Starting phenix.real_space_refine on Mon Jul 6 09:53:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhx_12342/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.map" model { file = "/net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nhx_12342/07_2026/7nhx_12342.cif" } 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-6108/lib/python3.11/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: 5.26, 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: 2.99 Conformation dependent library (CDL) restraints added in 985.0 milliseconds 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: 5.37 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: 8.41 Time building geometry restraints manager: 4.11 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: 14728 17.98 - 35.96: 1255 35.96 - 53.95: 296 53.95 - 71.93: 88 71.93 - 89.91: 17 Dihedral angle restraints: 16384 sinusoidal: 9222 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 16381 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: 1.080 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: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 14.575 89.912 6913 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/Z covalent geometry : bond 0.00300 / 0.13 (17899) covalent geometry : angle 0.67852 / 0.37 (24248) hydrogen bonds : bond 0.13744 / 9.19 ( 819) hydrogen bonds : angle 6.58132 / 4.73 ( 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 : 0.967 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: 0.4084 time to fit residues: 166.2532 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 : 0.994 ------------------------------------------------------------------------------- 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... 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 = 0.3830 r_free = 0.3830 target = 0.102394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.069039 restraints weight = 129757.021| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.30 r_work: 0.3026 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17899 Z= 0.207 Angle : 0.599 7.909 24248 Z= 0.324 Chirality : 0.040 0.333 2685 Planarity : 0.005 0.073 3046 Dihedral : 6.547 68.116 2592 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.58 % Allowed : 6.06 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2111 helix: 0.49 (0.16), residues: 951 sheet: -2.21 (0.31), residues: 244 loop : -1.86 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 706 TYR 0.016 0.001 TYR B 555 PHE 0.016 0.001 PHE C 330 TRP 0.017 0.001 TRP C 537 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (17899) covalent geometry : angle 0.59886 / 0.32 (24248) hydrogen bonds : bond 0.04459 / 2.95 ( 819) hydrogen bonds : angle 5.09570 / 3.63 ( 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 199 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.980 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 130 TYR cc_start: 0.8703 (t80) cc_final: 0.8499 (t80) REVERT: A 441 MET cc_start: 0.8626 (tpp) cc_final: 0.8377 (tpp) REVERT: C 365 MET cc_start: 0.3926 (mpp) cc_final: 0.3645 (mtm) REVERT: C 402 MET cc_start: 0.3577 (mmp) cc_final: 0.3054 (mtt) REVERT: C 475 MET cc_start: -0.2584 (mmm) cc_final: -0.3217 (mmm) REVERT: C 646 ARG cc_start: 0.7265 (ppt170) cc_final: 0.6861 (ppt170) outliers start: 11 outliers final: 4 residues processed: 193 average time/residue: 0.3313 time to fit residues: 94.1440 Evaluate side-chains 174 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 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: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066723 restraints weight = 130123.529| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.25 r_work: 0.2970 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17899 Z= 0.208 Angle : 0.559 7.328 24248 Z= 0.300 Chirality : 0.040 0.341 2685 Planarity : 0.005 0.054 3046 Dihedral : 6.606 70.630 2592 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 0.53 % Allowed : 6.85 % Favored : 92.61 % 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: -0.71 (0.18), residues: 2111 helix: 0.91 (0.17), residues: 959 sheet: -1.68 (0.32), residues: 232 loop : -1.63 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.014 0.001 TYR B 555 PHE 0.015 0.001 PHE C 595 TRP 0.016 0.001 TRP C 537 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (17899) covalent geometry : angle 0.55948 / 0.30 (24248) hydrogen bonds : bond 0.04196 / 2.79 ( 819) hydrogen bonds : angle 4.68533 / 3.34 ( 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 185 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.847 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: 0.8360 (ptm) cc_final: 0.8096 (ptm) REVERT: A 441 MET cc_start: 0.8647 (tpp) cc_final: 0.8443 (tpp) REVERT: B 655 MET cc_start: 0.8503 (tpp) cc_final: 0.8190 (tpp) REVERT: C 325 PHE cc_start: 0.6490 (t80) cc_final: 0.6136 (t80) REVERT: C 402 MET cc_start: 0.3596 (mmp) cc_final: 0.3014 (mtt) REVERT: C 475 MET cc_start: -0.2694 (mmm) cc_final: -0.3208 (mmm) REVERT: C 646 ARG cc_start: 0.7375 (ppt170) cc_final: 0.7001 (ppt170) outliers start: 10 outliers final: 7 residues processed: 179 average time/residue: 0.3351 time to fit residues: 88.2630 Evaluate side-chains 168 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG 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 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: 6.9990 chunk 44 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 209 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN B 671 ASN C 138 GLN C 236 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064537 restraints weight = 131067.039| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.24 r_work: 0.2926 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3245 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= 0.246 Angle : 0.564 7.792 24248 Z= 0.304 Chirality : 0.040 0.346 2685 Planarity : 0.004 0.045 3046 Dihedral : 6.728 71.345 2592 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 0.74 % Allowed : 7.60 % Favored : 91.66 % 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: -0.43 (0.18), residues: 2111 helix: 1.11 (0.17), residues: 948 sheet: -1.41 (0.32), residues: 235 loop : -1.46 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 293 TYR 0.014 0.001 TYR B 555 PHE 0.032 0.001 PHE C 580 TRP 0.015 0.001 TRP C 537 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.25 (17899) covalent geometry : angle 0.56433 / 0.30 (24248) hydrogen bonds : bond 0.04171 / 2.77 ( 819) hydrogen bonds : angle 4.64786 / 3.31 ( 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 182 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8333 (ptm) cc_final: 0.8074 (ptm) REVERT: A 549 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8386 (pt) REVERT: B 289 MET cc_start: 0.8835 (mmt) cc_final: 0.8528 (mmm) REVERT: B 655 MET cc_start: 0.8564 (tpp) cc_final: 0.8340 (tpp) REVERT: C 365 MET cc_start: 0.4438 (mpp) cc_final: 0.4108 (mtm) REVERT: C 402 MET cc_start: 0.3576 (mmp) cc_final: 0.3042 (mtt) REVERT: C 475 MET cc_start: -0.2786 (mmm) cc_final: -0.3204 (mmm) REVERT: C 570 MET cc_start: 0.8201 (tpp) cc_final: 0.7952 (tpp) REVERT: C 646 ARG cc_start: 0.7422 (ppt170) cc_final: 0.7017 (ppt170) REVERT: C 675 LEU cc_start: 0.8157 (tt) cc_final: 0.7551 (mp) outliers start: 14 outliers final: 10 residues processed: 177 average time/residue: 0.3305 time to fit residues: 87.5531 Evaluate side-chains 169 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 510 HIS B 158 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.098068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064276 restraints weight = 131305.393| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.22 r_work: 0.2914 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17899 Z= 0.223 Angle : 0.543 8.463 24248 Z= 0.291 Chirality : 0.039 0.347 2685 Planarity : 0.004 0.043 3046 Dihedral : 6.676 71.626 2592 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 0.69 % Allowed : 8.82 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.26 (0.18), residues: 2111 helix: 1.26 (0.17), residues: 947 sheet: -1.32 (0.33), residues: 230 loop : -1.37 (0.19), residues: 934 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 0.019 0.001 PHE A 105 TRP 0.014 0.001 TRP C 537 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (17899) covalent geometry : angle 0.54260 / 0.29 (24248) hydrogen bonds : bond 0.04029 / 2.67 ( 819) hydrogen bonds : angle 4.54803 / 3.24 ( 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 173 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.840 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: 0.8309 (ptm) cc_final: 0.8101 (ptm) REVERT: A 549 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8427 (pt) REVERT: B 638 GLU cc_start: 0.8742 (tp30) cc_final: 0.8398 (tp30) REVERT: C 402 MET cc_start: 0.3626 (mmp) cc_final: 0.3035 (mtt) REVERT: C 475 MET cc_start: -0.2429 (mmm) cc_final: -0.2950 (mmm) REVERT: C 570 MET cc_start: 0.8305 (tpp) cc_final: 0.8035 (tpp) REVERT: C 646 ARG cc_start: 0.7440 (ppt170) cc_final: 0.7022 (ppt170) REVERT: C 675 LEU cc_start: 0.8178 (tt) cc_final: 0.7574 (mp) outliers start: 13 outliers final: 9 residues processed: 169 average time/residue: 0.3359 time to fit residues: 85.5387 Evaluate side-chains 161 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 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 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 B residue 494 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3782 r_free = 0.3782 target = 0.099484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065900 restraints weight = 129641.420| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.29 r_work: 0.2953 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17899 Z= 0.116 Angle : 0.494 8.409 24248 Z= 0.260 Chirality : 0.038 0.352 2685 Planarity : 0.004 0.042 3046 Dihedral : 6.421 70.703 2592 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.48 % Allowed : 9.30 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.18), residues: 2111 helix: 1.49 (0.17), residues: 949 sheet: -1.05 (0.35), residues: 215 loop : -1.29 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.011 0.001 TYR B 217 PHE 0.011 0.001 PHE C 438 TRP 0.012 0.001 TRP C 537 HIS 0.004 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (17899) covalent geometry : angle 0.49377 / 0.26 (24248) hydrogen bonds : bond 0.03636 / 2.40 ( 819) hydrogen bonds : angle 4.27060 / 3.05 ( 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 168 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8366 (mmmt) REVERT: A 155 MET cc_start: 0.8352 (ptm) cc_final: 0.8127 (ptm) REVERT: A 549 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8453 (pt) REVERT: B 289 MET cc_start: 0.8805 (mmt) cc_final: 0.8526 (mmm) REVERT: C 285 HIS cc_start: 0.8032 (m-70) cc_final: 0.7741 (m-70) REVERT: C 365 MET cc_start: 0.4527 (mpp) cc_final: 0.4179 (mtm) REVERT: C 402 MET cc_start: 0.3594 (mmp) cc_final: 0.3003 (mtt) REVERT: C 475 MET cc_start: -0.2732 (mmm) cc_final: -0.3175 (mmm) REVERT: C 570 MET cc_start: 0.8365 (tpp) cc_final: 0.8106 (tpp) REVERT: C 603 MET cc_start: 0.8966 (tpt) cc_final: 0.8743 (tpp) REVERT: C 646 ARG cc_start: 0.7457 (ppt170) cc_final: 0.7043 (ppt170) REVERT: C 675 LEU cc_start: 0.8187 (tt) cc_final: 0.7585 (mp) outliers start: 9 outliers final: 8 residues processed: 164 average time/residue: 0.3126 time to fit residues: 78.0556 Evaluate side-chains 163 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG 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 C residue 297 ILE Chi-restraints excluded: chain C residue 390 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 181 optimal weight: 30.0000 chunk 167 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 180 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.096662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.062830 restraints weight = 131930.371| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.17 r_work: 0.2885 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17899 Z= 0.298 Angle : 0.580 9.535 24248 Z= 0.314 Chirality : 0.041 0.351 2685 Planarity : 0.004 0.038 3046 Dihedral : 6.796 72.246 2592 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.80 % Allowed : 9.72 % Favored : 89.48 % 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: -0.24 (0.18), residues: 2111 helix: 1.22 (0.17), residues: 955 sheet: -1.06 (0.35), residues: 220 loop : -1.40 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 15 TYR 0.013 0.002 TYR B 555 PHE 0.016 0.002 PHE A 520 TRP 0.012 0.002 TRP C 537 HIS 0.006 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.30 (17899) covalent geometry : angle 0.58027 / 0.31 (24248) hydrogen bonds : bond 0.04262 / 2.84 ( 819) hydrogen bonds : angle 4.67862 / 3.34 ( 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 171 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.940 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 134 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8377 (mmmt) REVERT: A 155 MET cc_start: 0.8341 (ptm) cc_final: 0.8117 (ptm) REVERT: A 549 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8479 (pt) REVERT: B 289 MET cc_start: 0.8974 (mmt) cc_final: 0.8718 (mmm) REVERT: C 285 HIS cc_start: 0.8056 (m-70) cc_final: 0.7760 (m-70) REVERT: C 402 MET cc_start: 0.3575 (mmp) cc_final: 0.3046 (mtt) REVERT: C 570 MET cc_start: 0.8412 (tpp) cc_final: 0.8130 (tpp) REVERT: C 646 ARG cc_start: 0.7495 (ppt170) cc_final: 0.7055 (ppt170) REVERT: C 675 LEU cc_start: 0.8241 (tt) cc_final: 0.7654 (mp) outliers start: 15 outliers final: 12 residues processed: 164 average time/residue: 0.3225 time to fit residues: 80.2928 Evaluate side-chains 165 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 492 LYS 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 B residue 494 SER Chi-restraints excluded: chain B residue 688 MET 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: 5.9990 chunk 187 optimal weight: 30.0000 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3757 r_free = 0.3757 target = 0.098398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.064437 restraints weight = 130345.300| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.29 r_work: 0.2920 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3965 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= 0.141 Angle : 0.508 9.888 24248 Z= 0.269 Chirality : 0.038 0.353 2685 Planarity : 0.004 0.040 3046 Dihedral : 6.514 71.410 2592 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 0.53 % Allowed : 10.20 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2111 helix: 1.44 (0.17), residues: 957 sheet: -0.94 (0.36), residues: 215 loop : -1.29 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.012 0.001 TYR B 217 PHE 0.019 0.001 PHE C 580 TRP 0.010 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (17899) covalent geometry : angle 0.50782 / 0.27 (24248) hydrogen bonds : bond 0.03748 / 2.48 ( 819) hydrogen bonds : angle 4.31292 / 3.08 ( 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 163 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.933 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 134 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8357 (mmmt) REVERT: A 155 MET cc_start: 0.8279 (ptm) cc_final: 0.8063 (ptm) REVERT: A 549 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8538 (pt) REVERT: B 289 MET cc_start: 0.8820 (mmt) cc_final: 0.8565 (mmm) REVERT: C 285 HIS cc_start: 0.8017 (m-70) cc_final: 0.7726 (m-70) REVERT: C 402 MET cc_start: 0.3712 (mmp) cc_final: 0.3139 (mtt) REVERT: C 570 MET cc_start: 0.8450 (tpp) cc_final: 0.8183 (tpp) REVERT: C 646 ARG cc_start: 0.7421 (ppt170) cc_final: 0.7000 (ppt170) REVERT: C 675 LEU cc_start: 0.8123 (tt) cc_final: 0.7489 (mp) outliers start: 10 outliers final: 7 residues processed: 157 average time/residue: 0.3321 time to fit residues: 79.0013 Evaluate side-chains 160 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 146 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 187 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3770 r_free = 0.3770 target = 0.099110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065227 restraints weight = 129749.629| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.32 r_work: 0.2939 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17899 Z= 0.120 Angle : 0.501 12.336 24248 Z= 0.261 Chirality : 0.038 0.344 2685 Planarity : 0.004 0.038 3046 Dihedral : 6.306 70.108 2592 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 0.32 % Allowed : 10.47 % Favored : 89.21 % 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: 1.65 (0.17), residues: 957 sheet: -1.01 (0.36), residues: 224 loop : -1.16 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 318 TYR 0.010 0.001 TYR A 130 PHE 0.024 0.001 PHE C 438 TRP 0.015 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17899) covalent geometry : angle 0.50122 / 0.26 (24248) hydrogen bonds : bond 0.03475 / 2.30 ( 819) hydrogen bonds : angle 4.13249 / 2.95 ( 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 159 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.961 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 134 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8357 (mmmt) REVERT: A 155 MET cc_start: 0.8321 (ptm) cc_final: 0.8104 (ptm) REVERT: A 549 LEU cc_start: 0.8956 (mp) cc_final: 0.8516 (pt) REVERT: B 289 MET cc_start: 0.8830 (mmt) cc_final: 0.8588 (mmm) REVERT: B 655 MET cc_start: 0.8657 (tpp) cc_final: 0.8418 (tpp) REVERT: C 285 HIS cc_start: 0.8036 (m-70) cc_final: 0.7744 (m-70) REVERT: C 402 MET cc_start: 0.3799 (mmp) cc_final: 0.3208 (mtt) REVERT: C 570 MET cc_start: 0.8445 (tpp) cc_final: 0.8180 (tpp) REVERT: C 646 ARG cc_start: 0.7424 (ppt170) cc_final: 0.6997 (ppt170) REVERT: C 675 LEU cc_start: 0.8119 (tt) cc_final: 0.7476 (mp) outliers start: 6 outliers final: 6 residues processed: 156 average time/residue: 0.3100 time to fit residues: 73.7823 Evaluate side-chains 157 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 180 optimal weight: 50.0000 chunk 117 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 182 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.098174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064386 restraints weight = 130339.515| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.29 r_work: 0.2919 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17899 Z= 0.168 Angle : 0.516 10.522 24248 Z= 0.271 Chirality : 0.038 0.355 2685 Planarity : 0.004 0.037 3046 Dihedral : 6.388 70.740 2592 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 0.37 % Allowed : 10.63 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.18), residues: 2111 helix: 1.62 (0.17), residues: 958 sheet: -1.07 (0.35), residues: 224 loop : -1.18 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.017 0.001 TYR B 436 PHE 0.022 0.001 PHE C 438 TRP 0.012 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (17899) covalent geometry : angle 0.51612 / 0.27 (24248) hydrogen bonds : bond 0.03638 / 2.42 ( 819) hydrogen bonds : angle 4.21115 / 3.01 ( 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 159 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.887 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 134 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8361 (mmmt) REVERT: A 155 MET cc_start: 0.8284 (ptm) cc_final: 0.8075 (ptm) REVERT: A 549 LEU cc_start: 0.8920 (mp) cc_final: 0.8498 (pt) REVERT: B 289 MET cc_start: 0.8849 (mmt) cc_final: 0.8613 (mmm) REVERT: B 655 MET cc_start: 0.8623 (tpp) cc_final: 0.8399 (tpp) REVERT: C 285 HIS cc_start: 0.8041 (m-70) cc_final: 0.7754 (m-70) REVERT: C 402 MET cc_start: 0.3893 (mmp) cc_final: 0.3361 (mtt) REVERT: C 570 MET cc_start: 0.8531 (tpp) cc_final: 0.8265 (tpp) REVERT: C 675 LEU cc_start: 0.8101 (tt) cc_final: 0.7434 (mp) outliers start: 7 outliers final: 7 residues processed: 155 average time/residue: 0.3217 time to fit residues: 75.4027 Evaluate side-chains 159 residues out of total 1882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG 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 297 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: 3.9990 chunk 120 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 183 optimal weight: 40.0000 chunk 191 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3752 r_free = 0.3752 target = 0.098136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064213 restraints weight = 130387.465| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.29 r_work: 0.2917 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17899 Z= 0.166 Angle : 0.516 12.136 24248 Z= 0.271 Chirality : 0.038 0.352 2685 Planarity : 0.004 0.038 3046 Dihedral : 6.380 70.641 2592 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.43 % Allowed : 10.84 % Favored : 88.74 % 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: 0.21 (0.18), residues: 2111 helix: 1.63 (0.17), residues: 958 sheet: -1.04 (0.35), residues: 230 loop : -1.17 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 318 TYR 0.011 0.001 TYR B 217 PHE 0.045 0.001 PHE C 580 TRP 0.014 0.001 TRP C 537 HIS 0.005 0.001 HIS B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (17899) covalent geometry : angle 0.51591 / 0.27 (24248) hydrogen bonds : bond 0.03626 / 2.41 ( 819) hydrogen bonds : angle 4.19526 / 3.00 ( 2272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6913.36 seconds wall clock time: 118 minutes 21.99 seconds (7101.99 seconds total)