6901 (t80) cc_final: 0.6588 (t80) REVERT: D 113 ASP cc_start: 0.7227 (t0) cc_final: 0.6846 (t0) REVERT: D 454 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7931 (mtmt) REVERT: D 471 GLU cc_start: 0.7560 (mp0) cc_final: 0.7236 (mp0) REVERT: D 493 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7749 (tm-30) REVERT: D 512 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7072 (mt-10) REVERT: D 514 ARG cc_start: 0.7503 (tpt170) cc_final: 0.7224 (ttt90) REVERT: E 36 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8521 (tm-30) REVERT: E 130 LEU cc_start: 0.8935 (tt) cc_final: 0.8713 (mt) REVERT: E 254 ASP cc_start: 0.7759 (t70) cc_final: 0.7426 (t70) REVERT: E 297 ASP cc_start: 0.6843 (m-30) cc_final: 0.6092 (p0) REVERT: F 296 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7118 (ptp-110) REVERT: I 89 MET cc_start: 0.3658 (mmm) cc_final: 0.3430 (mmm) REVERT: I 268 LYS cc_start: 0.3257 (tppt) cc_final: 0.2865 (tttp) REVERT: I 318 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6452 (pptt) REVERT: I 418 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7220 (tt) REVERT: I 477 LYS cc_start: 0.8450 (mmtt) cc_final: 0.7839 (mtpt) outliers start: 84 outliers final: 45 residues processed: 369 average time/residue: 0.1645 time to fit residues: 97.1797 Evaluate side-chains 316 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 147 optimal weight: 4.9990 chunk 277 optimal weight: 0.0670 chunk 129 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 239 ASN C 342 ASN D 489 ASN E 82 GLN E 223 GLN E 320 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125494 restraints weight = 35943.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124550 restraints weight = 32312.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126193 restraints weight = 30445.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.126157 restraints weight = 20160.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126637 restraints weight = 18998.147| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25379 Z= 0.164 Angle : 0.633 13.493 34727 Z= 0.328 Chirality : 0.044 0.220 3960 Planarity : 0.004 0.047 4013 Dihedral : 19.358 167.819 4159 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.02 % Favored : 91.94 % Rotamer: Outliers : 4.02 % Allowed : 19.49 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.15), residues: 2718 helix: -1.14 (0.14), residues: 1376 sheet: -2.72 (0.34), residues: 185 loop : -2.74 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 288 TYR 0.028 0.002 TYR I 291 PHE 0.039 0.002 PHE I 126 TRP 0.012 0.001 TRP F 378 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (25375) covalent geometry : angle 0.63263 / 0.33 (34727) hydrogen bonds : bond 0.04040 / 2.47 ( 813) hydrogen bonds : angle 4.47253 / 3.07 ( 2309) Misc. bond : bond 0.00037 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 285 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 382 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7005 (mt) REVERT: A 422 ILE cc_start: 0.9326 (tp) cc_final: 0.9092 (tt) REVERT: B 262 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7638 (t) REVERT: B 341 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8628 (t) REVERT: B 380 THR cc_start: 0.8004 (p) cc_final: 0.7672 (t) REVERT: C 100 ARG cc_start: 0.7280 (mmt180) cc_final: 0.6757 (ptp-170) REVERT: C 412 PHE cc_start: 0.6957 (t80) cc_final: 0.6625 (t80) REVERT: C 448 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: D 113 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6871 (t0) REVERT: D 120 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: D 258 GLU cc_start: 0.7234 (mp0) cc_final: 0.6918 (mp0) REVERT: D 454 LYS cc_start: 0.8527 (ttpt) cc_final: 0.7967 (mtmt) REVERT: D 471 GLU cc_start: 0.7556 (mp0) cc_final: 0.7255 (mp0) REVERT: D 493 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 512 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7109 (mt-10) REVERT: D 514 ARG cc_start: 0.7526 (tpt170) cc_final: 0.7301 (ttt90) REVERT: E 130 LEU cc_start: 0.8923 (tt) cc_final: 0.8713 (mt) REVERT: E 254 ASP cc_start: 0.7758 (t70) cc_final: 0.7472 (t70) REVERT: E 297 ASP cc_start: 0.6925 (m-30) cc_final: 0.6071 (p0) REVERT: F 296 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7140 (ptp-110) REVERT: I 89 MET cc_start: 0.3762 (mmm) cc_final: 0.3524 (mmm) REVERT: I 268 LYS cc_start: 0.3268 (tppt) cc_final: 0.2880 (tttp) REVERT: I 318 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6487 (pptt) REVERT: I 418 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7195 (tt) REVERT: I 477 LYS cc_start: 0.8387 (mmtt) cc_final: 0.7850 (mtpt) outliers start: 102 outliers final: 66 residues processed: 366 average time/residue: 0.1539 time to fit residues: 91.0775 Evaluate side-chains 343 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 269 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain C residue 614 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 193 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 ASN E 82 GLN E 223 GLN E 391 GLN I 302 GLN I 400 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123799 restraints weight = 36199.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122870 restraints weight = 32293.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124155 restraints weight = 32132.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124451 restraints weight = 20683.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124697 restraints weight = 19148.343| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25379 Z= 0.226 Angle : 0.671 14.445 34727 Z= 0.347 Chirality : 0.046 0.206 3960 Planarity : 0.004 0.051 4013 Dihedral : 19.412 166.922 4157 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.35 % Favored : 91.61 % Rotamer: Outliers : 4.06 % Allowed : 20.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.15), residues: 2718 helix: -1.13 (0.14), residues: 1375 sheet: -2.82 (0.34), residues: 185 loop : -2.74 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 271 TYR 0.018 0.002 TYR C 61 PHE 0.036 0.002 PHE I 126 TRP 0.010 0.001 TRP F 378 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (25375) covalent geometry : angle 0.67072 / 0.35 (34727) hydrogen bonds : bond 0.04187 / 2.57 ( 813) hydrogen bonds : angle 4.53099 / 3.11 ( 2309) Misc. bond : bond 0.00031 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 282 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 382 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7059 (mt) REVERT: A 422 ILE cc_start: 0.9328 (tp) cc_final: 0.9103 (tt) REVERT: A 526 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6434 (mt-10) REVERT: B 262 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7623 (t) REVERT: B 341 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8611 (t) REVERT: C 100 ARG cc_start: 0.7205 (mmt180) cc_final: 0.6763 (ptp90) REVERT: C 412 PHE cc_start: 0.6988 (t80) cc_final: 0.6625 (t80) REVERT: C 448 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: D 113 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6921 (t0) REVERT: D 120 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: D 258 GLU cc_start: 0.7251 (mp0) cc_final: 0.6947 (mp0) REVERT: D 454 LYS cc_start: 0.8556 (ttpt) cc_final: 0.7990 (mtmt) REVERT: D 471 GLU cc_start: 0.7616 (mp0) cc_final: 0.7345 (mp0) REVERT: D 493 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7734 (tm-30) REVERT: D 512 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7184 (mt-10) REVERT: D 514 ARG cc_start: 0.7536 (tpt170) cc_final: 0.7289 (ttt90) REVERT: E 130 LEU cc_start: 0.8939 (tt) cc_final: 0.8729 (mt) REVERT: E 254 ASP cc_start: 0.7774 (t70) cc_final: 0.7538 (t70) REVERT: E 297 ASP cc_start: 0.7024 (m-30) cc_final: 0.6121 (p0) REVERT: F 296 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7222 (ptp-110) REVERT: I 89 MET cc_start: 0.3934 (mmm) cc_final: 0.3638 (mmm) REVERT: I 268 LYS cc_start: 0.3203 (tppt) cc_final: 0.2895 (tttp) REVERT: I 318 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6547 (pptt) REVERT: I 418 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7285 (tt) REVERT: I 477 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7798 (mtpt) REVERT: I 499 TYR cc_start: 0.2479 (OUTLIER) cc_final: 0.1001 (m-10) outliers start: 103 outliers final: 71 residues processed: 359 average time/residue: 0.1591 time to fit residues: 92.6168 Evaluate side-chains 346 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 266 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain C residue 614 ARG Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 233 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 342 ILE Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 254 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 273 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN A 600 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN B 493 GLN C 241 ASN E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126465 restraints weight = 35794.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126562 restraints weight = 31333.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127709 restraints weight = 29570.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127811 restraints weight = 18662.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128144 restraints weight = 17557.311| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25379 Z= 0.127 Angle : 0.604 13.609 34727 Z= 0.314 Chirality : 0.043 0.220 3960 Planarity : 0.004 0.045 4013 Dihedral : 19.211 170.390 4157 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.40 % Favored : 92.57 % Rotamer: Outliers : 3.66 % Allowed : 21.26 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.15), residues: 2718 helix: -0.85 (0.14), residues: 1369 sheet: -2.70 (0.34), residues: 185 loop : -2.58 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 317 TYR 0.029 0.001 TYR I 291 PHE 0.032 0.001 PHE I 126 TRP 0.012 0.001 TRP F 378 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (25375) covalent geometry : angle 0.60392 / 0.31 (34727) hydrogen bonds : bond 0.03724 / 2.25 ( 813) hydrogen bonds : angle 4.30141 / 2.96 ( 2309) Misc. bond : bond 0.00042 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 295 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 422 ILE cc_start: 0.9319 (tp) cc_final: 0.9099 (tt) REVERT: B 262 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7609 (t) REVERT: B 380 THR cc_start: 0.7972 (p) cc_final: 0.7614 (t) REVERT: C 100 ARG cc_start: 0.7124 (mmt180) cc_final: 0.6729 (ptp90) REVERT: C 241 ASN cc_start: 0.7200 (OUTLIER) cc_final: 0.6650 (t0) REVERT: C 412 PHE cc_start: 0.6944 (t80) cc_final: 0.6620 (t80) REVERT: C 448 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7106 (pm20) REVERT: D 113 ASP cc_start: 0.7327 (t0) cc_final: 0.6961 (t0) REVERT: D 120 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: D 258 GLU cc_start: 0.7259 (mp0) cc_final: 0.6969 (mp0) REVERT: D 454 LYS cc_start: 0.8531 (ttpt) cc_final: 0.7968 (mtmt) REVERT: D 471 GLU cc_start: 0.7540 (mp0) cc_final: 0.7278 (mp0) REVERT: D 493 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7712 (tm-30) REVERT: D 512 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7080 (mt-10) REVERT: D 514 ARG cc_start: 0.7474 (tpt170) cc_final: 0.7205 (ttt90) REVERT: E 96 ASP cc_start: 0.7047 (t0) cc_final: 0.6779 (p0) REVERT: E 254 ASP cc_start: 0.7743 (t70) cc_final: 0.7519 (t70) REVERT: E 297 ASP cc_start: 0.6868 (m-30) cc_final: 0.6032 (p0) REVERT: F 296 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7143 (ptp-110) REVERT: I 87 GLN cc_start: 0.4096 (tm-30) cc_final: 0.3603 (mt0) REVERT: I 89 MET cc_start: 0.3914 (mmm) cc_final: 0.3623 (mmm) REVERT: I 268 LYS cc_start: 0.3168 (tppt) cc_final: 0.2858 (tttp) REVERT: I 318 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6557 (pptt) REVERT: I 418 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7285 (tt) REVERT: I 477 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7779 (mtpt) outliers start: 93 outliers final: 59 residues processed: 364 average time/residue: 0.1586 time to fit residues: 93.9937 Evaluate side-chains 342 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 277 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 232 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 163 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 241 ASN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.158114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124022 restraints weight = 36064.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123021 restraints weight = 32369.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124211 restraints weight = 33526.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.124579 restraints weight = 21598.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124826 restraints weight = 19697.497| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25379 Z= 0.230 Angle : 0.680 14.195 34727 Z= 0.349 Chirality : 0.047 0.340 3960 Planarity : 0.004 0.048 4013 Dihedral : 19.307 167.100 4157 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.61 % Favored : 91.35 % Rotamer: Outliers : 3.78 % Allowed : 21.69 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.15), residues: 2718 helix: -0.92 (0.14), residues: 1372 sheet: -2.71 (0.35), residues: 182 loop : -2.62 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 614 TYR 0.024 0.002 TYR I 291 PHE 0.041 0.002 PHE I 126 TRP 0.010 0.001 TRP C 58 HIS 0.006 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (25375) covalent geometry : angle 0.68042 / 0.35 (34727) hydrogen bonds : bond 0.04075 / 2.49 ( 813) hydrogen bonds : angle 4.46978 / 3.06 ( 2309) Misc. bond : bond 0.00043 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 382 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7106 (mt) REVERT: A 422 ILE cc_start: 0.9327 (tp) cc_final: 0.9101 (tt) REVERT: A 566 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: B 262 THR cc_start: 0.7932 (OUTLIER) cc_final: 0.7562 (t) REVERT: B 341 SER cc_start: 0.9250 (OUTLIER) cc_final: 0.8611 (t) REVERT: C 100 ARG cc_start: 0.7214 (mmt180) cc_final: 0.6780 (ptp90) REVERT: C 412 PHE cc_start: 0.7047 (t80) cc_final: 0.6705 (t80) REVERT: C 448 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: D 113 ASP cc_start: 0.7317 (t0) cc_final: 0.6917 (t0) REVERT: D 120 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: D 255 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7165 (p0) REVERT: D 454 LYS cc_start: 0.8548 (ttpt) cc_final: 0.7976 (mtmt) REVERT: D 471 GLU cc_start: 0.7628 (mp0) cc_final: 0.7389 (mp0) REVERT: D 493 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 512 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7211 (mt-10) REVERT: D 514 ARG cc_start: 0.7505 (tpt170) cc_final: 0.7237 (ttt90) REVERT: E 254 ASP cc_start: 0.7812 (t70) cc_final: 0.7599 (t70) REVERT: E 297 ASP cc_start: 0.7020 (m-30) cc_final: 0.6103 (p0) REVERT: F 296 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7184 (ptp-110) REVERT: I 268 LYS cc_start: 0.3117 (tppt) cc_final: 0.2717 (tptm) REVERT: I 318 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6671 (pptt) REVERT: I 418 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7392 (tt) REVERT: I 477 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7801 (mtpt) REVERT: I 499 TYR cc_start: 0.2358 (OUTLIER) cc_final: 0.0812 (m-10) REVERT: I 511 PHE cc_start: 0.3901 (m-10) cc_final: 0.3689 (m-10) outliers start: 96 outliers final: 72 residues processed: 357 average time/residue: 0.1515 time to fit residues: 88.1434 Evaluate side-chains 348 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 266 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 890 CYS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 65 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 229 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.162013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127856 restraints weight = 35947.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127623 restraints weight = 31338.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128750 restraints weight = 30396.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129237 restraints weight = 19360.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129617 restraints weight = 17749.696| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25379 Z= 0.117 Angle : 0.609 12.649 34727 Z= 0.316 Chirality : 0.043 0.317 3960 Planarity : 0.003 0.046 4013 Dihedral : 19.039 172.049 4157 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 3.07 % Allowed : 22.40 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.16), residues: 2718 helix: -0.64 (0.14), residues: 1370 sheet: -2.56 (0.35), residues: 183 loop : -2.44 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 478 TYR 0.028 0.002 TYR C 61 PHE 0.043 0.001 PHE I 126 TRP 0.014 0.001 TRP F 378 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (25375) covalent geometry : angle 0.60938 / 0.32 (34727) hydrogen bonds : bond 0.03512 / 2.11 ( 813) hydrogen bonds : angle 4.20690 / 2.89 ( 2309) Misc. bond : bond 0.00038 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 291 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 ILE cc_start: 0.9317 (tp) cc_final: 0.9094 (tt) REVERT: A 566 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: A 808 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8749 (tt) REVERT: B 262 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7384 (t) REVERT: B 380 THR cc_start: 0.7925 (p) cc_final: 0.7568 (t) REVERT: B 390 ARG cc_start: 0.8676 (tpt170) cc_final: 0.8309 (tpp-160) REVERT: C 100 ARG cc_start: 0.7079 (mmt180) cc_final: 0.6722 (ptp90) REVERT: C 412 PHE cc_start: 0.6971 (t80) cc_final: 0.6653 (t80) REVERT: C 448 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: D 113 ASP cc_start: 0.7280 (t0) cc_final: 0.6932 (t0) REVERT: D 255 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.7008 (p0) REVERT: D 454 LYS cc_start: 0.8512 (ttpt) cc_final: 0.7960 (mtmt) REVERT: D 471 GLU cc_start: 0.7543 (mp0) cc_final: 0.7283 (mp0) REVERT: D 493 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 512 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7093 (mt-10) REVERT: D 514 ARG cc_start: 0.7439 (tpt170) cc_final: 0.7184 (ttt90) REVERT: E 96 ASP cc_start: 0.7020 (t0) cc_final: 0.6710 (p0) REVERT: E 171 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8409 (tt) REVERT: E 254 ASP cc_start: 0.7719 (t70) cc_final: 0.7503 (t70) REVERT: E 297 ASP cc_start: 0.6771 (m-30) cc_final: 0.5966 (p0) REVERT: F 296 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7183 (ptp-110) REVERT: I 87 GLN cc_start: 0.4013 (tm-30) cc_final: 0.3578 (mt0) REVERT: I 318 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6660 (pptt) REVERT: I 477 LYS cc_start: 0.8297 (mmtt) cc_final: 0.7812 (mtpt) REVERT: I 499 TYR cc_start: 0.2255 (OUTLIER) cc_final: 0.0849 (m-10) outliers start: 78 outliers final: 58 residues processed: 351 average time/residue: 0.1505 time to fit residues: 86.3205 Evaluate side-chains 328 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 279 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 242 optimal weight: 40.0000 chunk 186 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 275 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN B 493 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123383 restraints weight = 36217.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122642 restraints weight = 32290.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123540 restraints weight = 34058.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124300 restraints weight = 21552.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124448 restraints weight = 19100.416| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25379 Z= 0.265 Angle : 0.713 14.542 34727 Z= 0.366 Chirality : 0.048 0.280 3960 Planarity : 0.004 0.047 4013 Dihedral : 19.225 166.570 4156 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 2.99 % Allowed : 22.76 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.15), residues: 2718 helix: -0.81 (0.14), residues: 1374 sheet: -2.71 (0.35), residues: 183 loop : -2.59 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 271 TYR 0.051 0.002 TYR C 23 PHE 0.048 0.002 PHE I 126 TRP 0.013 0.002 TRP C 58 HIS 0.007 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.27 (25375) covalent geometry : angle 0.71331 / 0.37 (34727) hydrogen bonds : bond 0.04104 / 2.51 ( 813) hydrogen bonds : angle 4.46113 / 3.05 ( 2309) Misc. bond : bond 0.00051 / 0.03 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 382 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7126 (mt) REVERT: A 422 ILE cc_start: 0.9340 (tp) cc_final: 0.9109 (tt) REVERT: A 566 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: A 808 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8912 (tt) REVERT: C 100 ARG cc_start: 0.7233 (mmt180) cc_final: 0.6798 (ptp90) REVERT: C 412 PHE cc_start: 0.6999 (t80) cc_final: 0.6661 (t80) REVERT: C 448 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: D 113 ASP cc_start: 0.7420 (t0) cc_final: 0.6975 (t0) REVERT: D 116 LEU cc_start: 0.7971 (mm) cc_final: 0.7767 (mt) REVERT: D 120 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: D 255 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.7191 (p0) REVERT: D 454 LYS cc_start: 0.8520 (ttpt) cc_final: 0.7925 (mttt) REVERT: D 471 GLU cc_start: 0.7661 (mp0) cc_final: 0.7411 (mp0) REVERT: D 493 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7718 (tm-30) REVERT: D 512 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7173 (mt-10) REVERT: D 514 ARG cc_start: 0.7505 (tpt170) cc_final: 0.7213 (ttt90) REVERT: E 171 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8504 (tt) REVERT: E 297 ASP cc_start: 0.6959 (m-30) cc_final: 0.6081 (p0) REVERT: F 296 ARG cc_start: 0.7640 (mtp85) cc_final: 0.7267 (ptp-110) REVERT: I 87 GLN cc_start: 0.4227 (tm-30) cc_final: 0.3775 (mt0) REVERT: I 318 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6758 (pptt) REVERT: I 477 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7815 (mtpt) REVERT: I 499 TYR cc_start: 0.2340 (OUTLIER) cc_final: 0.0732 (m-10) outliers start: 76 outliers final: 63 residues processed: 325 average time/residue: 0.1569 time to fit residues: 82.1832 Evaluate side-chains 326 residues out of total 2540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 720 HIS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 409 ASP Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 556 PHE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 611 CYS Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 257 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 272 LEU Chi-restraints excluded: chain I residue 285 THR Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 499 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 209 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 118 optimal weight: 0.3980 chunk 31 optimal weight: 0.0980 chunk 250 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127787 restraints weight = 35759.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127473 restraints weight = 30414.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128443 restraints weight = 30852.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.129055 restraints weight = 19870.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129252 restraints weight = 17965.653| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25379 Z= 0.116 Angle : 0.618 12.412 34727 Z= 0.320 Chirality : 0.043 0.287 3960 Planarity : 0.004 0.046 4013 Dihedral : 18.964 172.347 4156 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.66 % Favored : 93.30 % Rotamer: Outliers : 2.76 % Allowed : 23.07 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.16), residues: 2718 helix: -0.56 (0.14), residues: 1382 sheet: -2.53 (0.35), residues: 183 loop : -2.40 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 478 TYR 0.048 0.002 TYR C 23 PHE 0.048 0.001 PHE I 126 TRP 0.015 0.001 TRP F 378 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (25375) covalent geometry : angle 0.61776 / 0.32 (34727) hydrogen bonds : bond 0.03460 / 2.06 ( 813) hydrogen bonds : angle 4.18610 / 2.87 ( 2309) Misc. bond : bond 0.00051 / 0.03 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3651.57 seconds wall clock time: 64 minutes 15.35 seconds (3855.35 seconds total)