Starting phenix.real_space_refine on Fri Mar 6 21:02:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nhx_12342/03_2026/7nhx_12342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhx_12342/03_2026/7nhx_12342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nhx_12342/03_2026/7nhx_12342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhx_12342/03_2026/7nhx_12342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nhx_12342/03_2026/7nhx_12342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhx_12342/03_2026/7nhx_12342.map" } resolution = 3.23 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= 0.002 sd= 0.018 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 23 5.49 5 S 123 5.16 5 C 10942 2.51 5 N 3070 2.21 5 O 3354 1.98 5 H 17149 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34661 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 11619 Classifications: {'peptide': 729} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 698} Chain breaks: 2 Chain: "C" Number of atoms: 10772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 10772 Classifications: {'peptide': 676} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 5.20, per 1000 atoms: 0.15 Number of scatterers: 34661 At special positions: 0 Unit cell: (130.35, 105.6, 146.85, 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 123 16.00 P 23 15.00 O 3354 8.00 N 3070 7.00 C 10942 6.00 H 17149 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: 2.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 24 sheets defined 50.1% alpha, 12.2% beta 3 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.757A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.103A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.512A pdb=" N ALA A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 4.050A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.238A 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: 3.894A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.839A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.967A pdb=" N GLU A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.634A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.665A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (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 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.366A 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: 4.017A 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: 3.639A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.671A 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: 3.669A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 removed outlier: 3.628A 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 4 through 11 Processing helix chain 'B' and resid 17 through 22 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 124 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 174 removed outlier: 3.911A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.207A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.576A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.587A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.522A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.824A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 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 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.792A pdb=" N LYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.758A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.582A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.514A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.786A pdb=" N LYS B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.681A pdb=" N VAL B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.628A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.264A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.146A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.019A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.602A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.061A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.789A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.709A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.721A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.533A pdb=" N VAL C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (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: 3.652A 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 450 removed outlier: 4.789A pdb=" N GLY C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 460 removed outlier: 3.960A pdb=" N GLY C 459 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 564 removed outlier: 4.352A 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 583 removed outlier: 3.537A pdb=" N LEU C 583 " --> pdb=" O PRO C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 4.613A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) removed outlier: 3.604A 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 sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.767A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.819A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.710A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.828A pdb=" N ASN A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.062A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 619 through 623 removed outlier: 6.094A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (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 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 185 removed outlier: 3.532A pdb=" N GLY B 206 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.901A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 4.543A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AB9, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AC1, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.142A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (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 removed outlier: 3.738A pdb=" N SER C 474 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 504 through 505 removed outlier: 6.496A 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 657 through 658 removed outlier: 5.925A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17119 1.00 - 1.21: 30 1.21 - 1.41: 7229 1.41 - 1.62: 10454 1.62 - 1.82: 216 Bond restraints: 35048 Sorted by residual: bond pdb=" NE2 GLN C 581 " pdb="HE22 GLN C 581 " ideal model delta sigma weight residual 0.860 0.800 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 0.860 0.804 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" ND2 ASN C 422 " pdb="HD22 ASN C 422 " ideal model delta sigma weight residual 0.860 0.822 0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" CB PRO C 453 " pdb=" CG PRO C 453 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" ND2 ASN C 540 " pdb="HD22 ASN C 540 " ideal model delta sigma weight residual 0.860 0.828 0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 35043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.29: 63248 7.29 - 14.57: 8 14.57 - 21.86: 4 21.86 - 29.15: 0 29.15 - 36.44: 3 Bond angle restraints: 63263 Sorted by residual: angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 73.56 36.44 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 74.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 109.00 73.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CD GLN C 426 " pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 120.00 140.88 -20.88 3.00e+00 1.11e-01 4.84e+01 angle pdb="HE21 GLN C 426 " pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 120.00 99.17 20.83 3.00e+00 1.11e-01 4.82e+01 ... (remaining 63258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14762 17.98 - 35.96: 1268 35.96 - 53.95: 310 53.95 - 71.93: 108 71.93 - 89.91: 23 Dihedral angle restraints: 16471 sinusoidal: 9309 harmonic: 7162 Sorted by residual: dihedral pdb=" CA GLN A 180 " pdb=" C GLN A 180 " pdb=" N GLU A 181 " pdb=" CA GLU A 181 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+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 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL A 127 " pdb=" C VAL A 127 " pdb=" N HIS A 128 " pdb=" CA HIS A 128 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 16468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2236 0.054 - 0.109: 376 0.109 - 0.163: 68 0.163 - 0.217: 3 0.217 - 0.272: 2 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CG LEU C 183 " pdb=" CB LEU C 183 " pdb=" CD1 LEU C 183 " pdb=" CD2 LEU C 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA MET C 536 " pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CB MET C 536 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LYS C 187 " pdb=" N LYS C 187 " pdb=" C LYS C 187 " pdb=" CB LYS C 187 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2682 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 581 " 0.067 2.00e-02 2.50e+03 9.58e-02 1.38e+02 pdb=" CD GLN C 581 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 581 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN C 581 " -0.158 2.00e-02 2.50e+03 pdb="HE21 GLN C 581 " -0.026 2.00e-02 2.50e+03 pdb="HE22 GLN C 581 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 422 " -0.048 2.00e-02 2.50e+03 9.22e-02 1.27e+02 pdb=" CG ASN C 422 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 422 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 422 " -0.156 2.00e-02 2.50e+03 pdb="HD21 ASN C 422 " -0.027 2.00e-02 2.50e+03 pdb="HD22 ASN C 422 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 426 " 0.049 2.00e-02 2.50e+03 9.19e-02 1.27e+02 pdb=" CD GLN C 426 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN C 426 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN C 426 " -0.161 2.00e-02 2.50e+03 pdb="HE21 GLN C 426 " -0.035 2.00e-02 2.50e+03 pdb="HE22 GLN C 426 " 0.145 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 935 2.12 - 2.74: 61900 2.74 - 3.36: 99780 3.36 - 3.98: 127647 3.98 - 4.60: 201966 Nonbonded interactions: 492228 Sorted by model distance: nonbonded pdb="HH12 ARG B 706 " pdb=" OE1 GLN C 160 " model vdw 1.496 2.450 nonbonded pdb=" OD2 ASP C 499 " pdb="HH21 ARG C 503 " model vdw 1.506 2.450 nonbonded pdb=" H ASN A 513 " pdb=" OD2 ASP A 516 " model vdw 1.511 2.450 nonbonded pdb=" OD1 ASN B 136 " pdb="HD21 ASN B 225 " model vdw 1.534 2.450 nonbonded pdb="HD22 ASN B 676 " pdb=" O4' U E 5 " model vdw 1.541 2.450 ... (remaining 492223 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: 1.290 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: 0.150 Extract box with map and model: 0.390 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.780 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.003 0.087 17899 Z= 0.134 Angle : 0.679 10.272 24248 Z= 0.369 Chirality : 0.043 0.272 2685 Planarity : 0.006 0.121 3046 Dihedral : 15.183 89.912 6991 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.68 (0.16), residues: 2111 helix: -0.99 (0.14), residues: 945 sheet: -2.70 (0.29), residues: 243 loop : -2.28 (0.17), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 192 TYR 0.023 0.001 TYR B 30 PHE 0.019 0.001 PHE C 323 TRP 0.024 0.001 TRP C 537 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00300 (17899) covalent geometry : angle 0.67852 (24248) hydrogen bonds : bond 0.13744 ( 819) hydrogen bonds : angle 6.58132 ( 2272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.938 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: 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 51 PHE cc_start: 0.6805 (m-10) cc_final: 0.6586 (m-10) REVERT: C 365 MET cc_start: 0.3947 (mpp) cc_final: 0.3452 (mtm) REVERT: C 402 MET cc_start: 0.3536 (mmp) cc_final: 0.2988 (mtt) REVERT: C 473 MET cc_start: 0.7354 (ttp) cc_final: 0.7097 (tmm) REVERT: C 475 MET cc_start: -0.1992 (mmm) cc_final: -0.3024 (mmm) REVERT: C 611 ASP cc_start: 0.7035 (m-30) cc_final: 0.6358 (m-30) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.4098 time to fit residues: 164.2245 Evaluate side-chains 186 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 437 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.102143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.068757 restraints weight = 129826.579| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.28 r_work: 0.3020 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17899 Z= 0.205 Angle : 0.597 7.339 24248 Z= 0.323 Chirality : 0.040 0.334 2685 Planarity : 0.005 0.072 3046 Dihedral : 9.610 73.264 2670 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.69 % Allowed : 6.22 % Favored : 93.09 % 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: -1.20 (0.17), residues: 2111 helix: 0.52 (0.16), residues: 951 sheet: -2.18 (0.30), residues: 252 loop : -1.80 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 706 TYR 0.017 0.001 TYR B 555 PHE 0.019 0.001 PHE C 330 TRP 0.017 0.001 TRP C 537 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00453 (17899) covalent geometry : angle 0.59722 (24248) hydrogen bonds : bond 0.04396 ( 819) hydrogen bonds : angle 5.03550 ( 2272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.761 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8177 (m-10) cc_final: 0.7972 (m-10) REVERT: A 441 MET cc_start: 0.8634 (tpp) cc_final: 0.8394 (tpp) REVERT: B 603 ASN cc_start: 0.8857 (m-40) cc_final: 0.8550 (m110) REVERT: C 365 MET cc_start: 0.3885 (mpp) cc_final: 0.3454 (mtm) REVERT: C 402 MET cc_start: 0.3592 (mmp) cc_final: 0.3064 (mtt) REVERT: C 475 MET cc_start: -0.2345 (mmm) cc_final: -0.2996 (mmm) REVERT: C 646 ARG cc_start: 0.7271 (ppt170) cc_final: 0.6849 (ppt170) outliers start: 13 outliers final: 5 residues processed: 197 average time/residue: 0.3566 time to fit residues: 101.1863 Evaluate side-chains 174 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 18 optimal weight: 20.0000 chunk 205 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 102 optimal weight: 0.0770 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 = 0.3815 r_free = 0.3815 target = 0.101586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068086 restraints weight = 129667.191| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.26 r_work: 0.3003 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17899 Z= 0.153 Angle : 0.526 7.862 24248 Z= 0.281 Chirality : 0.038 0.343 2685 Planarity : 0.004 0.054 3046 Dihedral : 9.481 73.484 2670 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 0.48 % Allowed : 6.64 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.18), residues: 2111 helix: 1.00 (0.17), residues: 954 sheet: -1.65 (0.32), residues: 234 loop : -1.59 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 493 TYR 0.014 0.001 TYR B 555 PHE 0.014 0.001 PHE C 595 TRP 0.015 0.001 TRP C 537 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00337 (17899) covalent geometry : angle 0.52597 (24248) hydrogen bonds : bond 0.03999 ( 819) hydrogen bonds : angle 4.57805 ( 2272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 1.062 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7994 (ppp) cc_final: 0.7794 (ppp) REVERT: A 51 PHE cc_start: 0.8209 (m-10) cc_final: 0.7995 (m-10) REVERT: A 155 MET cc_start: 0.8403 (ptm) cc_final: 0.8114 (ptm) REVERT: A 441 MET cc_start: 0.8616 (tpp) cc_final: 0.8411 (tpp) REVERT: C 325 PHE cc_start: 0.6421 (t80) cc_final: 0.6037 (t80) REVERT: C 402 MET cc_start: 0.3569 (mmp) cc_final: 0.2991 (mtt) REVERT: C 475 MET cc_start: -0.2625 (mmm) cc_final: -0.3149 (mmm) REVERT: C 646 ARG cc_start: 0.7359 (ppt170) cc_final: 0.6959 (ppt170) outliers start: 9 outliers final: 6 residues processed: 178 average time/residue: 0.3352 time to fit residues: 88.0923 Evaluate side-chains 169 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 530 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 29 optimal weight: 5.9990 chunk 170 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 176 optimal weight: 30.0000 chunk 209 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 510 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.098579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.064833 restraints weight = 131122.051| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.25 r_work: 0.2925 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17899 Z= 0.259 Angle : 0.574 6.929 24248 Z= 0.311 Chirality : 0.040 0.343 2685 Planarity : 0.004 0.045 3046 Dihedral : 9.628 73.890 2670 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.74 % Allowed : 7.23 % Favored : 92.03 % 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: -0.38 (0.18), residues: 2111 helix: 1.16 (0.17), residues: 939 sheet: -1.46 (0.32), residues: 235 loop : -1.39 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.014 0.002 TYR B 555 PHE 0.027 0.001 PHE C 580 TRP 0.016 0.001 TRP C 537 HIS 0.007 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00571 (17899) covalent geometry : angle 0.57423 (24248) hydrogen bonds : bond 0.04294 ( 819) hydrogen bonds : angle 4.72195 ( 2272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.995 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: symmetry clash REVERT: A 155 MET cc_start: 0.8358 (ptm) cc_final: 0.8100 (ptm) REVERT: A 549 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8370 (pt) REVERT: B 289 MET cc_start: 0.8845 (mmt) cc_final: 0.8532 (mmm) REVERT: B 655 MET cc_start: 0.8569 (tpp) cc_final: 0.8321 (tpp) REVERT: C 365 MET cc_start: 0.4384 (mpp) cc_final: 0.4042 (mtm) REVERT: C 402 MET cc_start: 0.3512 (mmp) cc_final: 0.2979 (mtt) REVERT: C 475 MET cc_start: -0.2753 (mmm) cc_final: -0.3171 (mmm) REVERT: C 570 MET cc_start: 0.8161 (tpp) cc_final: 0.7908 (tpp) REVERT: C 646 ARG cc_start: 0.7462 (ppt170) cc_final: 0.7070 (ppt170) outliers start: 14 outliers final: 10 residues processed: 175 average time/residue: 0.3170 time to fit residues: 82.4540 Evaluate side-chains 163 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 671 ASN C 138 GLN C 236 GLN ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064691 restraints weight = 130781.279| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.26 r_work: 0.2923 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17899 Z= 0.218 Angle : 0.545 8.973 24248 Z= 0.291 Chirality : 0.040 0.349 2685 Planarity : 0.004 0.040 3046 Dihedral : 9.579 75.421 2670 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 0.58 % Allowed : 8.87 % Favored : 90.54 % 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: -0.23 (0.18), residues: 2111 helix: 1.28 (0.17), residues: 941 sheet: -1.30 (0.33), residues: 232 loop : -1.35 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.012 0.001 TYR B 555 PHE 0.017 0.001 PHE A 105 TRP 0.013 0.001 TRP C 537 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00485 (17899) covalent geometry : angle 0.54519 (24248) hydrogen bonds : bond 0.04024 ( 819) hydrogen bonds : angle 4.56701 ( 2272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.956 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: A 549 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8429 (pt) REVERT: B 655 MET cc_start: 0.8594 (tpp) cc_final: 0.8334 (tpp) REVERT: C 402 MET cc_start: 0.3601 (mmp) cc_final: 0.2980 (mtt) REVERT: C 475 MET cc_start: -0.2654 (mmm) cc_final: -0.3141 (mmm) REVERT: C 570 MET cc_start: 0.8260 (tpp) cc_final: 0.7989 (tpp) REVERT: C 646 ARG cc_start: 0.7426 (ppt170) cc_final: 0.7001 (ppt170) REVERT: C 675 LEU cc_start: 0.8123 (tt) cc_final: 0.7517 (mp) outliers start: 11 outliers final: 7 residues processed: 163 average time/residue: 0.3133 time to fit residues: 76.7196 Evaluate side-chains 158 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 162 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.100721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067012 restraints weight = 128949.833| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.26 r_work: 0.2982 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17899 Z= 0.095 Angle : 0.492 12.582 24248 Z= 0.257 Chirality : 0.038 0.353 2685 Planarity : 0.004 0.039 3046 Dihedral : 9.380 75.321 2670 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 0.37 % Allowed : 9.25 % Favored : 90.38 % 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: 0.09 (0.18), residues: 2111 helix: 1.54 (0.17), residues: 950 sheet: -0.96 (0.35), residues: 217 loop : -1.25 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.010 0.001 TYR B 217 PHE 0.011 0.001 PHE C 438 TRP 0.011 0.001 TRP C 537 HIS 0.003 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00211 (17899) covalent geometry : angle 0.49213 (24248) hydrogen bonds : bond 0.03494 ( 819) hydrogen bonds : angle 4.19300 ( 2272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.919 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: A 1 MET cc_start: 0.7953 (ppp) cc_final: 0.7731 (ppp) REVERT: A 549 LEU cc_start: 0.8898 (mp) cc_final: 0.8414 (pt) REVERT: B 289 MET cc_start: 0.8740 (mmt) cc_final: 0.8458 (mmm) REVERT: C 285 HIS cc_start: 0.8051 (m-70) cc_final: 0.7751 (m-70) REVERT: C 365 MET cc_start: 0.4530 (mpp) cc_final: 0.4125 (mtm) REVERT: C 402 MET cc_start: 0.3595 (mmp) cc_final: 0.3034 (mtt) REVERT: C 475 MET cc_start: -0.2855 (mmm) cc_final: -0.3290 (mmm) REVERT: C 570 MET cc_start: 0.8371 (tpp) cc_final: 0.8108 (tpp) REVERT: C 646 ARG cc_start: 0.7475 (ppt170) cc_final: 0.7080 (ppt170) REVERT: C 675 LEU cc_start: 0.8126 (tt) cc_final: 0.7523 (mp) outliers start: 7 outliers final: 7 residues processed: 157 average time/residue: 0.3147 time to fit residues: 75.0871 Evaluate side-chains 157 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 181 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.098420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064444 restraints weight = 130522.650| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.28 r_work: 0.2917 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17899 Z= 0.223 Angle : 0.526 10.534 24248 Z= 0.281 Chirality : 0.039 0.346 2685 Planarity : 0.004 0.036 3046 Dihedral : 9.459 77.169 2670 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 0.48 % Allowed : 9.51 % Favored : 90.01 % 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: 0.11 (0.18), residues: 2111 helix: 1.56 (0.17), residues: 940 sheet: -0.95 (0.35), residues: 215 loop : -1.22 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.013 0.001 TYR B 555 PHE 0.023 0.001 PHE B 185 TRP 0.012 0.001 TRP C 537 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd covalent geometry : bond 0.00494 (17899) covalent geometry : angle 0.52607 (24248) hydrogen bonds : bond 0.03834 ( 819) hydrogen bonds : angle 4.40203 ( 2272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.838 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: A 549 LEU cc_start: 0.8931 (mp) cc_final: 0.8466 (pt) REVERT: B 289 MET cc_start: 0.8864 (mmt) cc_final: 0.8591 (mmm) REVERT: B 638 GLU cc_start: 0.8796 (tp30) cc_final: 0.8480 (tp30) REVERT: C 285 HIS cc_start: 0.8080 (m-70) cc_final: 0.7784 (m-70) REVERT: C 365 MET cc_start: 0.4608 (mpp) cc_final: 0.4358 (mtm) REVERT: C 402 MET cc_start: 0.3719 (mmp) cc_final: 0.3204 (mtt) REVERT: C 475 MET cc_start: -0.2934 (mmm) cc_final: -0.3364 (mmm) REVERT: C 570 MET cc_start: 0.8378 (tpp) cc_final: 0.8102 (tpp) REVERT: C 646 ARG cc_start: 0.7440 (ppt170) cc_final: 0.7030 (ppt170) REVERT: C 675 LEU cc_start: 0.8140 (tt) cc_final: 0.7558 (mp) outliers start: 9 outliers final: 9 residues processed: 157 average time/residue: 0.3049 time to fit residues: 72.9417 Evaluate side-chains 159 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 15 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 187 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065046 restraints weight = 130143.095| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.32 r_work: 0.2931 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17899 Z= 0.156 Angle : 0.503 10.573 24248 Z= 0.266 Chirality : 0.038 0.349 2685 Planarity : 0.004 0.036 3046 Dihedral : 9.445 77.888 2670 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 0.37 % Allowed : 9.94 % Favored : 89.69 % 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: 0.14 (0.18), residues: 2111 helix: 1.55 (0.17), residues: 951 sheet: -0.85 (0.35), residues: 215 loop : -1.21 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.011 0.001 TYR B 217 PHE 0.019 0.001 PHE C 438 TRP 0.011 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00346 (17899) covalent geometry : angle 0.50344 (24248) hydrogen bonds : bond 0.03671 ( 819) hydrogen bonds : angle 4.27212 ( 2272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.946 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: A 137 LYS cc_start: 0.9595 (tppt) cc_final: 0.9349 (tppt) REVERT: A 549 LEU cc_start: 0.8960 (mp) cc_final: 0.8504 (pt) REVERT: B 289 MET cc_start: 0.8814 (mmt) cc_final: 0.8557 (mmm) REVERT: C 285 HIS cc_start: 0.8063 (m-70) cc_final: 0.7770 (m-70) REVERT: C 402 MET cc_start: 0.3713 (mmp) cc_final: 0.3188 (mtt) REVERT: C 475 MET cc_start: -0.2936 (mmm) cc_final: -0.3359 (mmm) REVERT: C 570 MET cc_start: 0.8430 (tpp) cc_final: 0.8154 (tpp) REVERT: C 646 ARG cc_start: 0.7421 (ppt170) cc_final: 0.7018 (ppt170) REVERT: C 675 LEU cc_start: 0.8076 (tt) cc_final: 0.7471 (mp) outliers start: 7 outliers final: 5 residues processed: 157 average time/residue: 0.3038 time to fit residues: 73.5326 Evaluate side-chains 156 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 146 optimal weight: 0.1980 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.065628 restraints weight = 129690.698| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.29 r_work: 0.2951 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17899 Z= 0.120 Angle : 0.492 11.647 24248 Z= 0.257 Chirality : 0.038 0.350 2685 Planarity : 0.004 0.036 3046 Dihedral : 9.372 77.917 2670 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.32 % Allowed : 9.99 % Favored : 89.69 % 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: 0.29 (0.18), residues: 2111 helix: 1.69 (0.17), residues: 952 sheet: -0.88 (0.35), residues: 224 loop : -1.12 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 318 TYR 0.010 0.001 TYR B 217 PHE 0.029 0.001 PHE C 580 TRP 0.012 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00268 (17899) covalent geometry : angle 0.49172 (24248) hydrogen bonds : bond 0.03461 ( 819) hydrogen bonds : angle 4.11402 ( 2272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.976 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: A 137 LYS cc_start: 0.9608 (tppt) cc_final: 0.9378 (tppt) REVERT: A 549 LEU cc_start: 0.8934 (mp) cc_final: 0.8474 (pt) REVERT: B 289 MET cc_start: 0.8808 (mmt) cc_final: 0.8560 (mmm) REVERT: C 285 HIS cc_start: 0.8086 (m-70) cc_final: 0.7785 (m-70) REVERT: C 402 MET cc_start: 0.3853 (mmp) cc_final: 0.3271 (mtt) REVERT: C 475 MET cc_start: -0.2980 (mmm) cc_final: -0.3351 (mmm) REVERT: C 570 MET cc_start: 0.8429 (tpp) cc_final: 0.8170 (tpp) REVERT: C 646 ARG cc_start: 0.7457 (ppt170) cc_final: 0.7042 (ppt170) REVERT: C 675 LEU cc_start: 0.8111 (tt) cc_final: 0.7546 (mp) outliers start: 6 outliers final: 6 residues processed: 160 average time/residue: 0.3214 time to fit residues: 78.4696 Evaluate side-chains 159 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 177 optimal weight: 0.0770 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 180 optimal weight: 50.0000 chunk 117 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 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 = 0.3781 r_free = 0.3781 target = 0.099630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065878 restraints weight = 129348.920| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.30 r_work: 0.2957 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17899 Z= 0.114 Angle : 0.492 11.067 24248 Z= 0.256 Chirality : 0.038 0.353 2685 Planarity : 0.004 0.036 3046 Dihedral : 9.341 77.370 2670 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 0.37 % Allowed : 10.10 % Favored : 89.53 % 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: 0.31 (0.19), residues: 2111 helix: 1.68 (0.17), residues: 970 sheet: -0.86 (0.35), residues: 224 loop : -1.13 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 493 TYR 0.020 0.001 TYR B 436 PHE 0.021 0.001 PHE C 438 TRP 0.011 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00256 (17899) covalent geometry : angle 0.49229 (24248) hydrogen bonds : bond 0.03407 ( 819) hydrogen bonds : angle 4.06873 ( 2272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.963 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 1 MET cc_start: 0.7961 (ppp) cc_final: 0.7706 (ppp) REVERT: A 137 LYS cc_start: 0.9601 (tppt) cc_final: 0.9368 (tppt) REVERT: A 549 LEU cc_start: 0.8935 (mp) cc_final: 0.8478 (pt) REVERT: B 289 MET cc_start: 0.8803 (mmt) cc_final: 0.8561 (mmm) REVERT: B 655 MET cc_start: 0.8660 (tpp) cc_final: 0.8416 (tpp) REVERT: C 285 HIS cc_start: 0.8097 (m-70) cc_final: 0.7800 (m-70) REVERT: C 402 MET cc_start: 0.3945 (mmp) cc_final: 0.3385 (mtt) REVERT: C 475 MET cc_start: -0.2990 (mmm) cc_final: -0.3318 (mmm) REVERT: C 570 MET cc_start: 0.8477 (tpp) cc_final: 0.8216 (tpp) REVERT: C 646 ARG cc_start: 0.7465 (ppt170) cc_final: 0.7045 (ppt170) REVERT: C 675 LEU cc_start: 0.8124 (tt) cc_final: 0.7557 (mp) outliers start: 7 outliers final: 7 residues processed: 157 average time/residue: 0.2931 time to fit residues: 70.2023 Evaluate side-chains 157 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 114 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 183 optimal weight: 50.0000 chunk 191 optimal weight: 40.0000 chunk 164 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.066853 restraints weight = 129177.498| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.34 r_work: 0.2978 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17899 Z= 0.093 Angle : 0.487 11.593 24248 Z= 0.252 Chirality : 0.037 0.354 2685 Planarity : 0.004 0.035 3046 Dihedral : 9.248 75.684 2670 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.32 % Allowed : 10.04 % Favored : 89.64 % 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: 0.44 (0.19), residues: 2111 helix: 1.77 (0.17), residues: 971 sheet: -0.83 (0.35), residues: 224 loop : -1.05 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 318 TYR 0.009 0.001 TYR B 555 PHE 0.048 0.001 PHE C 580 TRP 0.011 0.001 TRP C 537 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00210 (17899) covalent geometry : angle 0.48707 (24248) hydrogen bonds : bond 0.03238 ( 819) hydrogen bonds : angle 3.96070 ( 2272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7440.80 seconds wall clock time: 126 minutes 54.52 seconds (7614.52 seconds total)