Starting phenix.real_space_refine on Tue Sep 15 06:06:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rr7_4986/09_2026/6rr7_4986_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rr7_4986/09_2026/6rr7_4986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rr7_4986/09_2026/6rr7_4986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rr7_4986/09_2026/6rr7_4986.map" model { file = "/net/cci-nas-00/data/ceres_data/6rr7_4986/09_2026/6rr7_4986_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rr7_4986/09_2026/6rr7_4986_trim.cif" } resolution = 3.01 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= 0.009 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 32 5.49 5 S 128 5.16 5 C 11395 2.51 5 N 3202 2.21 5 O 3532 1.98 5 H 18001 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s 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: 36290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11578 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 11887 Classifications: {'peptide': 744} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 11832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 11832 Classifications: {'peptide': 737} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 708} Chain: "F" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 187 Unusual residues: {'M7G': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3} Link IDs: {'rna2p': 4, None: 1} Not linked: pdbres="M7G F 0 " pdbres=" A F 1 " Chain: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 346 Classifications: {'RNA': 11} Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 460 Classifications: {'RNA': 14} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 10} Time building chain proxies: 6.35, per 1000 atoms: 0.17 Number of scatterers: 36290 At special positions: 0 Unit cell: (106.33, 141.05, 141.05, 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 128 16.00 P 32 15.00 O 3532 8.00 N 3202 7.00 C 11395 6.00 H 18001 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4138 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 25 sheets defined 47.0% alpha, 12.8% beta 6 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.759A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.739A pdb=" N VAL A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 126 through 138 removed outlier: 4.527A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.970A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.045A pdb=" N ARG A 192 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.643A pdb=" N ALA A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.631A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.932A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.637A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.506A pdb=" N TYR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.169A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.934A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.591A pdb=" N LYS A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.603A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 removed outlier: 3.782A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.534A pdb=" N ALA B 17 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.678A pdb=" N PHE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.723A pdb=" N VAL B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.672A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.613A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.589A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.752A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.552A pdb=" N MET B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 412 through 425 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 518 through 536 removed outlier: 3.651A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.555A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.760A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.684A pdb=" N VAL B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 677 Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.300A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.883A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.506A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 755 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.704A pdb=" N GLN C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.058A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.511A pdb=" N ILE C 63 " --> pdb=" O ASP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.836A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.508A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.978A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.530A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.640A pdb=" N VAL C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.584A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 564 removed outlier: 4.354A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.658A pdb=" N TYR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 709 through 713 removed outlier: 4.030A pdb=" N LEU C 713 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.338A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 147 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.434A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324 removed outlier: 10.294A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.768A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.571A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 184 Processing sheet with id=AB1, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 350 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 59 removed outlier: 4.823A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.670A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.848A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB9, first strand: chain 'C' and resid 323 through 325 Processing sheet with id=AC1, first strand: chain 'C' and resid 332 through 334 removed outlier: 6.123A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC4, first strand: chain 'C' and resid 497 through 498 removed outlier: 6.737A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC6, first strand: chain 'C' and resid 656 through 658 removed outlier: 5.761A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 694 through 699 removed outlier: 6.913A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 8.94 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 17970 1.03 - 1.22: 50 1.22 - 1.42: 7760 1.42 - 1.61: 10696 1.61 - 1.81: 228 Bond restraints: 36704 Sorted by residual: bond pdb=" C3' M7G F 0 " pdb=" C4' M7G F 0 " ideal model delta sigma weight residual 1.528 1.306 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C8 M7G F 0 " pdb=" N7 M7G F 0 " ideal model delta sigma weight residual 1.315 1.506 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C4' M7G F 0 " pdb=" O4' M7G F 0 " ideal model delta sigma weight residual 1.433 1.608 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C8 M7G F 0 " pdb=" N9 M7G F 0 " ideal model delta sigma weight residual 1.341 1.508 -0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C2 M7G F 0 " pdb=" N3 M7G F 0 " ideal model delta sigma weight residual 1.317 1.467 -0.150 2.00e-02 2.50e+03 5.62e+01 ... (remaining 36699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 64317 1.98 - 3.95: 1811 3.95 - 5.93: 152 5.93 - 7.91: 24 7.91 - 9.88: 4 Bond angle restraints: 66308 Sorted by residual: angle pdb=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 113.38 -3.98 8.00e-01 1.56e+00 2.47e+01 angle pdb=" O4' A D 7 " pdb=" C1' A D 7 " pdb=" N9 A D 7 " ideal model delta sigma weight residual 108.20 112.02 -3.82 8.00e-01 1.56e+00 2.28e+01 angle pdb=" N1 U F 5 " pdb=" C2 U F 5 " pdb=" O2 U F 5 " ideal model delta sigma weight residual 122.80 126.07 -3.27 7.00e-01 2.04e+00 2.18e+01 angle pdb=" O2 U F 5 " pdb=" C2 U F 5 " pdb=" N3 U F 5 " ideal model delta sigma weight residual 122.20 119.07 3.13 7.00e-01 2.04e+00 2.00e+01 angle pdb=" C2' A D 4 " pdb=" C1' A D 4 " pdb=" N9 A D 4 " ideal model delta sigma weight residual 112.00 116.84 -4.84 1.10e+00 8.26e-01 1.94e+01 ... (remaining 66303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 16627 34.80 - 69.59: 591 69.59 - 104.39: 31 104.39 - 139.19: 0 139.19 - 173.99: 2 Dihedral angle restraints: 17251 sinusoidal: 9817 harmonic: 7434 Sorted by residual: dihedral pdb=" O4' C F 4 " pdb=" C1' C F 4 " pdb=" N1 C F 4 " pdb=" C2 C F 4 " ideal model delta sinusoidal sigma weight residual -128.00 45.99 -173.99 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U F 3 " pdb=" C1' U F 3 " pdb=" N1 U F 3 " pdb=" C2 U F 3 " ideal model delta sinusoidal sigma weight residual -128.00 37.85 -165.85 1 1.70e+01 3.46e-03 6.54e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta harmonic sigma weight residual -180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 17248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1747 0.044 - 0.089: 806 0.089 - 0.133: 226 0.133 - 0.178: 27 0.178 - 0.222: 9 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C1' U E 11 " pdb=" O4' U E 11 " pdb=" C2' U E 11 " pdb=" N1 U E 11 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL B 170 " pdb=" CA VAL B 170 " pdb=" CG1 VAL B 170 " pdb=" CG2 VAL B 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C1' A D 4 " pdb=" O4' A D 4 " pdb=" C2' A D 4 " pdb=" N9 A D 4 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2812 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 464 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO C 465 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 465 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 465 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 4 " -0.038 2.00e-02 2.50e+03 1.59e-02 8.25e+00 pdb=" N9 A D 4 " 0.041 2.00e-02 2.50e+03 pdb=" C8 A D 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 4 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 4 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A D 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 4 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A D 4 " 0.001 2.00e-02 2.50e+03 pdb=" H8 A D 4 " 0.003 2.00e-02 2.50e+03 pdb=" H2 A D 4 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 393 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 394 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " 0.035 5.00e-02 4.00e+02 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 125 1.92 - 2.59: 40310 2.59 - 3.26: 104816 3.26 - 3.93: 135968 3.93 - 4.60: 223286 Nonbonded interactions: 504505 Sorted by model distance: nonbonded pdb=" O3B M7G F 0 " pdb=" OP2 A F 1 " model vdw 1.252 2.800 nonbonded pdb=" O3B M7G F 0 " pdb=" P A F 1 " model vdw 1.583 3.200 nonbonded pdb=" O LEU A 655 " pdb=" HG SER A 659 " model vdw 1.646 2.450 nonbonded pdb=" OD1 ASN B 276 " pdb="HH11 ARG C 142 " model vdw 1.663 2.450 nonbonded pdb=" O PHE A 658 " pdb=" HG SER A 662 " model vdw 1.672 2.450 ... (remaining 504500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.260 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 40.910 Find NCS groups from input model: 0.240 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.010 0.222 18703 Z= 0.415 Angle : 0.879 9.882 25368 Z= 0.492 Chirality : 0.053 0.222 2815 Planarity : 0.006 0.078 3163 Dihedral : 15.817 173.986 7367 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: -3.62 (0.15), residues: 2189 helix: -1.82 (0.14), residues: 927 sheet: -2.36 (0.27), residues: 274 loop : -2.95 (0.16), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 663 TYR 0.020 0.002 TYR A 540 PHE 0.022 0.002 PHE A 520 TRP 0.017 0.002 TRP A 368 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.42 (18703) covalent geometry : angle 0.87938 / 0.49 (25368) hydrogen bonds : bond 0.14401 / 9.34 ( 815) hydrogen bonds : angle 6.04579 / 4.21 ( 2243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ILE cc_start: 0.8185 (pt) cc_final: 0.7975 (mm) REVERT: C 1 MET cc_start: 0.6481 (tpp) cc_final: 0.6256 (tpt) REVERT: C 177 LEU cc_start: 0.7973 (mt) cc_final: 0.7679 (mp) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.4622 time to fit residues: 235.8434 Evaluate side-chains 268 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN A 142 ASN A 217 GLN A 228 ASN B 137 GLN B 153 ASN B 642 ASN C 540 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129785 restraints weight = 58169.308| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.63 r_work: 0.3204 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18703 Z= 0.135 Angle : 0.595 5.090 25368 Z= 0.320 Chirality : 0.040 0.166 2815 Planarity : 0.005 0.085 3163 Dihedral : 11.835 174.697 2888 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.46 % Allowed : 7.44 % Favored : 92.10 % 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: -2.44 (0.16), residues: 2189 helix: -0.55 (0.16), residues: 935 sheet: -2.00 (0.28), residues: 273 loop : -2.57 (0.17), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 721 TYR 0.011 0.001 TYR C 34 PHE 0.014 0.001 PHE B 185 TRP 0.010 0.001 TRP C 78 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (18703) covalent geometry : angle 0.59487 / 0.32 (25368) hydrogen bonds : bond 0.05792 / 3.81 ( 815) hydrogen bonds : angle 4.91943 / 3.46 ( 2243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 279 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ILE cc_start: 0.8374 (pt) cc_final: 0.8086 (mm) REVERT: B 179 MET cc_start: 0.7582 (tpt) cc_final: 0.7322 (tpt) REVERT: B 232 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6532 (mt-10) REVERT: C 241 GLU cc_start: 0.7594 (tt0) cc_final: 0.7222 (mp0) REVERT: C 300 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6726 (mp10) outliers start: 9 outliers final: 6 residues processed: 284 average time/residue: 0.3907 time to fit residues: 158.1283 Evaluate side-chains 273 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 266 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 132 optimal weight: 0.0070 chunk 161 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 228 ASN B 137 GLN B 306 ASN B 485 ASN C 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127274 restraints weight = 58701.656| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.39 r_work: 0.3212 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18703 Z= 0.148 Angle : 0.559 12.374 25368 Z= 0.298 Chirality : 0.040 0.158 2815 Planarity : 0.005 0.054 3163 Dihedral : 11.591 174.734 2888 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.82 % Allowed : 8.72 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2189 helix: 0.06 (0.17), residues: 943 sheet: -1.71 (0.29), residues: 274 loop : -2.29 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.011 0.001 TYR C 360 PHE 0.019 0.001 PHE A 191 TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (18703) covalent geometry : angle 0.55940 / 0.30 (25368) hydrogen bonds : bond 0.05135 / 3.40 ( 815) hydrogen bonds : angle 4.59787 / 3.24 ( 2243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 621 ILE cc_start: 0.8505 (pt) cc_final: 0.8196 (mm) REVERT: B 179 MET cc_start: 0.7849 (tpt) cc_final: 0.7516 (tpt) REVERT: B 232 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6537 (mt-10) outliers start: 16 outliers final: 10 residues processed: 275 average time/residue: 0.4212 time to fit residues: 164.8443 Evaluate side-chains 271 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 260 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 138 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN B 485 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118703 restraints weight = 59327.302| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.51 r_work: 0.3002 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18703 Z= 0.244 Angle : 0.622 5.626 25368 Z= 0.335 Chirality : 0.044 0.169 2815 Planarity : 0.005 0.055 3163 Dihedral : 11.658 174.041 2888 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.87 % Allowed : 9.85 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.17), residues: 2189 helix: 0.09 (0.17), residues: 941 sheet: -1.61 (0.29), residues: 276 loop : -2.19 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.015 0.002 TYR B 559 PHE 0.018 0.002 PHE B 185 TRP 0.012 0.002 TRP A 368 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.24 (18703) covalent geometry : angle 0.62215 / 0.34 (25368) hydrogen bonds : bond 0.06011 / 4.00 ( 815) hydrogen bonds : angle 4.65338 / 3.27 ( 2243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 266 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (mt) REVERT: A 248 GLN cc_start: 0.8691 (mt0) cc_final: 0.8490 (mt0) REVERT: A 424 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7094 (pt0) REVERT: A 512 ARG cc_start: 0.6998 (mmm160) cc_final: 0.6797 (mmm160) REVERT: A 579 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8282 (ttt) REVERT: A 621 ILE cc_start: 0.8673 (pt) cc_final: 0.8304 (mm) REVERT: B 179 MET cc_start: 0.8061 (tpt) cc_final: 0.7670 (tpt) REVERT: C 300 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: C 648 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8599 (mt) outliers start: 17 outliers final: 12 residues processed: 275 average time/residue: 0.4047 time to fit residues: 159.4673 Evaluate side-chains 263 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 247 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 187 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124429 restraints weight = 59044.621| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.44 r_work: 0.3065 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18703 Z= 0.165 Angle : 0.555 5.802 25368 Z= 0.300 Chirality : 0.041 0.262 2815 Planarity : 0.005 0.060 3163 Dihedral : 11.552 174.451 2888 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.82 % Allowed : 10.82 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2189 helix: 0.37 (0.17), residues: 941 sheet: -1.57 (0.29), residues: 276 loop : -2.06 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 170 TYR 0.011 0.001 TYR B 559 PHE 0.013 0.001 PHE A 520 TRP 0.010 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (18703) covalent geometry : angle 0.55514 / 0.30 (25368) hydrogen bonds : bond 0.05277 / 3.50 ( 815) hydrogen bonds : angle 4.51098 / 3.17 ( 2243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 621 ILE cc_start: 0.8631 (pt) cc_final: 0.8287 (mm) REVERT: B 92 MET cc_start: 0.8537 (mmm) cc_final: 0.7604 (mmp) REVERT: B 179 MET cc_start: 0.8080 (tpt) cc_final: 0.7640 (tpt) REVERT: B 287 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7722 (ttm110) REVERT: B 691 LYS cc_start: 0.8437 (mttt) cc_final: 0.8219 (mttm) REVERT: C 300 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: C 648 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8599 (mt) outliers start: 16 outliers final: 10 residues processed: 267 average time/residue: 0.4040 time to fit residues: 154.3891 Evaluate side-chains 263 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 250 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.0000 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.153421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124118 restraints weight = 59255.795| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.42 r_work: 0.3080 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18703 Z= 0.122 Angle : 0.513 5.639 25368 Z= 0.276 Chirality : 0.039 0.157 2815 Planarity : 0.004 0.055 3163 Dihedral : 11.374 174.644 2888 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.82 % Allowed : 11.28 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2189 helix: 0.69 (0.17), residues: 943 sheet: -1.47 (0.29), residues: 276 loop : -1.92 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.020 0.001 TYR A 305 PHE 0.013 0.001 PHE B 185 TRP 0.009 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (18703) covalent geometry : angle 0.51261 / 0.28 (25368) hydrogen bonds : bond 0.04626 / 3.06 ( 815) hydrogen bonds : angle 4.33810 / 3.04 ( 2243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 523 MET cc_start: 0.8835 (mtt) cc_final: 0.8623 (mtt) REVERT: A 579 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8143 (ttt) REVERT: B 92 MET cc_start: 0.8487 (mmm) cc_final: 0.7623 (mmp) REVERT: B 179 MET cc_start: 0.8139 (tpt) cc_final: 0.7688 (tpt) REVERT: B 523 MET cc_start: 0.8084 (tpt) cc_final: 0.7883 (tpt) REVERT: B 691 LYS cc_start: 0.8407 (mttt) cc_final: 0.8194 (mttm) REVERT: C 300 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: C 648 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8643 (mt) outliers start: 16 outliers final: 11 residues processed: 262 average time/residue: 0.4197 time to fit residues: 157.2928 Evaluate side-chains 265 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 141 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114194 restraints weight = 60536.620| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.63 r_work: 0.3048 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18703 Z= 0.126 Angle : 0.507 5.710 25368 Z= 0.273 Chirality : 0.039 0.156 2815 Planarity : 0.004 0.054 3163 Dihedral : 11.289 174.442 2888 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.97 % Allowed : 11.49 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.17), residues: 2189 helix: 0.84 (0.17), residues: 943 sheet: -1.39 (0.29), residues: 276 loop : -1.83 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.011 0.001 TYR A 305 PHE 0.014 0.001 PHE B 185 TRP 0.008 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18703) covalent geometry : angle 0.50651 / 0.27 (25368) hydrogen bonds : bond 0.04497 / 2.98 ( 815) hydrogen bonds : angle 4.26227 / 2.99 ( 2243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8699 (mt0) cc_final: 0.8468 (mt0) REVERT: A 523 MET cc_start: 0.8915 (mtt) cc_final: 0.8709 (mtt) REVERT: A 579 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8199 (ttt) REVERT: B 92 MET cc_start: 0.8524 (mmm) cc_final: 0.7692 (mmp) REVERT: B 691 LYS cc_start: 0.8282 (mttt) cc_final: 0.8029 (mttm) REVERT: C 51 MET cc_start: 0.8979 (mmp) cc_final: 0.8608 (mmp) REVERT: C 300 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: C 648 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8602 (mt) outliers start: 19 outliers final: 12 residues processed: 265 average time/residue: 0.4040 time to fit residues: 154.7194 Evaluate side-chains 262 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 247 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 648 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 160 optimal weight: 5.9990 chunk 151 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 97 optimal weight: 0.0570 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123981 restraints weight = 59260.462| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.39 r_work: 0.3149 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18703 Z= 0.094 Angle : 0.480 6.734 25368 Z= 0.257 Chirality : 0.038 0.152 2815 Planarity : 0.004 0.048 3163 Dihedral : 11.162 174.641 2888 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.46 % Allowed : 12.26 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2189 helix: 1.12 (0.17), residues: 943 sheet: -1.28 (0.30), residues: 266 loop : -1.66 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 204 TYR 0.009 0.001 TYR C 360 PHE 0.012 0.001 PHE B 185 TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (18703) covalent geometry : angle 0.47997 / 0.26 (25368) hydrogen bonds : bond 0.03954 / 2.61 ( 815) hydrogen bonds : angle 4.12595 / 2.89 ( 2243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 257 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8724 (mt0) cc_final: 0.8474 (mt0) REVERT: A 309 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8395 (mtmt) REVERT: A 523 MET cc_start: 0.8817 (mtt) cc_final: 0.8584 (mtt) REVERT: B 92 MET cc_start: 0.8450 (mmm) cc_final: 0.7655 (mmp) REVERT: B 523 MET cc_start: 0.8019 (tpt) cc_final: 0.7799 (tpt) REVERT: B 691 LYS cc_start: 0.8348 (mttt) cc_final: 0.8116 (mttm) REVERT: C 51 MET cc_start: 0.8919 (mmp) cc_final: 0.8514 (mmp) REVERT: C 300 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: C 628 GLN cc_start: 0.7225 (mm110) cc_final: 0.6909 (mm-40) outliers start: 9 outliers final: 7 residues processed: 260 average time/residue: 0.4282 time to fit residues: 158.7850 Evaluate side-chains 257 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 249 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 202 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115227 restraints weight = 60502.952| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.60 r_work: 0.3019 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18703 Z= 0.154 Angle : 0.511 6.296 25368 Z= 0.274 Chirality : 0.039 0.156 2815 Planarity : 0.004 0.050 3163 Dihedral : 11.197 174.021 2888 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.62 % Allowed : 12.10 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 2189 helix: 1.03 (0.17), residues: 943 sheet: -1.27 (0.29), residues: 276 loop : -1.68 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 204 TYR 0.021 0.001 TYR A 305 PHE 0.013 0.001 PHE B 185 TRP 0.008 0.001 TRP A 368 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (18703) covalent geometry : angle 0.51094 / 0.27 (25368) hydrogen bonds : bond 0.04509 / 3.00 ( 815) hydrogen bonds : angle 4.18518 / 2.93 ( 2243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 249 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8734 (mt0) cc_final: 0.8490 (mt0) REVERT: A 309 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8300 (mtmt) REVERT: A 523 MET cc_start: 0.8959 (mtt) cc_final: 0.8751 (mtt) REVERT: A 579 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8228 (ttt) REVERT: B 92 MET cc_start: 0.8540 (mmm) cc_final: 0.7734 (mmp) REVERT: B 117 THR cc_start: 0.8814 (t) cc_final: 0.8590 (m) REVERT: B 523 MET cc_start: 0.8198 (tpt) cc_final: 0.7987 (tpt) REVERT: B 691 LYS cc_start: 0.8286 (mttt) cc_final: 0.8019 (mttm) REVERT: B 706 ARG cc_start: 0.7995 (mmm-85) cc_final: 0.7411 (mtm-85) REVERT: C 51 MET cc_start: 0.8998 (mmp) cc_final: 0.8599 (mmp) REVERT: C 300 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6891 (mp10) REVERT: C 628 GLN cc_start: 0.7282 (mm110) cc_final: 0.6982 (mm-40) outliers start: 12 outliers final: 10 residues processed: 253 average time/residue: 0.4184 time to fit residues: 151.5586 Evaluate side-chains 258 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 70 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 196 optimal weight: 0.0980 chunk 189 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116153 restraints weight = 60439.673| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.72 r_work: 0.3000 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18703 Z= 0.122 Angle : 0.496 5.594 25368 Z= 0.266 Chirality : 0.039 0.160 2815 Planarity : 0.004 0.051 3163 Dihedral : 11.184 174.012 2888 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.62 % Allowed : 12.15 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2189 helix: 1.07 (0.17), residues: 950 sheet: -1.21 (0.29), residues: 276 loop : -1.63 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 204 TYR 0.009 0.001 TYR C 360 PHE 0.013 0.001 PHE B 185 TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (18703) covalent geometry : angle 0.49562 / 0.27 (25368) hydrogen bonds : bond 0.04315 / 2.86 ( 815) hydrogen bonds : angle 4.15020 / 2.90 ( 2243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4378 Ramachandran restraints generated. 2189 Oldfield, 0 Emsley, 2189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 250 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLN cc_start: 0.8724 (mt0) cc_final: 0.8467 (mt0) REVERT: A 309 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8194 (mtmt) REVERT: A 579 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8226 (ttt) REVERT: B 92 MET cc_start: 0.8547 (mmm) cc_final: 0.7760 (mmp) REVERT: B 117 THR cc_start: 0.8746 (t) cc_final: 0.8523 (m) REVERT: B 523 MET cc_start: 0.8226 (tpt) cc_final: 0.8015 (tpt) REVERT: B 691 LYS cc_start: 0.8171 (mttt) cc_final: 0.7887 (mttm) REVERT: B 706 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7367 (mtm-85) REVERT: C 51 MET cc_start: 0.9017 (mmp) cc_final: 0.8645 (mmp) REVERT: C 300 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: C 315 MET cc_start: 0.7927 (mtt) cc_final: 0.7581 (mtt) REVERT: C 628 GLN cc_start: 0.7283 (mm110) cc_final: 0.6993 (mm-40) outliers start: 12 outliers final: 10 residues processed: 254 average time/residue: 0.4220 time to fit residues: 153.3939 Evaluate side-chains 260 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 248 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 409 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 198 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114935 restraints weight = 60247.832| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.74 r_work: 0.3028 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18703 Z= 0.159 Angle : 0.520 5.528 25368 Z= 0.279 Chirality : 0.040 0.160 2815 Planarity : 0.004 0.050 3163 Dihedral : 11.238 173.534 2888 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.72 % Allowed : 12.15 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2189 helix: 0.97 (0.17), residues: 951 sheet: -1.21 (0.29), residues: 277 loop : -1.65 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 204 TYR 0.010 0.001 TYR C 360 PHE 0.013 0.001 PHE A 191 TRP 0.008 0.001 TRP A 368 HIS 0.003 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (18703) covalent geometry : angle 0.51965 / 0.28 (25368) hydrogen bonds : bond 0.04673 / 3.11 ( 815) hydrogen bonds : angle 4.20995 / 2.94 ( 2243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9458.31 seconds wall clock time: 160 minutes 59.57 seconds (9659.57 seconds total)