Starting phenix.real_space_refine on Fri Jul 3 15:29:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.map" model { file = "/net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t0s_10358/07_2026/6t0s_10358.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 43 5.49 5 Mg 2 5.21 5 S 92 5.16 5 C 9083 2.51 5 N 2553 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 14651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 5769 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 25, 'TRANS': 682} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 708, 5769 Classifications: {'peptide': 708} Link IDs: {'PTRANS': 25, 'TRANS': 682} Chain breaks: 2 bond proxies already assigned to first conformer: 5879 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5947 Classifications: {'peptide': 743} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 714} Chain breaks: 1 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2012 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain: "V" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 690 Classifications: {'RNA': 33} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna2p': 12, 'rna3p': 20} Chain breaks: 2 Chain: "M" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 491 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 491 " occ=0.50 Time building chain proxies: 3.48, per 1000 atoms: 0.24 Number of scatterers: 14651 At special positions: 0 Unit cell: (97.2, 119.07, 117.45, 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 92 16.00 P 43 15.00 Mg 2 11.99 O 2878 8.00 N 2553 7.00 C 9083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 612.1 milliseconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 17 sheets defined 50.7% alpha, 13.8% beta 11 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.560A pdb=" N PHE A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 96 Processing helix chain 'A' and resid 126 through 138 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 185 removed outlier: 3.523A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.628A pdb=" N ALA A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.801A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.522A pdb=" N GLN A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 Processing helix chain 'A' and resid 528 through 533 removed outlier: 4.175A pdb=" N GLU A 533 " --> pdb=" O HIS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 578 through 598 removed outlier: 3.780A pdb=" N GLN A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 4.269A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 Processing helix chain 'A' and resid 692 through 713 Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.580A pdb=" N ILE B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.616A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 4.064A pdb=" N THR B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 139 through 152 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.618A pdb=" N GLY B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.650A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.744A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 373 removed outlier: 3.731A pdb=" N LEU B 373 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.700A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.533A pdb=" N SER B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.740A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 removed outlier: 3.557A pdb=" N LEU B 509 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.738A pdb=" N ILE B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 613 through 616 removed outlier: 3.631A pdb=" N MET B 616 " --> pdb=" O TRP B 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 616' Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 683 through 697 removed outlier: 3.703A pdb=" N GLU B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 0 through 13 removed outlier: 3.504A pdb=" N ILE C 4 " --> pdb=" O GLY C 0 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 33 removed outlier: 4.288A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.670A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.922A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 4.041A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 removed outlier: 4.151A pdb=" N LEU C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.993A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.617A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 3.852A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.657A pdb=" N GLY A 121 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.282A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.803A pdb=" N AARG A 491 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 486 " --> pdb=" O AARG A 491 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.508A pdb=" N LYS A 318 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N MET A 543 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ALA A 320 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N GLY A 541 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 556 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 542 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 554 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 544 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ILE A 552 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N AARG A 491 " --> pdb=" O ASP A 486 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP A 486 " --> pdb=" O AARG A 491 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374 removed outlier: 5.952A pdb=" N GLU A 372 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N GLN B 367 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N MET A 374 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 623 through 626 removed outlier: 6.593A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 187 Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 192 Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.920A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 59 Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.628A pdb=" N GLN C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.264A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4111 1.34 - 1.45: 2727 1.45 - 1.57: 7949 1.57 - 1.69: 82 1.69 - 1.81: 160 Bond restraints: 15029 Sorted by residual: bond pdb=" N THR C 176 " pdb=" CA THR C 176 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.43e+00 bond pdb=" N LEU C 177 " pdb=" CA LEU C 177 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.25e-02 6.40e+03 5.62e+00 bond pdb=" N ARG C 175 " pdb=" CA ARG C 175 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.05e+00 bond pdb=" N GLY C 173 " pdb=" CA GLY C 173 " ideal model delta sigma weight residual 1.449 1.476 -0.027 1.68e-02 3.54e+03 2.50e+00 bond pdb=" N ALA C 174 " pdb=" CA ALA C 174 " ideal model delta sigma weight residual 1.464 1.482 -0.018 1.20e-02 6.94e+03 2.18e+00 ... (remaining 15024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 19882 1.49 - 2.99: 488 2.99 - 4.48: 70 4.48 - 5.97: 15 5.97 - 7.46: 7 Bond angle restraints: 20462 Sorted by residual: angle pdb=" CA GLY C 173 " pdb=" C GLY C 173 " pdb=" O GLY C 173 " ideal model delta sigma weight residual 122.01 118.21 3.80 1.19e+00 7.06e-01 1.02e+01 angle pdb=" N LEU B 509 " pdb=" CA LEU B 509 " pdb=" C LEU B 509 " ideal model delta sigma weight residual 109.81 116.19 -6.38 2.21e+00 2.05e-01 8.32e+00 angle pdb=" CA LEU B 509 " pdb=" C LEU B 509 " pdb=" N PRO B 510 " ideal model delta sigma weight residual 118.44 122.74 -4.30 1.59e+00 3.96e-01 7.31e+00 angle pdb=" CA TRP C 49 " pdb=" CB TRP C 49 " pdb=" CG TRP C 49 " ideal model delta sigma weight residual 113.60 118.68 -5.08 1.90e+00 2.77e-01 7.16e+00 angle pdb=" N ALA B 340 " pdb=" CA ALA B 340 " pdb=" C ALA B 340 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.75e+00 ... (remaining 20457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 8232 16.88 - 33.76: 633 33.76 - 50.65: 153 50.65 - 67.53: 38 67.53 - 84.41: 10 Dihedral angle restraints: 9066 sinusoidal: 4097 harmonic: 4969 Sorted by residual: dihedral pdb=" O4' C V 40 " pdb=" C1' C V 40 " pdb=" N1 C V 40 " pdb=" C2 C V 40 " ideal model delta sinusoidal sigma weight residual -128.00 -70.50 -57.50 1 1.70e+01 3.46e-03 1.54e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER A 583 " pdb=" C SER A 583 " pdb=" N LEU A 584 " pdb=" CA LEU A 584 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 9063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1415 0.033 - 0.066: 611 0.066 - 0.099: 160 0.099 - 0.131: 71 0.131 - 0.164: 13 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CA LEU C 177 " pdb=" N LEU C 177 " pdb=" C LEU C 177 " pdb=" CB LEU C 177 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 2267 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 137 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO B 138 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 219 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 220 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO A 620 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.031 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 323 2.67 - 3.23: 12366 3.23 - 3.78: 23941 3.78 - 4.34: 33660 4.34 - 4.90: 54129 Nonbonded interactions: 124419 Sorted by model distance: nonbonded pdb=" OD1 ASP B 446 " pdb="MG MG B 802 " model vdw 2.109 2.170 nonbonded pdb=" O ARG C 175 " pdb=" NH1 ARG C 175 " model vdw 2.211 3.120 nonbonded pdb=" O ALA B 113 " pdb=" OG1 THR B 117 " model vdw 2.266 3.040 nonbonded pdb=" O ILE B 219 " pdb=" OG1 THR B 223 " model vdw 2.285 3.040 nonbonded pdb=" O SER B 524 " pdb=" OG1 THR B 528 " model vdw 2.298 3.040 ... (remaining 124414 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=0.50 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 0.049 15029 Z= 0.165 Angle : 0.596 7.463 20462 Z= 0.345 Chirality : 0.042 0.164 2270 Planarity : 0.006 0.058 2478 Dihedral : 13.173 84.409 5850 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.69 % Allowed : 6.41 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.16), residues: 1691 helix: -2.20 (0.13), residues: 817 sheet: -1.68 (0.36), residues: 167 loop : -1.95 (0.19), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 578 TYR 0.020 0.002 TYR B 557 PHE 0.015 0.002 PHE A 211 TRP 0.021 0.002 TRP C 49 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (15029) covalent geometry : angle 0.59623 / 0.35 (20462) hydrogen bonds : bond 0.16713 / 11.10 ( 705) hydrogen bonds : angle 6.69484 / 4.70 ( 1957) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 310 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6545 (ttmt) REVERT: A 67 ASP cc_start: 0.5455 (OUTLIER) cc_final: 0.4670 (m-30) REVERT: A 129 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6235 (t0) REVERT: A 148 PHE cc_start: 0.8164 (m-80) cc_final: 0.7921 (m-80) REVERT: A 174 ARG cc_start: 0.7184 (tpt90) cc_final: 0.6536 (tpt-90) REVERT: A 490 GLN cc_start: 0.7350 (mt0) cc_final: 0.6797 (mm110) REVERT: A 624 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7584 (mm-30) REVERT: B 109 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 314 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8687 (t0) REVERT: B 353 ARG cc_start: 0.7129 (ptt180) cc_final: 0.5744 (mtm-85) REVERT: B 392 ILE cc_start: 0.8899 (tt) cc_final: 0.8620 (tt) REVERT: B 571 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7648 (mmp80) REVERT: B 638 GLU cc_start: 0.5515 (OUTLIER) cc_final: 0.3570 (tt0) REVERT: B 680 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6527 (mtm-85) REVERT: C 152 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6723 (ptmm) REVERT: C 157 ARG cc_start: 0.7274 (mmt90) cc_final: 0.7037 (mmt-90) REVERT: C 197 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7566 (mmtt) outliers start: 71 outliers final: 29 residues processed: 362 average time/residue: 0.1395 time to fit residues: 72.4921 Evaluate side-chains 256 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 198 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 217 GLN A 239 ASN A 508 ASN B 58 ASN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 629 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118848 restraints weight = 27697.028| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.86 r_work: 0.3124 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15029 Z= 0.153 Angle : 0.516 9.328 20462 Z= 0.274 Chirality : 0.040 0.165 2270 Planarity : 0.004 0.053 2478 Dihedral : 9.204 84.487 2443 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.17 % Allowed : 10.05 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -1.36 (0.19), residues: 1691 helix: -0.20 (0.17), residues: 820 sheet: -1.04 (0.38), residues: 165 loop : -1.62 (0.20), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 175 TYR 0.024 0.001 TYR B 557 PHE 0.015 0.001 PHE A 211 TRP 0.022 0.001 TRP A 188 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (15029) covalent geometry : angle 0.51558 / 0.27 (20462) hydrogen bonds : bond 0.04435 / 3.00 ( 705) hydrogen bonds : angle 4.51192 / 3.17 ( 1957) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 0.427 Fit side-chains REVERT: A 18 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 174 ARG cc_start: 0.7235 (tpt90) cc_final: 0.7025 (tpt-90) REVERT: A 315 TRP cc_start: 0.8063 (OUTLIER) cc_final: 0.7720 (p90) REVERT: A 375 ASP cc_start: 0.7870 (m-30) cc_final: 0.7622 (m-30) REVERT: A 490 GLN cc_start: 0.7801 (mt0) cc_final: 0.7018 (mm110) REVERT: A 707 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8087 (mppt) REVERT: B 238 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8950 (mmp80) REVERT: B 314 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8711 (t0) REVERT: B 392 ILE cc_start: 0.9139 (tt) cc_final: 0.8904 (tt) REVERT: B 433 LYS cc_start: 0.7391 (mttt) cc_final: 0.7098 (mtpt) REVERT: B 638 GLU cc_start: 0.5553 (OUTLIER) cc_final: 0.3448 (tt0) REVERT: B 680 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6772 (mtm180) REVERT: B 683 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8193 (mm) REVERT: C 28 MET cc_start: 0.8949 (ttp) cc_final: 0.8741 (ttp) REVERT: C 152 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6746 (ptmm) REVERT: C 208 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8351 (mt-10) outliers start: 48 outliers final: 33 residues processed: 261 average time/residue: 0.1092 time to fit residues: 41.9058 Evaluate side-chains 243 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 0.0010 chunk 69 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 0.0570 chunk 104 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.3908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 100 ASN A 239 ASN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 372 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118833 restraints weight = 30578.797| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.18 r_work: 0.3103 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15029 Z= 0.123 Angle : 0.478 9.027 20462 Z= 0.252 Chirality : 0.039 0.148 2270 Planarity : 0.004 0.051 2478 Dihedral : 8.823 84.848 2413 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.11 % Allowed : 10.77 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.54 (0.20), residues: 1691 helix: 0.63 (0.18), residues: 819 sheet: -0.83 (0.39), residues: 163 loop : -1.37 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 124 TYR 0.022 0.001 TYR A 131 PHE 0.011 0.001 PHE A 211 TRP 0.019 0.001 TRP A 188 HIS 0.002 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15029) covalent geometry : angle 0.47787 / 0.25 (20462) hydrogen bonds : bond 0.03903 / 2.63 ( 705) hydrogen bonds : angle 4.22090 / 2.97 ( 1957) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 0.595 Fit side-chains REVERT: A 122 VAL cc_start: 0.7613 (t) cc_final: 0.7278 (m) REVERT: A 174 ARG cc_start: 0.7196 (tpt90) cc_final: 0.6884 (tpt-90) REVERT: A 377 GLU cc_start: 0.7222 (mp0) cc_final: 0.6992 (pm20) REVERT: A 490 GLN cc_start: 0.7803 (mt0) cc_final: 0.7288 (mm110) REVERT: A 707 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8063 (mppt) REVERT: B 238 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8968 (mmp80) REVERT: B 314 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8784 (t0) REVERT: B 392 ILE cc_start: 0.9150 (tt) cc_final: 0.8947 (tt) REVERT: B 433 LYS cc_start: 0.7398 (mttt) cc_final: 0.7073 (mtpt) REVERT: B 638 GLU cc_start: 0.5519 (OUTLIER) cc_final: 0.3535 (tt0) REVERT: B 680 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6693 (mtm180) REVERT: B 683 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8294 (mm) REVERT: C 8 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7636 (ttm) REVERT: C 152 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6716 (ptmm) REVERT: C 197 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7745 (mmtt) REVERT: C 208 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8517 (mt-10) outliers start: 47 outliers final: 32 residues processed: 255 average time/residue: 0.1200 time to fit residues: 44.7599 Evaluate side-chains 248 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 169 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 239 ASN A 508 ASN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.119644 restraints weight = 26033.844| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.82 r_work: 0.3152 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15029 Z= 0.114 Angle : 0.462 9.574 20462 Z= 0.243 Chirality : 0.038 0.146 2270 Planarity : 0.004 0.048 2478 Dihedral : 8.512 85.326 2406 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.24 % Allowed : 11.76 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.03 (0.20), residues: 1691 helix: 1.11 (0.18), residues: 819 sheet: -0.64 (0.39), residues: 163 loop : -1.19 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 124 TYR 0.022 0.001 TYR A 131 PHE 0.012 0.001 PHE A 211 TRP 0.016 0.001 TRP A 188 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15029) covalent geometry : angle 0.46225 / 0.24 (20462) hydrogen bonds : bond 0.03631 / 2.45 ( 705) hydrogen bonds : angle 4.06250 / 2.87 ( 1957) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.561 Fit side-chains REVERT: A 60 THR cc_start: 0.7644 (p) cc_final: 0.7367 (m) REVERT: A 83 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (tm-30) REVERT: A 100 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.7027 (m110) REVERT: A 174 ARG cc_start: 0.7244 (tpt90) cc_final: 0.6983 (tpt-90) REVERT: A 192 ARG cc_start: 0.7419 (ttt180) cc_final: 0.6759 (mtp-110) REVERT: A 224 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8355 (pmtt) REVERT: A 243 GLU cc_start: 0.7762 (tp30) cc_final: 0.7553 (mm-30) REVERT: A 374 MET cc_start: 0.7186 (mtm) cc_final: 0.6145 (tpt) REVERT: A 490 GLN cc_start: 0.7898 (mt0) cc_final: 0.7252 (mm110) REVERT: A 707 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8054 (mppt) REVERT: B 238 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8971 (mmp80) REVERT: B 314 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8720 (t0) REVERT: B 353 ARG cc_start: 0.7784 (ptt180) cc_final: 0.7574 (ptt180) REVERT: B 392 ILE cc_start: 0.9126 (tt) cc_final: 0.8901 (tt) REVERT: B 433 LYS cc_start: 0.7371 (mttt) cc_final: 0.7113 (mtpt) REVERT: B 457 GLU cc_start: 0.8038 (mp0) cc_final: 0.7819 (pt0) REVERT: B 638 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.3564 (tt0) REVERT: B 680 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6727 (mtm180) REVERT: B 683 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8338 (mm) REVERT: C 8 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7535 (ttm) REVERT: C 152 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6717 (ptmm) REVERT: C 177 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7239 (mp) REVERT: C 208 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8345 (mt-10) outliers start: 49 outliers final: 29 residues processed: 255 average time/residue: 0.1231 time to fit residues: 45.3978 Evaluate side-chains 244 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 157 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.120591 restraints weight = 30467.648| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.19 r_work: 0.3112 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15029 Z= 0.093 Angle : 0.444 9.161 20462 Z= 0.235 Chirality : 0.037 0.142 2270 Planarity : 0.003 0.047 2478 Dihedral : 8.354 85.320 2401 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.17 % Allowed : 11.90 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.30 (0.20), residues: 1691 helix: 1.37 (0.19), residues: 819 sheet: -0.50 (0.39), residues: 167 loop : -1.01 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 118 TYR 0.022 0.001 TYR A 131 PHE 0.010 0.001 PHE A 211 TRP 0.014 0.001 TRP A 188 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (15029) covalent geometry : angle 0.44438 / 0.23 (20462) hydrogen bonds : bond 0.03375 / 2.27 ( 705) hydrogen bonds : angle 3.97561 / 2.81 ( 1957) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.557 Fit side-chains REVERT: A 60 THR cc_start: 0.7677 (p) cc_final: 0.7398 (m) REVERT: A 63 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6329 (ttmt) REVERT: A 83 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 174 ARG cc_start: 0.7205 (tpt90) cc_final: 0.6929 (tpt-90) REVERT: A 192 ARG cc_start: 0.7341 (ttt180) cc_final: 0.6760 (mtp-110) REVERT: A 243 GLU cc_start: 0.7797 (tp30) cc_final: 0.7565 (mm-30) REVERT: A 374 MET cc_start: 0.7230 (mtm) cc_final: 0.6166 (tpt) REVERT: A 490 GLN cc_start: 0.7939 (mt0) cc_final: 0.7278 (mm110) REVERT: A 707 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8040 (mppt) REVERT: B 314 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8774 (t0) REVERT: B 353 ARG cc_start: 0.7607 (ptt180) cc_final: 0.7354 (ptt180) REVERT: B 392 ILE cc_start: 0.9128 (tt) cc_final: 0.8885 (tt) REVERT: B 433 LYS cc_start: 0.7366 (mttt) cc_final: 0.7112 (mtpt) REVERT: B 457 GLU cc_start: 0.8117 (mp0) cc_final: 0.7854 (pt0) REVERT: B 638 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.3464 (tt0) REVERT: B 680 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6668 (mtm-85) REVERT: B 683 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 702 SER cc_start: 0.8395 (p) cc_final: 0.8156 (t) REVERT: C 8 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7640 (ttm) REVERT: C 134 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8606 (mttt) REVERT: C 152 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6755 (ptmm) REVERT: C 177 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7356 (mp) REVERT: C 197 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7711 (mmtt) REVERT: C 208 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8422 (mt-10) outliers start: 48 outliers final: 29 residues processed: 246 average time/residue: 0.1237 time to fit residues: 44.5829 Evaluate side-chains 246 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 411 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 45 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 239 ASN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 679 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.116042 restraints weight = 29079.548| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.85 r_work: 0.3056 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15029 Z= 0.241 Angle : 0.565 11.285 20462 Z= 0.296 Chirality : 0.043 0.176 2270 Planarity : 0.004 0.051 2478 Dihedral : 8.539 86.006 2392 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.90 % Allowed : 11.63 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.06 (0.20), residues: 1691 helix: 1.12 (0.18), residues: 818 sheet: -0.50 (0.40), residues: 162 loop : -1.08 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 118 TYR 0.023 0.002 TYR B 557 PHE 0.020 0.002 PHE A 211 TRP 0.016 0.002 TRP A 188 HIS 0.004 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (15029) covalent geometry : angle 0.56545 / 0.30 (20462) hydrogen bonds : bond 0.04518 / 3.06 ( 705) hydrogen bonds : angle 4.24856 / 2.99 ( 1957) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.542 Fit side-chains REVERT: A 60 THR cc_start: 0.7794 (p) cc_final: 0.7478 (m) REVERT: A 63 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6127 (ttmt) REVERT: A 174 ARG cc_start: 0.7316 (tpt90) cc_final: 0.6983 (tpt-90) REVERT: A 192 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6592 (mtp-110) REVERT: A 224 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8249 (pmtt) REVERT: A 228 GLN cc_start: 0.8687 (tt0) cc_final: 0.8133 (tt0) REVERT: A 374 MET cc_start: 0.7309 (mtm) cc_final: 0.6207 (tpt) REVERT: A 490 GLN cc_start: 0.8016 (mt0) cc_final: 0.7423 (mm110) REVERT: A 707 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8177 (mppt) REVERT: B 238 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.9019 (mmp80) REVERT: B 314 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8733 (t0) REVERT: B 353 ARG cc_start: 0.7852 (ptt180) cc_final: 0.7579 (ptt180) REVERT: B 392 ILE cc_start: 0.9162 (tt) cc_final: 0.8875 (tt) REVERT: B 396 MET cc_start: 0.9019 (mmm) cc_final: 0.8816 (mmm) REVERT: B 433 LYS cc_start: 0.7507 (mttt) cc_final: 0.7186 (mtpt) REVERT: B 638 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.3727 (tt0) REVERT: B 680 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6778 (mtm180) REVERT: B 683 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8309 (mm) REVERT: C 8 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7582 (ttm) REVERT: C 62 ARG cc_start: 0.8247 (ptp90) cc_final: 0.7764 (ptm-80) REVERT: C 134 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8565 (mttt) REVERT: C 152 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6724 (ptmm) REVERT: C 197 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7798 (mmtt) REVERT: C 208 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8421 (mt-10) outliers start: 59 outliers final: 33 residues processed: 248 average time/residue: 0.1291 time to fit residues: 46.3806 Evaluate side-chains 239 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 141 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.148151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120052 restraints weight = 42138.806| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.21 r_work: 0.3103 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15029 Z= 0.103 Angle : 0.458 9.852 20462 Z= 0.242 Chirality : 0.038 0.147 2270 Planarity : 0.003 0.047 2478 Dihedral : 8.237 84.774 2389 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.97 % Allowed : 12.69 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.37 (0.20), residues: 1691 helix: 1.41 (0.19), residues: 820 sheet: -0.52 (0.39), residues: 176 loop : -0.94 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 118 TYR 0.023 0.001 TYR A 131 PHE 0.010 0.001 PHE A 211 TRP 0.016 0.001 TRP C 49 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15029) covalent geometry : angle 0.45841 / 0.24 (20462) hydrogen bonds : bond 0.03472 / 2.34 ( 705) hydrogen bonds : angle 4.01804 / 2.83 ( 1957) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.517 Fit side-chains REVERT: A 60 THR cc_start: 0.7763 (p) cc_final: 0.7466 (m) REVERT: A 63 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6328 (ttmt) REVERT: A 174 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6926 (tpt-90) REVERT: A 192 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6757 (mtp-110) REVERT: A 224 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.7986 (pmtt) REVERT: A 374 MET cc_start: 0.7062 (mtm) cc_final: 0.6101 (tpt) REVERT: A 490 GLN cc_start: 0.7788 (mt0) cc_final: 0.7225 (mm110) REVERT: A 707 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7988 (mppt) REVERT: B 238 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8969 (mmp80) REVERT: B 314 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8638 (t0) REVERT: B 353 ARG cc_start: 0.7312 (ptt180) cc_final: 0.7048 (ptt180) REVERT: B 392 ILE cc_start: 0.9066 (tt) cc_final: 0.8850 (tt) REVERT: B 433 LYS cc_start: 0.7304 (mttt) cc_final: 0.7068 (mtpt) REVERT: B 599 TYR cc_start: 0.9005 (m-80) cc_final: 0.8792 (m-80) REVERT: B 638 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.3574 (tt0) REVERT: B 680 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6717 (mtm180) REVERT: B 683 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8316 (mm) REVERT: C 8 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7446 (ttm) REVERT: C 134 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8462 (mttt) REVERT: C 152 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6780 (ptmm) REVERT: C 197 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7785 (mmtp) REVERT: C 208 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8223 (mt-10) outliers start: 45 outliers final: 29 residues processed: 238 average time/residue: 0.1315 time to fit residues: 45.5642 Evaluate side-chains 245 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 40 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.145733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.118396 restraints weight = 33204.227| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.92 r_work: 0.3069 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15029 Z= 0.184 Angle : 0.511 10.825 20462 Z= 0.268 Chirality : 0.041 0.164 2270 Planarity : 0.004 0.057 2478 Dihedral : 8.298 85.602 2389 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.24 % Allowed : 12.56 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1691 helix: 1.34 (0.19), residues: 819 sheet: -0.51 (0.39), residues: 171 loop : -0.94 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 124 TYR 0.021 0.002 TYR A 131 PHE 0.018 0.001 PHE A 211 TRP 0.014 0.001 TRP A 188 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (15029) covalent geometry : angle 0.51055 / 0.27 (20462) hydrogen bonds : bond 0.04009 / 2.70 ( 705) hydrogen bonds : angle 4.12672 / 2.90 ( 1957) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 60 THR cc_start: 0.7847 (p) cc_final: 0.7530 (m) REVERT: A 122 VAL cc_start: 0.7657 (t) cc_final: 0.7364 (m) REVERT: A 174 ARG cc_start: 0.7337 (tpt90) cc_final: 0.6753 (tpt-90) REVERT: A 192 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6612 (mtp-110) REVERT: A 224 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8059 (pmtt) REVERT: A 300 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 374 MET cc_start: 0.7327 (mtm) cc_final: 0.6241 (tpt) REVERT: A 490 GLN cc_start: 0.7970 (mt0) cc_final: 0.7349 (mm110) REVERT: A 707 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8155 (mppt) REVERT: B 238 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.9014 (mmp80) REVERT: B 314 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8694 (t0) REVERT: B 353 ARG cc_start: 0.7629 (ptt180) cc_final: 0.7355 (ptt180) REVERT: B 433 LYS cc_start: 0.7446 (mttt) cc_final: 0.7152 (mtpt) REVERT: B 638 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.3649 (tt0) REVERT: B 680 ARG cc_start: 0.7365 (mtt180) cc_final: 0.6761 (mtm180) REVERT: B 683 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8344 (mm) REVERT: C 8 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7642 (ttm) REVERT: C 134 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8569 (mttt) REVERT: C 152 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6754 (ptmm) REVERT: C 197 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7892 (mmtp) REVERT: C 208 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8429 (mt-10) outliers start: 49 outliers final: 35 residues processed: 240 average time/residue: 0.1366 time to fit residues: 47.6776 Evaluate side-chains 246 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.119843 restraints weight = 24101.040| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.74 r_work: 0.3146 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15029 Z= 0.100 Angle : 0.453 9.993 20462 Z= 0.239 Chirality : 0.038 0.144 2270 Planarity : 0.003 0.047 2478 Dihedral : 8.166 85.034 2389 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.78 % Allowed : 12.95 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1691 helix: 1.52 (0.19), residues: 824 sheet: -0.46 (0.40), residues: 169 loop : -0.82 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 124 TYR 0.023 0.001 TYR A 131 PHE 0.011 0.001 PHE A 211 TRP 0.016 0.001 TRP C 49 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (15029) covalent geometry : angle 0.45314 / 0.24 (20462) hydrogen bonds : bond 0.03416 / 2.30 ( 705) hydrogen bonds : angle 3.99170 / 2.82 ( 1957) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.553 Fit side-chains REVERT: A 60 THR cc_start: 0.7812 (p) cc_final: 0.7538 (m) REVERT: A 63 LYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6326 (ttmt) REVERT: A 122 VAL cc_start: 0.7627 (t) cc_final: 0.7324 (m) REVERT: A 174 ARG cc_start: 0.7217 (tpt90) cc_final: 0.6891 (tpt-90) REVERT: A 192 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6654 (mtp-110) REVERT: A 224 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8039 (pmtt) REVERT: A 374 MET cc_start: 0.7089 (mtm) cc_final: 0.6108 (tpt) REVERT: A 490 GLN cc_start: 0.7822 (mt0) cc_final: 0.7165 (mm110) REVERT: A 707 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8016 (mppt) REVERT: B 238 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8944 (mmp80) REVERT: B 314 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8659 (t0) REVERT: B 353 ARG cc_start: 0.7365 (ptt180) cc_final: 0.7079 (ptt180) REVERT: B 433 LYS cc_start: 0.7346 (mttt) cc_final: 0.7068 (mtpt) REVERT: B 638 GLU cc_start: 0.5320 (OUTLIER) cc_final: 0.3426 (tt0) REVERT: B 680 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6641 (mtm180) REVERT: B 683 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8236 (mm) REVERT: B 702 SER cc_start: 0.8373 (p) cc_final: 0.8088 (t) REVERT: B 705 TYR cc_start: 0.8825 (t80) cc_final: 0.8597 (t80) REVERT: C 8 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7591 (ttm) REVERT: C 10 MET cc_start: 0.7597 (mtp) cc_final: 0.7396 (mtp) REVERT: C 134 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8505 (mttt) REVERT: C 152 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6706 (ptmm) REVERT: C 197 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7740 (mmtp) REVERT: C 208 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8381 (mt-10) outliers start: 42 outliers final: 29 residues processed: 242 average time/residue: 0.1360 time to fit residues: 47.6665 Evaluate side-chains 247 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 23 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN B 413 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118715 restraints weight = 31669.855| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.01 r_work: 0.3117 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 15029 Z= 0.140 Angle : 0.717 59.196 20462 Z= 0.428 Chirality : 0.039 0.373 2270 Planarity : 0.004 0.048 2478 Dihedral : 8.169 85.012 2389 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.91 % Allowed : 13.02 % Favored : 84.07 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.54 % 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: 0.54 (0.21), residues: 1691 helix: 1.52 (0.19), residues: 824 sheet: -0.45 (0.40), residues: 169 loop : -0.81 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.000 ARG A 124 TYR 0.023 0.001 TYR A 131 PHE 0.009 0.001 PHE A 211 TRP 0.015 0.001 TRP C 49 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (15029) covalent geometry : angle 0.71748 / 0.43 (20462) hydrogen bonds : bond 0.03426 / 2.30 ( 705) hydrogen bonds : angle 3.99354 / 2.82 ( 1957) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 0.416 Fit side-chains REVERT: A 60 THR cc_start: 0.7827 (p) cc_final: 0.7557 (m) REVERT: A 63 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6337 (ttmt) REVERT: A 122 VAL cc_start: 0.7640 (t) cc_final: 0.7334 (m) REVERT: A 174 ARG cc_start: 0.7227 (tpt90) cc_final: 0.6896 (tpt-90) REVERT: A 192 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6642 (mtp-110) REVERT: A 224 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8062 (pmtt) REVERT: A 374 MET cc_start: 0.7132 (mtm) cc_final: 0.6127 (tpt) REVERT: A 391 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8488 (mp0) REVERT: A 490 GLN cc_start: 0.7852 (mt0) cc_final: 0.7184 (mm110) REVERT: A 707 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8052 (mppt) REVERT: B 238 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8946 (mmp80) REVERT: B 314 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8682 (t0) REVERT: B 353 ARG cc_start: 0.7412 (ptt180) cc_final: 0.7119 (ptt180) REVERT: B 433 LYS cc_start: 0.7357 (mttt) cc_final: 0.7070 (mtpt) REVERT: B 638 GLU cc_start: 0.5312 (OUTLIER) cc_final: 0.3405 (tt0) REVERT: B 680 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6630 (mtm180) REVERT: B 683 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8279 (mm) REVERT: B 702 SER cc_start: 0.8386 (p) cc_final: 0.8108 (t) REVERT: C 8 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7646 (ttm) REVERT: C 10 MET cc_start: 0.7638 (mtp) cc_final: 0.7434 (mtp) REVERT: C 134 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8531 (mttt) REVERT: C 152 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6714 (ptmm) REVERT: C 197 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7768 (mmtp) REVERT: C 208 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8450 (mt-10) outliers start: 44 outliers final: 32 residues processed: 234 average time/residue: 0.1210 time to fit residues: 40.9729 Evaluate side-chains 250 residues out of total 1511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 748 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 152 LYS Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain C residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8563 > 50: distance: 37 - 43: 3.779 distance: 43 - 44: 4.960 distance: 44 - 45: 6.155 distance: 44 - 47: 6.606 distance: 45 - 46: 8.141 distance: 45 - 54: 5.825 distance: 47 - 48: 9.517 distance: 48 - 49: 9.167 distance: 49 - 50: 6.643 distance: 50 - 51: 3.925 distance: 51 - 53: 8.683 distance: 55 - 56: 3.086 distance: 55 - 58: 4.766 distance: 56 - 57: 16.082 distance: 58 - 59: 5.315 distance: 58 - 60: 10.165 distance: 61 - 62: 13.027 distance: 62 - 63: 3.964 distance: 62 - 65: 11.684 distance: 63 - 64: 8.111 distance: 63 - 67: 11.064 distance: 65 - 66: 16.103 distance: 67 - 68: 12.209 distance: 68 - 69: 8.569 distance: 68 - 71: 9.182 distance: 69 - 70: 8.089 distance: 69 - 75: 12.291 distance: 71 - 72: 5.306 distance: 71 - 73: 25.350 distance: 72 - 74: 11.949 distance: 75 - 76: 10.340 distance: 76 - 77: 7.330 distance: 76 - 79: 14.827 distance: 77 - 78: 5.414 distance: 77 - 81: 12.031 distance: 79 - 80: 23.728 distance: 81 - 82: 7.077 distance: 82 - 83: 11.911 distance: 82 - 85: 11.309 distance: 83 - 84: 10.019 distance: 83 - 88: 7.438 distance: 85 - 86: 17.005 distance: 85 - 87: 18.381 distance: 88 - 89: 9.096 distance: 89 - 90: 8.949 distance: 89 - 92: 13.107 distance: 90 - 91: 15.947 distance: 90 - 96: 20.943 distance: 92 - 93: 4.212 distance: 92 - 94: 22.173 distance: 93 - 95: 10.039 distance: 96 - 97: 10.843 distance: 97 - 98: 22.613 distance: 97 - 100: 8.383 distance: 98 - 99: 21.620 distance: 98 - 104: 15.311 distance: 100 - 101: 15.638 distance: 101 - 102: 33.125 distance: 102 - 103: 13.344 distance: 104 - 105: 12.089 distance: 105 - 106: 16.133 distance: 105 - 108: 22.511 distance: 106 - 107: 17.893 distance: 106 - 113: 12.961 distance: 108 - 109: 4.240 distance: 109 - 110: 18.424 distance: 110 - 111: 16.620 distance: 111 - 112: 20.728 distance: 113 - 114: 20.787 distance: 114 - 115: 17.842 distance: 114 - 117: 10.464 distance: 115 - 116: 22.131 distance: 115 - 120: 20.893 distance: 117 - 118: 12.329 distance: 118 - 119: 23.197