Starting phenix.real_space_refine on Mon May 4 22:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xvi_67289/05_2026/9xvi_67289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xvi_67289/05_2026/9xvi_67289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xvi_67289/05_2026/9xvi_67289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xvi_67289/05_2026/9xvi_67289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xvi_67289/05_2026/9xvi_67289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xvi_67289/05_2026/9xvi_67289.map" } resolution = 3.65 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= 0.028 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 15130 2.51 5 N 3992 2.21 5 O 4458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23700 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5793 Classifications: {'peptide': 718} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 681} Chain: "C" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6057 Classifications: {'peptide': 764} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 721} Chain breaks: 2 Chain: "B" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5793 Classifications: {'peptide': 718} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 681} Chain: "D" Number of atoms: 6057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6057 Classifications: {'peptide': 764} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 721} Chain breaks: 2 Time building chain proxies: 5.51, per 1000 atoms: 0.23 Number of scatterers: 23700 At special positions: 0 Unit cell: (97.97, 269.66, 109.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4458 8.00 N 3992 7.00 C 15130 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: 1.79 Conformation dependent library (CDL) restraints added in 903.7 milliseconds 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 34 sheets defined 23.0% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.918A pdb=" N ARG A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 181 through 186 removed outlier: 4.543A pdb=" N THR A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.663A pdb=" N LYS A 192 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.127A pdb=" N LEU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.610A pdb=" N ASN A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 3.744A pdb=" N TYR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 319' Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.589A pdb=" N LEU A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 376 through 379 removed outlier: 3.642A pdb=" N TRP A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 446 through 458 removed outlier: 4.103A pdb=" N ARG A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.624A pdb=" N PHE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.223A pdb=" N VAL A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 556 removed outlier: 4.085A pdb=" N ARG A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 552 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 591 through 598 removed outlier: 3.858A pdb=" N LYS A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 596 " --> pdb=" O TRP A 592 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 Processing helix chain 'A' and resid 705 through 712 removed outlier: 3.563A pdb=" N ALA A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 Processing helix chain 'C' and resid 290 through 294 removed outlier: 4.037A pdb=" N LEU C 294 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.981A pdb=" N ALA C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 373 through 388 removed outlier: 3.545A pdb=" N MET C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS C 379 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 380 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.715A pdb=" N SER C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 453 Processing helix chain 'C' and resid 462 through 467 Processing helix chain 'C' and resid 477 through 485 Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.839A pdb=" N ARG C 533 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 4.301A pdb=" N VAL C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER C 578 " --> pdb=" O VAL C 574 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 579 " --> pdb=" O ASP C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 579' Processing helix chain 'C' and resid 606 through 621 removed outlier: 3.667A pdb=" N GLN C 610 " --> pdb=" O ARG C 606 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 614 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 646 removed outlier: 3.587A pdb=" N SER C 645 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG C 646 " --> pdb=" O LEU C 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 642 through 646' Processing helix chain 'C' and resid 656 through 676 removed outlier: 3.881A pdb=" N SER C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 672 " --> pdb=" O PHE C 668 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG C 673 " --> pdb=" O MET C 669 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.933A pdb=" N ARG B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 181 through 186 removed outlier: 4.537A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.685A pdb=" N LYS B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 205 through 213 removed outlier: 4.078A pdb=" N LEU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 285 removed outlier: 3.584A pdb=" N ASN B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 319 removed outlier: 3.800A pdb=" N TYR B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 319' Processing helix chain 'B' and resid 343 through 359 removed outlier: 3.646A pdb=" N LEU B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET B 359 " --> pdb=" O TRP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'B' and resid 376 through 379 removed outlier: 3.623A pdb=" N TRP B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 446 through 458 removed outlier: 4.085A pdb=" N ARG B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 451 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.619A pdb=" N PHE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 498 through 503 removed outlier: 4.223A pdb=" N VAL B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 removed outlier: 3.965A pdb=" N ARG B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 552 " --> pdb=" O MET B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 593 through 598 removed outlier: 3.745A pdb=" N GLU B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 616 Processing helix chain 'B' and resid 705 through 712 removed outlier: 3.569A pdb=" N GLN B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 719 Processing helix chain 'D' and resid 290 through 294 removed outlier: 4.040A pdb=" N LEU D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'D' and resid 320 through 326 removed outlier: 3.999A pdb=" N ALA D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 334 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.927A pdb=" N LYS D 379 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 426 removed outlier: 3.733A pdb=" N SER D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 453 Processing helix chain 'D' and resid 461 through 467 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.840A pdb=" N ARG D 533 " --> pdb=" O ARG D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 579 removed outlier: 4.308A pdb=" N VAL D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 579 " --> pdb=" O ASP D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 573 through 579' Processing helix chain 'D' and resid 606 through 621 removed outlier: 3.695A pdb=" N GLN D 610 " --> pdb=" O ARG D 606 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ARG D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 614 " --> pdb=" O GLN D 610 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 646 removed outlier: 3.548A pdb=" N SER D 645 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG D 646 " --> pdb=" O LEU D 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 642 through 646' Processing helix chain 'D' and resid 656 through 676 removed outlier: 3.922A pdb=" N SER D 671 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG D 673 " --> pdb=" O MET D 669 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 76 removed outlier: 4.677A pdb=" N ALA A 55 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 54 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180 removed outlier: 6.030A pdb=" N TYR A 178 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 292 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 363 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 420 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TRP A 445 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA A 422 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU A 444 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER A 487 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET A 563 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 489 " --> pdb=" O MET A 563 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR A 565 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.733A pdb=" N GLU A 224 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY A 251 " --> pdb=" O GLU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 631 through 633 removed outlier: 3.571A pdb=" N ALA A 650 " --> pdb=" O HIS A 633 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU A 660 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 733 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER A 735 " --> pdb=" O TRP A 684 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP A 684 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 672 through 675 Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 31 removed outlier: 3.532A pdb=" N LEU C 111 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 31 removed outlier: 3.518A pdb=" N ILE C 51 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.848A pdb=" N LEU C 130 " --> pdb=" O MET C 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 181 removed outlier: 3.601A pdb=" N VAL C 222 " --> pdb=" O TRP C 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 205 through 206 removed outlier: 3.870A pdb=" N TYR C 233 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 231 removed outlier: 3.626A pdb=" N GLY C 271 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 299 removed outlier: 6.056A pdb=" N TYR C 297 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL C 338 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU C 395 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 340 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 456 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU C 494 " --> pdb=" O ALA C 518 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU C 520 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA C 496 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLU C 519 " --> pdb=" O PHE C 562 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER C 561 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 626 " --> pdb=" O SER C 561 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN C 563 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN C 628 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 692 through 694 removed outlier: 3.764A pdb=" N PHE C 739 " --> pdb=" O PHE C 805 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 766 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 806 " --> pdb=" O ARG C 764 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ARG C 764 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 749 through 752 Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AC1, first strand: chain 'B' and resid 72 through 76 removed outlier: 4.695A pdb=" N ALA B 55 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 54 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC3, first strand: chain 'B' and resid 177 through 180 removed outlier: 5.998A pdb=" N TYR B 178 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 363 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 420 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP B 445 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA B 422 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU B 444 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER B 487 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N MET B 563 " --> pdb=" O SER B 487 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 489 " --> pdb=" O MET B 563 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR B 565 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.802A pdb=" N GLU B 224 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY B 251 " --> pdb=" O GLU B 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 631 through 633 removed outlier: 3.545A pdb=" N ALA B 650 " --> pdb=" O HIS B 633 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU B 660 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU B 733 " --> pdb=" O PRO B 686 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER B 735 " --> pdb=" O TRP B 684 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N TRP B 684 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 672 through 675 Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 31 removed outlier: 3.540A pdb=" N LEU D 111 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 25 through 31 removed outlier: 3.535A pdb=" N ILE D 51 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.853A pdb=" N LEU D 130 " --> pdb=" O MET D 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 99 through 102 Processing sheet with id=AD2, first strand: chain 'D' and resid 176 through 181 removed outlier: 3.598A pdb=" N VAL D 222 " --> pdb=" O TRP D 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 205 through 206 removed outlier: 3.856A pdb=" N TYR D 233 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 230 through 231 removed outlier: 3.627A pdb=" N GLY D 271 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 296 through 299 removed outlier: 6.055A pdb=" N TYR D 297 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL D 338 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU D 395 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU D 340 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY D 456 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 494 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU D 520 " --> pdb=" O LEU D 494 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA D 496 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU D 519 " --> pdb=" O PHE D 562 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER D 561 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL D 626 " --> pdb=" O SER D 561 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN D 563 " --> pdb=" O VAL D 626 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 692 through 694 removed outlier: 3.750A pdb=" N PHE D 739 " --> pdb=" O PHE D 805 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 766 " --> pdb=" O LEU D 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU D 806 " --> pdb=" O ARG D 764 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG D 764 " --> pdb=" O GLU D 806 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 749 through 752 650 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4176 1.32 - 1.45: 6768 1.45 - 1.57: 13224 1.57 - 1.69: 0 1.69 - 1.81: 182 Bond restraints: 24350 Sorted by residual: bond pdb=" CA ARG B 103 " pdb=" CB ARG B 103 " ideal model delta sigma weight residual 1.529 1.480 0.050 1.54e-02 4.22e+03 1.04e+01 bond pdb=" CA ARG A 103 " pdb=" CB ARG A 103 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.54e-02 4.22e+03 9.82e+00 bond pdb=" C ARG A 103 " pdb=" O ARG A 103 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.19e-02 7.06e+03 8.14e+00 bond pdb=" C ARG B 103 " pdb=" O ARG B 103 " ideal model delta sigma weight residual 1.235 1.202 0.033 1.19e-02 7.06e+03 7.53e+00 bond pdb=" N ARG B 103 " pdb=" CA ARG B 103 " ideal model delta sigma weight residual 1.461 1.483 -0.022 1.19e-02 7.06e+03 3.56e+00 ... (remaining 24345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 32607 2.40 - 4.81: 384 4.81 - 7.21: 27 7.21 - 9.61: 4 9.61 - 12.01: 4 Bond angle restraints: 33026 Sorted by residual: angle pdb=" C ARG B 103 " pdb=" CA ARG B 103 " pdb=" CB ARG B 103 " ideal model delta sigma weight residual 110.62 98.61 12.01 1.46e+00 4.69e-01 6.77e+01 angle pdb=" C ARG A 103 " pdb=" CA ARG A 103 " pdb=" CB ARG A 103 " ideal model delta sigma weight residual 110.62 98.78 11.84 1.46e+00 4.69e-01 6.58e+01 angle pdb=" N VAL A 557 " pdb=" CA VAL A 557 " pdb=" C VAL A 557 " ideal model delta sigma weight residual 113.53 107.87 5.66 9.80e-01 1.04e+00 3.34e+01 angle pdb=" N VAL B 557 " pdb=" CA VAL B 557 " pdb=" C VAL B 557 " ideal model delta sigma weight residual 113.53 107.94 5.59 9.80e-01 1.04e+00 3.25e+01 angle pdb=" N ARG B 103 " pdb=" CA ARG B 103 " pdb=" C ARG B 103 " ideal model delta sigma weight residual 107.80 116.67 -8.87 1.73e+00 3.34e-01 2.63e+01 ... (remaining 33021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13041 17.94 - 35.89: 1070 35.89 - 53.83: 196 53.83 - 71.78: 32 71.78 - 89.72: 19 Dihedral angle restraints: 14358 sinusoidal: 5774 harmonic: 8584 Sorted by residual: dihedral pdb=" C ARG A 103 " pdb=" N ARG A 103 " pdb=" CA ARG A 103 " pdb=" CB ARG A 103 " ideal model delta harmonic sigma weight residual -122.60 -108.21 -14.39 0 2.50e+00 1.60e-01 3.31e+01 dihedral pdb=" C ARG B 103 " pdb=" N ARG B 103 " pdb=" CA ARG B 103 " pdb=" CB ARG B 103 " ideal model delta harmonic sigma weight residual -122.60 -108.90 -13.70 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA GLY D 774 " pdb=" C GLY D 774 " pdb=" N PHE D 775 " pdb=" CA PHE D 775 " ideal model delta harmonic sigma weight residual -180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 14355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2886 0.054 - 0.108: 523 0.108 - 0.163: 79 0.163 - 0.217: 2 0.217 - 0.271: 2 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CB ILE B 639 " pdb=" CA ILE B 639 " pdb=" CG1 ILE B 639 " pdb=" CG2 ILE B 639 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE A 639 " pdb=" CA ILE A 639 " pdb=" CG1 ILE A 639 " pdb=" CG2 ILE A 639 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ARG A 103 " pdb=" N ARG A 103 " pdb=" C ARG A 103 " pdb=" CB ARG A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 3489 not shown) Planarity restraints: 4294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 77 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.79e+00 pdb=" N PRO A 78 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 77 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO B 78 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 78 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 78 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 474 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.37e+00 pdb=" N PRO B 475 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " -0.032 5.00e-02 4.00e+02 ... (remaining 4291 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1158 2.73 - 3.27: 22613 3.27 - 3.82: 36243 3.82 - 4.36: 42978 4.36 - 4.90: 74886 Nonbonded interactions: 177878 Sorted by model distance: nonbonded pdb=" OD1 ASP C 746 " pdb=" ND1 HIS C 747 " model vdw 2.189 3.120 nonbonded pdb=" OD1 ASP D 746 " pdb=" ND1 HIS D 747 " model vdw 2.194 3.120 nonbonded pdb=" OD1 ASP D 737 " pdb=" OG1 THR D 807 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASP C 737 " pdb=" OG1 THR C 807 " model vdw 2.211 3.040 nonbonded pdb=" O ILE C 576 " pdb=" OG SER C 589 " model vdw 2.218 3.040 ... (remaining 177873 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.790 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.002 0.050 24350 Z= 0.123 Angle : 0.618 12.014 33026 Z= 0.343 Chirality : 0.043 0.271 3492 Planarity : 0.005 0.065 4294 Dihedral : 13.586 89.722 8850 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.55 % Favored : 91.18 % Rotamer: Outliers : 0.08 % Allowed : 0.15 % Favored : 99.77 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.13 % 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: -1.48 (0.15), residues: 2948 helix: 0.27 (0.24), residues: 498 sheet: 0.30 (0.21), residues: 666 loop : -1.98 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 80 TYR 0.021 0.001 TYR B 230 PHE 0.015 0.001 PHE B 337 TRP 0.016 0.001 TRP C 693 HIS 0.005 0.001 HIS D 747 Details of bonding type rmsd covalent geometry : bond 0.00233 (24350) covalent geometry : angle 0.61809 (33026) hydrogen bonds : bond 0.16642 ( 598) hydrogen bonds : angle 6.42151 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 613 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8007 (mtt-85) REVERT: A 112 GLU cc_start: 0.7233 (pm20) cc_final: 0.6791 (pm20) REVERT: A 192 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8694 (mmtm) REVERT: A 492 CYS cc_start: 0.8590 (m) cc_final: 0.8261 (m) REVERT: A 521 GLU cc_start: 0.6515 (tp30) cc_final: 0.6131 (pt0) REVERT: A 528 ASN cc_start: 0.8510 (p0) cc_final: 0.8005 (p0) REVERT: A 534 ASP cc_start: 0.7781 (t70) cc_final: 0.7567 (t0) REVERT: A 597 GLU cc_start: 0.8377 (tt0) cc_final: 0.8050 (mt-10) REVERT: A 628 LYS cc_start: 0.8875 (tppt) cc_final: 0.8673 (ttmm) REVERT: C 116 GLU cc_start: 0.7657 (mp0) cc_final: 0.6994 (tp30) REVERT: C 120 LYS cc_start: 0.5801 (ptpp) cc_final: 0.5294 (tttt) REVERT: C 227 ASP cc_start: 0.7509 (t0) cc_final: 0.6970 (p0) REVERT: C 526 ARG cc_start: 0.6020 (ttp-170) cc_final: 0.5696 (ttp-170) REVERT: C 535 ARG cc_start: 0.8776 (ptm160) cc_final: 0.8122 (ptt90) REVERT: C 546 CYS cc_start: 0.8909 (m) cc_final: 0.8668 (p) REVERT: C 548 SER cc_start: 0.6575 (m) cc_final: 0.5965 (t) REVERT: C 575 ASP cc_start: 0.6338 (t70) cc_final: 0.5699 (t70) REVERT: C 627 LEU cc_start: 0.8056 (tp) cc_final: 0.7850 (tp) REVERT: C 652 ASN cc_start: 0.7435 (m-40) cc_final: 0.6627 (t0) REVERT: C 668 PHE cc_start: 0.7977 (t80) cc_final: 0.7617 (t80) REVERT: C 683 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7214 (mmt90) REVERT: C 685 PHE cc_start: 0.6157 (m-10) cc_final: 0.5678 (m-10) REVERT: C 747 HIS cc_start: 0.7262 (p-80) cc_final: 0.6951 (p90) REVERT: B 30 LEU cc_start: 0.8317 (mp) cc_final: 0.8016 (mt) REVERT: B 49 SER cc_start: 0.9245 (t) cc_final: 0.8871 (p) REVERT: B 192 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8608 (mmtm) REVERT: B 435 MET cc_start: 0.8063 (pmm) cc_final: 0.7856 (pmm) REVERT: B 534 ASP cc_start: 0.7843 (t70) cc_final: 0.7642 (t0) REVERT: B 597 GLU cc_start: 0.8346 (tt0) cc_final: 0.8042 (mt-10) REVERT: B 628 LYS cc_start: 0.8931 (tppt) cc_final: 0.8683 (ttmm) REVERT: D 116 GLU cc_start: 0.7567 (mp0) cc_final: 0.6829 (tp30) REVERT: D 120 LYS cc_start: 0.6104 (ptpp) cc_final: 0.5678 (tttt) REVERT: D 147 ARG cc_start: 0.7484 (mtp-110) cc_final: 0.7013 (mtm110) REVERT: D 227 ASP cc_start: 0.7498 (t0) cc_final: 0.7035 (p0) REVERT: D 292 GLU cc_start: 0.8396 (pm20) cc_final: 0.8069 (pt0) REVERT: D 535 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8081 (ptt90) REVERT: D 546 CYS cc_start: 0.8798 (m) cc_final: 0.8593 (p) REVERT: D 548 SER cc_start: 0.6329 (m) cc_final: 0.5928 (t) REVERT: D 575 ASP cc_start: 0.6260 (t70) cc_final: 0.5434 (t70) REVERT: D 683 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7272 (mmt90) REVERT: D 685 PHE cc_start: 0.6173 (m-10) cc_final: 0.5709 (m-10) REVERT: D 747 HIS cc_start: 0.7422 (p-80) cc_final: 0.7117 (p90) outliers start: 2 outliers final: 1 residues processed: 615 average time/residue: 0.1645 time to fit residues: 156.5291 Evaluate side-chains 351 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain B residue 103 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 240 HIS A 476 ASN A 506 ASN A 510 ASN ** C 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 315 ASN B 340 ASN B 476 ASN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.184193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138486 restraints weight = 36995.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142505 restraints weight = 19510.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145123 restraints weight = 13193.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146684 restraints weight = 10409.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147695 restraints weight = 9043.837| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24350 Z= 0.133 Angle : 0.605 13.021 33026 Z= 0.313 Chirality : 0.045 0.268 3492 Planarity : 0.005 0.052 4294 Dihedral : 4.419 57.107 3238 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.75 % Favored : 90.98 % Rotamer: Outliers : 1.87 % Allowed : 8.31 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -1.45 (0.15), residues: 2948 helix: 0.41 (0.24), residues: 502 sheet: 0.25 (0.21), residues: 670 loop : -1.98 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 80 TYR 0.013 0.001 TYR D 434 PHE 0.025 0.001 PHE A 267 TRP 0.018 0.002 TRP D 651 HIS 0.005 0.001 HIS C 453 Details of bonding type rmsd covalent geometry : bond 0.00306 (24350) covalent geometry : angle 0.60456 (33026) hydrogen bonds : bond 0.03618 ( 598) hydrogen bonds : angle 5.11410 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8354 (mtp) cc_final: 0.8120 (mtp) REVERT: A 204 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6095 (mp0) REVERT: A 531 GLU cc_start: 0.7459 (mp0) cc_final: 0.7134 (mp0) REVERT: A 532 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 541 LYS cc_start: 0.8428 (mttt) cc_final: 0.8216 (ttmm) REVERT: A 655 ASP cc_start: 0.8657 (t0) cc_final: 0.8307 (t70) REVERT: C 100 GLU cc_start: 0.7179 (pp20) cc_final: 0.6763 (tm-30) REVERT: C 120 LYS cc_start: 0.5469 (ptpp) cc_final: 0.5248 (tttt) REVERT: C 147 ARG cc_start: 0.7615 (mtp-110) cc_final: 0.7289 (mtm110) REVERT: C 191 CYS cc_start: 0.6985 (m) cc_final: 0.4829 (p) REVERT: C 308 ARG cc_start: 0.8378 (tpm170) cc_final: 0.8170 (tpm170) REVERT: C 384 LYS cc_start: 0.8426 (tptt) cc_final: 0.8151 (tppt) REVERT: C 497 ASP cc_start: 0.8105 (t0) cc_final: 0.7770 (t0) REVERT: C 526 ARG cc_start: 0.6290 (ttp-170) cc_final: 0.5939 (ttp-170) REVERT: C 535 ARG cc_start: 0.8557 (ptm160) cc_final: 0.8237 (ptt90) REVERT: C 575 ASP cc_start: 0.6315 (t70) cc_final: 0.5824 (t70) REVERT: C 652 ASN cc_start: 0.7352 (m-40) cc_final: 0.6643 (t0) REVERT: C 683 ARG cc_start: 0.8267 (mtt90) cc_final: 0.7348 (mmt90) REVERT: B 112 GLU cc_start: 0.7332 (pm20) cc_final: 0.6969 (pm20) REVERT: B 478 TYR cc_start: 0.8779 (m-80) cc_final: 0.8393 (m-80) REVERT: B 531 GLU cc_start: 0.7467 (mp0) cc_final: 0.7195 (mp0) REVERT: B 532 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7120 (tm-30) REVERT: D 100 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6906 (tm-30) REVERT: D 116 GLU cc_start: 0.7531 (mp0) cc_final: 0.7134 (tp30) REVERT: D 147 ARG cc_start: 0.7573 (mtp-110) cc_final: 0.7371 (mtm110) REVERT: D 486 ASP cc_start: 0.8031 (t0) cc_final: 0.7593 (t0) REVERT: D 497 ASP cc_start: 0.8188 (t0) cc_final: 0.7809 (t0) REVERT: D 526 ARG cc_start: 0.6273 (ttp-170) cc_final: 0.5946 (ttp-170) REVERT: D 535 ARG cc_start: 0.8522 (ptm160) cc_final: 0.7977 (ptt90) REVERT: D 544 ARG cc_start: 0.7508 (mtt-85) cc_final: 0.7219 (mmm-85) REVERT: D 631 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7435 (t70) REVERT: D 683 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7333 (mmt90) REVERT: D 747 HIS cc_start: 0.7114 (p-80) cc_final: 0.6845 (p90) outliers start: 49 outliers final: 31 residues processed: 386 average time/residue: 0.1654 time to fit residues: 100.5850 Evaluate side-chains 320 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 647 LYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 615 GLU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 514 TRP Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 765 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 58 optimal weight: 0.5980 overall best weight: 0.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN B 240 HIS ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 473 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.179937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133548 restraints weight = 37207.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137461 restraints weight = 19703.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139990 restraints weight = 13453.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141443 restraints weight = 10713.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142504 restraints weight = 9384.410| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24350 Z= 0.120 Angle : 0.568 12.223 33026 Z= 0.292 Chirality : 0.044 0.278 3492 Planarity : 0.004 0.052 4294 Dihedral : 4.117 19.406 3230 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.18 % Favored : 91.55 % Rotamer: Outliers : 2.33 % Allowed : 10.64 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -1.42 (0.15), residues: 2948 helix: 0.40 (0.24), residues: 510 sheet: 0.30 (0.20), residues: 676 loop : -1.98 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 544 TYR 0.011 0.001 TYR B 581 PHE 0.025 0.001 PHE D 775 TRP 0.020 0.001 TRP D 226 HIS 0.004 0.001 HIS D 747 Details of bonding type rmsd covalent geometry : bond 0.00280 (24350) covalent geometry : angle 0.56799 (33026) hydrogen bonds : bond 0.03440 ( 598) hydrogen bonds : angle 4.81130 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 306 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 HIS cc_start: 0.5684 (m-70) cc_final: 0.5335 (m-70) REVERT: C 100 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: C 115 LEU cc_start: 0.7602 (mt) cc_final: 0.7380 (mt) REVERT: C 120 LYS cc_start: 0.5745 (ptpp) cc_final: 0.5538 (tttt) REVERT: C 308 ARG cc_start: 0.8308 (tpm170) cc_final: 0.8081 (tpm170) REVERT: C 362 MET cc_start: 0.6070 (ptm) cc_final: 0.5758 (ptm) REVERT: C 486 ASP cc_start: 0.8181 (t0) cc_final: 0.7867 (t0) REVERT: C 497 ASP cc_start: 0.8221 (t0) cc_final: 0.7877 (t0) REVERT: C 526 ARG cc_start: 0.6274 (ttp-170) cc_final: 0.5922 (ttp-170) REVERT: C 575 ASP cc_start: 0.6501 (t70) cc_final: 0.6273 (t70) REVERT: C 631 ASP cc_start: 0.8125 (t0) cc_final: 0.7775 (t70) REVERT: C 652 ASN cc_start: 0.7398 (m-40) cc_final: 0.6676 (t0) REVERT: C 683 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7357 (mmt90) REVERT: C 775 PHE cc_start: 0.6406 (p90) cc_final: 0.6022 (p90) REVERT: B 103 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7723 (ttm-80) REVERT: B 112 GLU cc_start: 0.7369 (pm20) cc_final: 0.6966 (pm20) REVERT: B 478 TYR cc_start: 0.8814 (m-80) cc_final: 0.8521 (m-80) REVERT: D 100 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7050 (tm-30) REVERT: D 116 GLU cc_start: 0.7475 (mp0) cc_final: 0.7146 (tp30) REVERT: D 147 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7408 (mtm110) REVERT: D 273 LEU cc_start: 0.8554 (mp) cc_final: 0.8324 (mp) REVERT: D 362 MET cc_start: 0.6156 (ptm) cc_final: 0.5836 (ptm) REVERT: D 486 ASP cc_start: 0.8089 (t0) cc_final: 0.7245 (t0) REVERT: D 526 ARG cc_start: 0.6276 (ttp-170) cc_final: 0.6023 (ttp-170) REVERT: D 535 ARG cc_start: 0.8554 (ptm160) cc_final: 0.8272 (ptt90) REVERT: D 631 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7734 (t70) REVERT: D 668 PHE cc_start: 0.7881 (t80) cc_final: 0.7648 (t80) REVERT: D 683 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7485 (mmt90) outliers start: 61 outliers final: 42 residues processed: 352 average time/residue: 0.1638 time to fit residues: 90.5342 Evaluate side-chains 300 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 514 TRP Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 647 LYS Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 782 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 514 TRP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 546 CYS Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 631 ASP Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 647 LYS Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 765 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2298 > 50: distance: 36 - 44: 27.118 distance: 44 - 45: 18.492 distance: 45 - 46: 47.355 distance: 45 - 48: 20.695 distance: 46 - 47: 41.167 distance: 46 - 52: 50.054 distance: 48 - 49: 44.449 distance: 49 - 50: 34.766 distance: 49 - 51: 24.870 distance: 52 - 53: 24.947 distance: 53 - 54: 25.031 distance: 53 - 56: 4.672 distance: 54 - 55: 18.191 distance: 54 - 57: 25.329 distance: 57 - 58: 12.766 distance: 57 - 175: 23.331 distance: 58 - 59: 23.391 distance: 58 - 61: 28.851 distance: 59 - 60: 47.993 distance: 59 - 64: 38.555 distance: 60 - 172: 31.826 distance: 61 - 62: 46.426 distance: 61 - 63: 51.515 distance: 64 - 65: 20.706 distance: 65 - 66: 17.993 distance: 65 - 68: 37.732 distance: 66 - 67: 21.989 distance: 66 - 72: 32.210 distance: 68 - 69: 46.334 distance: 69 - 70: 42.997 distance: 69 - 71: 7.596 distance: 72 - 73: 52.202 distance: 72 - 161: 22.696 distance: 73 - 74: 3.961 distance: 73 - 76: 17.980 distance: 74 - 75: 10.606 distance: 75 - 158: 27.118 distance: 76 - 77: 42.213 distance: 76 - 78: 48.894 distance: 79 - 80: 46.552 distance: 80 - 81: 52.839 distance: 80 - 83: 21.617 distance: 81 - 82: 55.946 distance: 81 - 85: 5.025 distance: 83 - 84: 21.455 distance: 85 - 86: 15.485 distance: 86 - 87: 13.290 distance: 86 - 89: 39.944 distance: 87 - 88: 56.929 distance: 87 - 93: 61.415 distance: 89 - 90: 32.912 distance: 90 - 91: 22.231 distance: 90 - 92: 37.007 distance: 93 - 94: 21.532 distance: 93 - 99: 21.603 distance: 94 - 95: 19.010 distance: 94 - 97: 38.173 distance: 95 - 96: 17.595 distance: 95 - 100: 47.107 distance: 97 - 98: 44.007 distance: 98 - 99: 47.092 distance: 100 - 101: 24.809 distance: 101 - 102: 15.914 distance: 101 - 104: 20.721 distance: 102 - 103: 45.257 distance: 102 - 108: 35.990 distance: 104 - 105: 33.789 distance: 105 - 106: 32.661 distance: 105 - 107: 13.417 distance: 108 - 109: 11.780 distance: 109 - 110: 14.834 distance: 109 - 112: 32.929 distance: 110 - 111: 22.897 distance: 110 - 119: 26.523 distance: 112 - 113: 50.013 distance: 113 - 114: 47.964 distance: 114 - 115: 35.213 distance: 115 - 116: 9.831 distance: 116 - 117: 10.319 distance: 116 - 118: 12.230