Starting phenix.real_space_refine on Fri Jun 20 15:53:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6on2_20133/06_2025/6on2_20133.cif Found real_map, /net/cci-nas-00/data/ceres_data/6on2_20133/06_2025/6on2_20133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6on2_20133/06_2025/6on2_20133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6on2_20133/06_2025/6on2_20133.map" model { file = "/net/cci-nas-00/data/ceres_data/6on2_20133/06_2025/6on2_20133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6on2_20133/06_2025/6on2_20133.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.014 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 16 5.49 5 Mg 5 5.21 5 S 138 5.16 5 C 15268 2.51 5 N 4307 2.21 5 O 4616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24350 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "B" Number of atoms: 4052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4052 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain: "C" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "D" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4001 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 24, 'TRANS': 493} Chain breaks: 1 Chain: "E" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4041 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 24, 'TRANS': 498} Chain: "F" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3955 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 24, 'TRANS': 487} Chain breaks: 1 Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.85, per 1000 atoms: 0.61 Number of scatterers: 24350 At special positions: 0 Unit cell: (131.1, 136.85, 129.95, 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 138 16.00 P 16 15.00 Mg 5 11.99 O 4616 8.00 N 4307 7.00 C 15268 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: 6.25 Conformation dependent library (CDL) restraints added in 3.3 seconds 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 28 sheets defined 47.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.590A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 285 through 300 removed outlier: 3.743A pdb=" N THR A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 327 through 341 Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.772A pdb=" N LYS A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.619A pdb=" N ALA A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.770A pdb=" N ASP A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.719A pdb=" N LYS A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.652A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 657 through 660 Processing helix chain 'A' and resid 681 through 694 removed outlier: 3.552A pdb=" N THR A 686 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.711A pdb=" N LYS A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 5.057A pdb=" N ARG A 742 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 747 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.732A pdb=" N VAL A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 264 through 279 Processing helix chain 'B' and resid 285 through 299 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 327 through 344 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.960A pdb=" N SER B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.303A pdb=" N ILE B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.823A pdb=" N GLU B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 451 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 515 removed outlier: 3.636A pdb=" N LYS B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 631 through 648 Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.545A pdb=" N MET B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.774A pdb=" N LYS B 722 " --> pdb=" O GLY B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 747 removed outlier: 4.173A pdb=" N ARG B 742 " --> pdb=" O ASP B 739 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 747 " --> pdb=" O LEU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 755 Processing helix chain 'B' and resid 762 through 770 removed outlier: 3.770A pdb=" N VAL B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 285 through 301 removed outlier: 3.618A pdb=" N VAL C 301 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 327 through 344 Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.876A pdb=" N GLN C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.529A pdb=" N GLU C 390 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 Processing helix chain 'C' and resid 439 through 444 removed outlier: 4.318A pdb=" N VAL C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 484 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 513 removed outlier: 3.535A pdb=" N LYS C 509 " --> pdb=" O HIS C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 Processing helix chain 'C' and resid 541 through 561 Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.679A pdb=" N GLN C 635 " --> pdb=" O GLY C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 Processing helix chain 'C' and resid 677 through 679 No H-bonds generated for 'chain 'C' and resid 677 through 679' Processing helix chain 'C' and resid 680 through 694 Processing helix chain 'C' and resid 718 through 730 removed outlier: 3.753A pdb=" N LYS C 722 " --> pdb=" O GLY C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 747 removed outlier: 4.804A pdb=" N ARG C 742 " --> pdb=" O ASP C 739 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 747 " --> pdb=" O LEU C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 755 Processing helix chain 'C' and resid 762 through 771 removed outlier: 3.840A pdb=" N VAL C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 264 through 280 removed outlier: 3.950A pdb=" N MET D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 Processing helix chain 'D' and resid 313 through 323 Processing helix chain 'D' and resid 327 through 341 Processing helix chain 'D' and resid 362 through 374 removed outlier: 3.624A pdb=" N GLY D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 405 through 414 removed outlier: 3.575A pdb=" N LYS D 409 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.546A pdb=" N MET D 428 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.845A pdb=" N ALA D 439 " --> pdb=" O ASP D 435 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 484 removed outlier: 4.045A pdb=" N ARG D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.532A pdb=" N LYS D 509 " --> pdb=" O HIS D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 536 removed outlier: 3.720A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 536 " --> pdb=" O ILE D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 562 removed outlier: 3.529A pdb=" N ASP D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 648 Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 677 through 679 No H-bonds generated for 'chain 'D' and resid 677 through 679' Processing helix chain 'D' and resid 680 through 694 removed outlier: 3.787A pdb=" N LEU D 692 " --> pdb=" O LEU D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 728 Processing helix chain 'D' and resid 739 through 747 removed outlier: 4.630A pdb=" N ARG D 742 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 747 " --> pdb=" O LEU D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 755 Processing helix chain 'D' and resid 762 through 771 Processing helix chain 'E' and resid 254 through 262 removed outlier: 3.982A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 281 Processing helix chain 'E' and resid 285 through 299 Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 327 through 342 Processing helix chain 'E' and resid 362 through 374 removed outlier: 3.709A pdb=" N GLY E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 404 through 414 Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.693A pdb=" N ALA E 439 " --> pdb=" O ASP E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.587A pdb=" N ASP E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 removed outlier: 3.583A pdb=" N LYS E 498 " --> pdb=" O THR E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 512 removed outlier: 3.516A pdb=" N GLU E 512 " --> pdb=" O PRO E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 Processing helix chain 'E' and resid 541 through 563 removed outlier: 3.914A pdb=" N LYS E 563 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 579 Processing helix chain 'E' and resid 631 through 648 Processing helix chain 'E' and resid 657 through 661 Processing helix chain 'E' and resid 677 through 679 No H-bonds generated for 'chain 'E' and resid 677 through 679' Processing helix chain 'E' and resid 680 through 694 removed outlier: 3.590A pdb=" N THR E 686 " --> pdb=" O ILE E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 729 removed outlier: 3.957A pdb=" N LYS E 722 " --> pdb=" O GLY E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 747 removed outlier: 4.351A pdb=" N ARG E 742 " --> pdb=" O ASP E 739 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE E 747 " --> pdb=" O LEU E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 755 removed outlier: 3.567A pdb=" N ILE E 752 " --> pdb=" O PRO E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 771 removed outlier: 3.783A pdb=" N VAL E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 769 " --> pdb=" O ASP E 765 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 771 " --> pdb=" O LEU E 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 261 removed outlier: 3.776A pdb=" N ALA F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 279 Processing helix chain 'F' and resid 285 through 297 Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 327 through 344 Processing helix chain 'F' and resid 364 through 374 removed outlier: 3.557A pdb=" N GLY F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 414 removed outlier: 3.840A pdb=" N MET F 410 " --> pdb=" O LEU F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 445 removed outlier: 4.363A pdb=" N VAL F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 removed outlier: 3.978A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 506 removed outlier: 3.567A pdb=" N LEU F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 515 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 542 through 561 Processing helix chain 'F' and resid 631 through 648 Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 694 removed outlier: 3.516A pdb=" N MET F 684 " --> pdb=" O ALA F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 730 removed outlier: 3.662A pdb=" N GLY F 730 " --> pdb=" O ALA F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 747 removed outlier: 4.721A pdb=" N ARG F 742 " --> pdb=" O ASP F 739 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 747 " --> pdb=" O LEU F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 755 Processing helix chain 'F' and resid 762 through 771 removed outlier: 3.755A pdb=" N VAL F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 769 " --> pdb=" O ASP F 765 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 771 " --> pdb=" O LEU F 767 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.205A pdb=" N GLN A 376 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU A 421 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 469 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N PHE A 420 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR A 471 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 422 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 352 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER A 472 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU A 354 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 351 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE A 488 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS A 353 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 523 removed outlier: 6.627A pdb=" N THR A 522 " --> pdb=" O ILE A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 627 removed outlier: 4.229A pdb=" N LYS A 623 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N GLN A 597 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N MET A 703 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 599 " --> pdb=" O MET A 703 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 734 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 760 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 736 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.606A pdb=" N GLU A 706 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 381 removed outlier: 7.370A pdb=" N VAL B 469 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 420 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR B 471 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 422 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 351 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 488 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N CYS B 353 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AA8, first strand: chain 'B' and resid 624 through 627 removed outlier: 9.684A pdb=" N GLN B 597 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N MET B 703 " --> pdb=" O GLN B 597 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 599 " --> pdb=" O MET B 703 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 702 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL B 734 " --> pdb=" O HIS B 758 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 760 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 736 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 706 through 707 Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 381 removed outlier: 7.574A pdb=" N VAL C 469 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 420 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR C 471 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU C 422 " --> pdb=" O THR C 471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.085A pdb=" N THR C 522 " --> pdb=" O ILE C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 598 through 603 Processing sheet with id=AB4, first strand: chain 'C' and resid 706 through 707 Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 737 removed outlier: 6.448A pdb=" N VAL C 734 " --> pdb=" O HIS C 758 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL C 760 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 736 " --> pdb=" O VAL C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 381 removed outlier: 6.771A pdb=" N GLN D 376 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU D 421 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL D 378 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP D 423 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N MET D 380 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 469 " --> pdb=" O PRO D 418 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE D 420 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR D 471 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU D 422 " --> pdb=" O THR D 471 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 351 " --> pdb=" O GLU D 486 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE D 488 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N CYS D 353 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 521 through 523 removed outlier: 6.632A pdb=" N THR D 522 " --> pdb=" O ILE D 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 624 through 627 removed outlier: 6.575A pdb=" N THR D 625 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL D 701 " --> pdb=" O GLN D 597 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR D 599 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET D 703 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 601 " --> pdb=" O MET D 703 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 702 " --> pdb=" O LEU D 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.568A pdb=" N GLU D 706 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 376 through 381 removed outlier: 6.675A pdb=" N GLN E 376 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 421 " --> pdb=" O GLN E 376 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP E 423 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET E 380 " --> pdb=" O ASP E 423 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL E 469 " --> pdb=" O PRO E 418 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE E 420 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR E 471 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU E 422 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU E 352 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ILE E 351 " --> pdb=" O GLU E 486 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'E' and resid 521 through 523 removed outlier: 6.968A pdb=" N THR E 522 " --> pdb=" O ILE E 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 624 through 627 removed outlier: 6.879A pdb=" N THR E 599 " --> pdb=" O MET E 703 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL E 734 " --> pdb=" O HIS E 758 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL E 760 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE E 736 " --> pdb=" O VAL E 760 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 706 through 707 Processing sheet with id=AC6, first strand: chain 'F' and resid 376 through 381 removed outlier: 6.522A pdb=" N GLN F 376 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU F 421 " --> pdb=" O GLN F 376 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL F 378 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASP F 423 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N MET F 380 " --> pdb=" O ASP F 423 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL F 469 " --> pdb=" O PRO F 418 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE F 420 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N THR F 471 " --> pdb=" O PHE F 420 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 422 " --> pdb=" O THR F 471 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU F 352 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER F 472 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU F 354 " --> pdb=" O SER F 472 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'F' and resid 521 through 523 removed outlier: 6.214A pdb=" N THR F 522 " --> pdb=" O ILE F 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 624 through 627 removed outlier: 9.563A pdb=" N GLN F 597 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N MET F 703 " --> pdb=" O GLN F 597 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR F 599 " --> pdb=" O MET F 703 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 734 " --> pdb=" O HIS F 758 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL F 760 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE F 736 " --> pdb=" O VAL F 760 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 706 through 707 1028 hydrogen bonds defined for protein. 2949 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: 8.79 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4769 1.33 - 1.45: 5039 1.45 - 1.57: 14621 1.57 - 1.69: 26 1.69 - 1.81: 246 Bond restraints: 24701 Sorted by residual: bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.17e+01 ... (remaining 24696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 33049 3.60 - 7.20: 288 7.20 - 10.80: 25 10.80 - 14.40: 3 14.40 - 18.00: 6 Bond angle restraints: 33371 Sorted by residual: angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 121.87 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 122.25 17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 122.34 17.53 1.00e+00 1.00e+00 3.07e+02 angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 122.75 17.12 1.00e+00 1.00e+00 2.93e+02 angle pdb=" PA ATP D 801 " pdb=" O3A ATP D 801 " pdb=" PB ATP D 801 " ideal model delta sigma weight residual 136.83 121.66 15.17 1.00e+00 1.00e+00 2.30e+02 ... (remaining 33366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.70: 15056 23.70 - 47.40: 357 47.40 - 71.10: 31 71.10 - 94.80: 4 94.80 - 118.50: 1 Dihedral angle restraints: 15449 sinusoidal: 6465 harmonic: 8984 Sorted by residual: dihedral pdb=" C5' ADP E 801 " pdb=" O5' ADP E 801 " pdb=" PA ADP E 801 " pdb=" O2A ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 -178.50 118.50 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA LEU A 422 " pdb=" C LEU A 422 " pdb=" N ASP A 423 " pdb=" CA ASP A 423 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA VAL E 668 " pdb=" C VAL E 668 " pdb=" N PRO E 669 " pdb=" CA PRO E 669 " ideal model delta harmonic sigma weight residual -180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 15446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2298 0.045 - 0.090: 1153 0.090 - 0.135: 330 0.135 - 0.181: 67 0.181 - 0.226: 15 Chirality restraints: 3863 Sorted by residual: chirality pdb=" CA VAL F 378 " pdb=" N VAL F 378 " pdb=" C VAL F 378 " pdb=" CB VAL F 378 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL F 581 " pdb=" CA VAL F 581 " pdb=" CG1 VAL F 581 " pdb=" CG2 VAL F 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO F 669 " pdb=" N PRO F 669 " pdb=" C PRO F 669 " pdb=" CB PRO F 669 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 3860 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 689 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C VAL A 689 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL A 689 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 690 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 690 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C SER C 690 " 0.048 2.00e-02 2.50e+03 pdb=" O SER C 690 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS C 691 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 684 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C MET C 684 " -0.047 2.00e-02 2.50e+03 pdb=" O MET C 684 " 0.018 2.00e-02 2.50e+03 pdb=" N CYS C 685 " 0.016 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 274 2.64 - 3.20: 20993 3.20 - 3.77: 37303 3.77 - 4.33: 53734 4.33 - 4.90: 86326 Nonbonded interactions: 198630 Sorted by model distance: nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 2.073 2.170 nonbonded pdb=" OG1 THR B 363 " pdb="MG MG B 802 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A 363 " pdb="MG MG A 802 " model vdw 2.081 2.170 nonbonded pdb=" O3G ATP A 801 " pdb="MG MG A 802 " model vdw 2.097 2.170 nonbonded pdb=" O2G ATP D 801 " pdb="MG MG D 802 " model vdw 2.112 2.170 ... (remaining 198625 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'B' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'C' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'D' and (resid 253 through 383 or resid 395 through 775)) selection = (chain 'E' and (resid 253 through 383 or resid 395 through 585 or resid 591 thro \ ugh 775)) selection = (chain 'F' and (resid 253 through 585 or resid 591 through 775)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.540 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.110 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.006 0.078 24701 Z= 0.313 Angle : 0.983 18.001 33371 Z= 0.605 Chirality : 0.057 0.226 3863 Planarity : 0.008 0.065 4272 Dihedral : 10.370 118.500 9663 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 0.42 % Allowed : 3.05 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.12), residues: 3112 helix: -3.11 (0.10), residues: 1343 sheet: -1.47 (0.22), residues: 492 loop : -2.38 (0.14), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 603 HIS 0.011 0.002 HIS A 324 PHE 0.026 0.003 PHE D 420 TYR 0.022 0.003 TYR C 493 ARG 0.015 0.001 ARG A 710 Details of bonding type rmsd hydrogen bonds : bond 0.15870 ( 1028) hydrogen bonds : angle 9.18181 ( 2949) covalent geometry : bond 0.00612 (24701) covalent geometry : angle 0.98315 (33371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 613 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7794 (p0) cc_final: 0.7567 (p0) REVERT: A 332 ASP cc_start: 0.7265 (m-30) cc_final: 0.7001 (m-30) REVERT: A 408 GLN cc_start: 0.8613 (mt0) cc_final: 0.8287 (mt0) REVERT: B 274 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7754 (tp30) REVERT: B 472 SER cc_start: 0.8867 (p) cc_final: 0.8663 (t) REVERT: C 604 THR cc_start: 0.8401 (p) cc_final: 0.8198 (p) REVERT: C 754 ASP cc_start: 0.7890 (m-30) cc_final: 0.7656 (m-30) REVERT: D 323 ASP cc_start: 0.7524 (p0) cc_final: 0.7244 (p0) REVERT: D 371 LYS cc_start: 0.8552 (tmtp) cc_final: 0.8314 (tttm) REVERT: D 410 MET cc_start: 0.9177 (mmm) cc_final: 0.8786 (mmm) REVERT: D 669 PRO cc_start: 0.8312 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: E 265 LYS cc_start: 0.7351 (mmmt) cc_final: 0.7077 (mmtt) REVERT: E 304 ASN cc_start: 0.7280 (m-40) cc_final: 0.6826 (m110) REVERT: E 388 GLU cc_start: 0.7707 (tt0) cc_final: 0.6793 (pm20) REVERT: E 406 LEU cc_start: 0.7517 (tm) cc_final: 0.7222 (tt) REVERT: E 440 LEU cc_start: 0.7660 (mt) cc_final: 0.7457 (mt) REVERT: E 453 ASN cc_start: 0.7668 (p0) cc_final: 0.7034 (p0) REVERT: E 538 GLU cc_start: 0.5868 (tt0) cc_final: 0.5620 (tt0) REVERT: F 402 MET cc_start: 0.5628 (mmm) cc_final: 0.5189 (ttm) REVERT: F 410 MET cc_start: 0.8701 (mmm) cc_final: 0.8468 (mmt) REVERT: F 487 VAL cc_start: 0.8410 (t) cc_final: 0.8156 (t) outliers start: 11 outliers final: 3 residues processed: 621 average time/residue: 1.6542 time to fit residues: 1148.5108 Evaluate side-chains 437 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 434 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain F residue 274 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 9.9990 chunk 234 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 158 optimal weight: 0.0050 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 281 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 324 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 394 HIS A 448 GLN A 473 ASN A 476 ASN A 500 ASN A 510 GLN A 639 GLN A 773 HIS ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 455 HIS B 500 ASN B 505 HIS B 558 ASN B 571 ASN C 453 ASN C 476 ASN D 304 ASN D 455 HIS D 473 ASN D 505 HIS D 758 HIS D 773 HIS E 408 GLN E 510 GLN E 639 GLN E 655 ASN F 500 ASN F 558 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106051 restraints weight = 37761.694| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.70 r_work: 0.3127 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24701 Z= 0.115 Angle : 0.578 9.674 33371 Z= 0.299 Chirality : 0.044 0.201 3863 Planarity : 0.005 0.045 4272 Dihedral : 8.129 103.320 3551 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.32 % Allowed : 13.45 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.14), residues: 3112 helix: -1.04 (0.13), residues: 1435 sheet: -0.98 (0.23), residues: 467 loop : -1.86 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 603 HIS 0.004 0.001 HIS C 667 PHE 0.006 0.001 PHE B 658 TYR 0.016 0.001 TYR A 294 ARG 0.007 0.001 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 1028) hydrogen bonds : angle 5.27223 ( 2949) covalent geometry : bond 0.00256 (24701) covalent geometry : angle 0.57813 (33371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 477 time to evaluate : 2.671 Fit side-chains REVERT: A 265 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8133 (tptt) REVERT: A 284 MET cc_start: 0.8454 (mmt) cc_final: 0.7929 (tpp) REVERT: A 332 ASP cc_start: 0.7867 (m-30) cc_final: 0.7663 (m-30) REVERT: A 347 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 432 MET cc_start: 0.6606 (mpm) cc_final: 0.5838 (ttp) REVERT: A 435 ASP cc_start: 0.8111 (t0) cc_final: 0.7811 (t70) REVERT: A 512 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8269 (tm-30) REVERT: A 660 GLU cc_start: 0.7152 (mp0) cc_final: 0.6721 (mp0) REVERT: B 346 LYS cc_start: 0.8437 (tptp) cc_final: 0.8234 (tptt) REVERT: B 425 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7799 (tp) REVERT: B 444 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8894 (pp) REVERT: C 396 ARG cc_start: 0.8355 (ptt-90) cc_final: 0.8121 (ptp-170) REVERT: C 432 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6085 (pp-130) REVERT: C 563 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: C 754 ASP cc_start: 0.8310 (m-30) cc_final: 0.8063 (m-30) REVERT: D 328 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: D 348 LYS cc_start: 0.8176 (mmpt) cc_final: 0.7802 (mmmt) REVERT: D 402 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7983 (mtt) REVERT: D 410 MET cc_start: 0.9195 (mmm) cc_final: 0.8909 (mmm) REVERT: E 304 ASN cc_start: 0.8059 (m-40) cc_final: 0.7423 (m110) REVERT: E 375 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8286 (ptm160) REVERT: E 386 ARG cc_start: 0.6855 (mpp-170) cc_final: 0.6538 (mtm110) REVERT: E 388 GLU cc_start: 0.7854 (tt0) cc_final: 0.6878 (pm20) REVERT: E 453 ASN cc_start: 0.7913 (p0) cc_final: 0.7482 (p0) REVERT: E 458 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7796 (mt-10) REVERT: E 517 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (mppt) REVERT: E 651 LYS cc_start: 0.7663 (pptt) cc_final: 0.7402 (pttt) REVERT: F 263 MET cc_start: 0.7194 (mtp) cc_final: 0.6052 (mpm) REVERT: F 269 GLU cc_start: 0.7136 (mp0) cc_final: 0.6769 (pp20) REVERT: F 402 MET cc_start: 0.5729 (mmm) cc_final: 0.5149 (ttm) outliers start: 61 outliers final: 16 residues processed: 504 average time/residue: 1.5956 time to fit residues: 906.1020 Evaluate side-chains 434 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 409 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 537 ARG Chi-restraints excluded: chain C residue 563 LYS Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 328 GLU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 153 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 80 optimal weight: 0.3980 chunk 242 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 367 GLN A 639 GLN B 449 ASN D 449 ASN D 727 HIS E 408 GLN E 639 GLN F 324 HIS F 449 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099135 restraints weight = 37222.575| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.58 r_work: 0.3070 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24701 Z= 0.166 Angle : 0.599 9.180 33371 Z= 0.305 Chirality : 0.046 0.196 3863 Planarity : 0.005 0.063 4272 Dihedral : 8.011 94.304 3548 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.28 % Allowed : 14.75 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3112 helix: -0.09 (0.14), residues: 1435 sheet: -0.77 (0.23), residues: 481 loop : -1.56 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 603 HIS 0.004 0.001 HIS F 667 PHE 0.014 0.002 PHE B 468 TYR 0.015 0.002 TYR C 398 ARG 0.006 0.001 ARG D 306 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 1028) hydrogen bonds : angle 4.82005 ( 2949) covalent geometry : bond 0.00394 (24701) covalent geometry : angle 0.59882 (33371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 437 time to evaluate : 2.780 Fit side-chains REVERT: A 265 LYS cc_start: 0.8479 (ptmm) cc_final: 0.8218 (tptt) REVERT: A 266 ASP cc_start: 0.7882 (t0) cc_final: 0.7565 (t0) REVERT: A 269 GLU cc_start: 0.8507 (pp20) cc_final: 0.8285 (pp20) REVERT: A 421 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8212 (tm) REVERT: A 432 MET cc_start: 0.6684 (mpm) cc_final: 0.5848 (ttp) REVERT: A 435 ASP cc_start: 0.8161 (t0) cc_final: 0.7878 (t70) REVERT: A 465 ASP cc_start: 0.7962 (t0) cc_final: 0.7723 (t70) REVERT: A 512 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 592 GLU cc_start: 0.8120 (tt0) cc_final: 0.7919 (tt0) REVERT: A 660 GLU cc_start: 0.7319 (mp0) cc_final: 0.6574 (mp0) REVERT: A 739 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: B 425 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7985 (tp) REVERT: B 460 ASP cc_start: 0.8813 (m-30) cc_final: 0.8569 (m-30) REVERT: B 650 ASP cc_start: 0.8324 (t70) cc_final: 0.8124 (t0) REVERT: C 265 LYS cc_start: 0.9115 (tttp) cc_final: 0.8823 (tmtm) REVERT: C 276 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: C 281 MET cc_start: 0.8928 (mtt) cc_final: 0.8708 (mtt) REVERT: C 328 GLU cc_start: 0.7999 (mp0) cc_final: 0.7671 (mp0) REVERT: C 432 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.6035 (pp-130) REVERT: C 754 ASP cc_start: 0.8296 (m-30) cc_final: 0.8048 (m-30) REVERT: E 375 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8277 (ptm160) REVERT: E 386 ARG cc_start: 0.6847 (mpp-170) cc_final: 0.6518 (mtm110) REVERT: E 388 GLU cc_start: 0.7861 (tt0) cc_final: 0.6857 (pm20) REVERT: E 453 ASN cc_start: 0.7896 (p0) cc_final: 0.7462 (p0) REVERT: E 458 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7817 (mt-10) REVERT: E 485 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: E 605 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6915 (tm-30) REVERT: F 280 MET cc_start: 0.5572 (mpp) cc_final: 0.4881 (tpt) REVERT: F 402 MET cc_start: 0.5776 (mmm) cc_final: 0.5226 (ttp) REVERT: F 513 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8093 (ptp-110) outliers start: 86 outliers final: 31 residues processed: 479 average time/residue: 1.6899 time to fit residues: 908.4761 Evaluate side-chains 433 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 394 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 513 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 chunk 165 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 367 GLN A 639 GLN D 341 GLN D 408 GLN D 727 HIS E 276 GLN E 424 GLN E 639 GLN F 449 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093104 restraints weight = 37813.254| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.57 r_work: 0.3072 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24701 Z= 0.156 Angle : 0.583 10.230 33371 Z= 0.294 Chirality : 0.045 0.183 3863 Planarity : 0.005 0.054 4272 Dihedral : 7.877 91.112 3548 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.12 % Allowed : 15.66 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3112 helix: 0.39 (0.14), residues: 1429 sheet: -0.52 (0.24), residues: 478 loop : -1.30 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 603 HIS 0.004 0.001 HIS C 324 PHE 0.011 0.001 PHE B 468 TYR 0.013 0.001 TYR C 398 ARG 0.007 0.001 ARG B 392 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1028) hydrogen bonds : angle 4.60815 ( 2949) covalent geometry : bond 0.00372 (24701) covalent geometry : angle 0.58319 (33371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 426 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8020 (t0) cc_final: 0.7727 (t0) REVERT: A 269 GLU cc_start: 0.8463 (pp20) cc_final: 0.8231 (pp20) REVERT: A 392 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7505 (mtp180) REVERT: A 402 MET cc_start: 0.8722 (ptm) cc_final: 0.8461 (ptp) REVERT: A 421 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 432 MET cc_start: 0.6649 (mpm) cc_final: 0.5754 (ttp) REVERT: A 435 ASP cc_start: 0.8077 (t0) cc_final: 0.7794 (t70) REVERT: A 512 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 592 GLU cc_start: 0.8171 (tt0) cc_final: 0.7941 (tt0) REVERT: A 660 GLU cc_start: 0.7341 (mp0) cc_final: 0.6541 (mp0) REVERT: A 738 ASP cc_start: 0.8553 (t70) cc_final: 0.8259 (t0) REVERT: A 739 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: B 321 ASP cc_start: 0.8817 (m-30) cc_final: 0.8499 (m-30) REVERT: B 650 ASP cc_start: 0.8334 (t70) cc_final: 0.8115 (t0) REVERT: B 684 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8041 (mtt) REVERT: C 276 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7956 (tp40) REVERT: C 432 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.6123 (pp-130) REVERT: C 573 ASP cc_start: 0.7994 (p0) cc_final: 0.7777 (p0) REVERT: C 583 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8465 (mptp) REVERT: C 651 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7547 (pttp) REVERT: C 754 ASP cc_start: 0.8230 (m-30) cc_final: 0.7986 (m-30) REVERT: D 341 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: D 465 ASP cc_start: 0.8681 (t70) cc_final: 0.8456 (t0) REVERT: E 284 MET cc_start: 0.5433 (tpp) cc_final: 0.5190 (tpp) REVERT: E 333 ARG cc_start: 0.7286 (tpp80) cc_final: 0.7069 (mmm160) REVERT: E 375 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8335 (ptm160) REVERT: E 386 ARG cc_start: 0.6840 (mpp-170) cc_final: 0.6430 (mtm110) REVERT: E 388 GLU cc_start: 0.7844 (tt0) cc_final: 0.6764 (pm20) REVERT: E 453 ASN cc_start: 0.8072 (p0) cc_final: 0.7593 (p0) REVERT: E 485 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8091 (mmm) REVERT: E 605 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6975 (tm-30) REVERT: E 651 LYS cc_start: 0.7923 (tmtt) cc_final: 0.7489 (ptpt) REVERT: F 280 MET cc_start: 0.5319 (mpp) cc_final: 0.4612 (tpt) REVERT: F 402 MET cc_start: 0.5798 (mmm) cc_final: 0.5210 (ttp) REVERT: F 517 LYS cc_start: 0.8006 (pmtt) cc_final: 0.7720 (pmtt) outliers start: 82 outliers final: 33 residues processed: 472 average time/residue: 1.8143 time to fit residues: 961.2313 Evaluate side-chains 431 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 388 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 634 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 35 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 241 optimal weight: 0.2980 chunk 175 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN D 341 GLN D 727 HIS F 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097981 restraints weight = 37526.874| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.58 r_work: 0.3118 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24701 Z= 0.101 Angle : 0.535 8.414 33371 Z= 0.269 Chirality : 0.043 0.166 3863 Planarity : 0.004 0.054 4272 Dihedral : 7.540 89.091 3548 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.52 % Allowed : 16.88 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3112 helix: 0.89 (0.14), residues: 1417 sheet: -0.33 (0.24), residues: 465 loop : -1.13 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 603 HIS 0.002 0.001 HIS C 324 PHE 0.006 0.001 PHE E 658 TYR 0.014 0.001 TYR A 626 ARG 0.009 0.000 ARG F 742 Details of bonding type rmsd hydrogen bonds : bond 0.02737 ( 1028) hydrogen bonds : angle 4.37845 ( 2949) covalent geometry : bond 0.00231 (24701) covalent geometry : angle 0.53488 (33371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 427 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.7973 (t0) cc_final: 0.7627 (t0) REVERT: A 269 GLU cc_start: 0.8401 (pp20) cc_final: 0.8166 (pp20) REVERT: A 395 ARG cc_start: 0.7471 (mpt90) cc_final: 0.7243 (tpp80) REVERT: A 402 MET cc_start: 0.8658 (ptm) cc_final: 0.8409 (ptp) REVERT: A 421 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8126 (tm) REVERT: A 425 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 432 MET cc_start: 0.6576 (mpm) cc_final: 0.5776 (ttp) REVERT: A 435 ASP cc_start: 0.8006 (t0) cc_final: 0.7634 (t70) REVERT: A 512 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 538 GLU cc_start: 0.7439 (pm20) cc_final: 0.6790 (pm20) REVERT: A 592 GLU cc_start: 0.8202 (tt0) cc_final: 0.7862 (tt0) REVERT: A 660 GLU cc_start: 0.7247 (mp0) cc_final: 0.6445 (mp0) REVERT: A 739 ASP cc_start: 0.8148 (p0) cc_final: 0.7691 (m-30) REVERT: B 321 ASP cc_start: 0.8791 (m-30) cc_final: 0.8482 (m-30) REVERT: B 346 LYS cc_start: 0.8427 (tptt) cc_final: 0.8172 (tppt) REVERT: B 425 ILE cc_start: 0.8578 (pt) cc_final: 0.8039 (tt) REVERT: B 512 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8378 (tm-30) REVERT: B 650 ASP cc_start: 0.8291 (t70) cc_final: 0.8051 (t0) REVERT: B 684 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: C 432 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.6037 (pp-130) REVERT: C 754 ASP cc_start: 0.8177 (m-30) cc_final: 0.7945 (m-30) REVERT: C 769 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8599 (mt) REVERT: D 274 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8197 (mm-30) REVERT: D 348 LYS cc_start: 0.8334 (mptp) cc_final: 0.7537 (ptmm) REVERT: D 465 ASP cc_start: 0.8701 (t70) cc_final: 0.8436 (t0) REVERT: D 679 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8640 (m) REVERT: E 263 MET cc_start: 0.7891 (mtp) cc_final: 0.7690 (mtp) REVERT: E 284 MET cc_start: 0.5520 (tpp) cc_final: 0.5273 (tpp) REVERT: E 298 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7589 (tpp) REVERT: E 375 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8179 (ptm160) REVERT: E 386 ARG cc_start: 0.6748 (mpp-170) cc_final: 0.6341 (mtm110) REVERT: E 388 GLU cc_start: 0.7738 (tt0) cc_final: 0.6637 (pm20) REVERT: E 420 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: E 423 ASP cc_start: 0.7536 (t70) cc_final: 0.7283 (t70) REVERT: E 453 ASN cc_start: 0.8107 (p0) cc_final: 0.7678 (p0) REVERT: E 458 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7793 (mt-10) REVERT: E 537 ARG cc_start: 0.7490 (tpm170) cc_final: 0.7050 (tpp-160) REVERT: E 605 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6908 (tm-30) REVERT: F 280 MET cc_start: 0.5024 (mpp) cc_final: 0.4386 (tpt) REVERT: F 402 MET cc_start: 0.5731 (mmm) cc_final: 0.5272 (ttm) REVERT: F 546 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7925 (mmm-85) outliers start: 66 outliers final: 24 residues processed: 465 average time/residue: 1.7257 time to fit residues: 896.3834 Evaluate side-chains 431 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 397 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 769 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 525 ASP Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 634 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 234 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 639 GLN B 449 ASN C 567 HIS E 455 HIS E 639 GLN E 727 HIS F 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.091788 restraints weight = 37903.207| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.60 r_work: 0.3000 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24701 Z= 0.255 Angle : 0.668 8.461 33371 Z= 0.337 Chirality : 0.049 0.245 3863 Planarity : 0.005 0.062 4272 Dihedral : 8.003 91.770 3548 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.47 % Allowed : 16.77 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3112 helix: 0.72 (0.14), residues: 1420 sheet: -0.30 (0.24), residues: 459 loop : -1.08 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 603 HIS 0.008 0.002 HIS C 324 PHE 0.037 0.002 PHE A 420 TYR 0.021 0.002 TYR C 398 ARG 0.008 0.001 ARG F 742 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1028) hydrogen bonds : angle 4.65295 ( 2949) covalent geometry : bond 0.00617 (24701) covalent geometry : angle 0.66846 (33371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 407 time to evaluate : 2.783 Fit side-chains revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8178 (t0) cc_final: 0.7755 (t0) REVERT: A 269 GLU cc_start: 0.8366 (pp20) cc_final: 0.8113 (pp20) REVERT: A 280 MET cc_start: 0.7540 (pmm) cc_final: 0.7278 (pmm) REVERT: A 512 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 592 GLU cc_start: 0.8227 (tt0) cc_final: 0.7912 (tt0) REVERT: A 604 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8449 (m) REVERT: A 739 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: B 321 ASP cc_start: 0.8913 (m-30) cc_final: 0.8623 (m-30) REVERT: B 346 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8218 (tppt) REVERT: B 396 ARG cc_start: 0.8946 (ptt-90) cc_final: 0.8510 (ptt-90) REVERT: B 650 ASP cc_start: 0.8457 (t70) cc_final: 0.8246 (t0) REVERT: C 255 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.5857 (pmmt) REVERT: C 265 LYS cc_start: 0.9011 (tttp) cc_final: 0.8725 (tmtm) REVERT: C 309 VAL cc_start: 0.9320 (t) cc_final: 0.9067 (m) REVERT: C 583 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8468 (mptp) REVERT: C 651 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7577 (pttp) REVERT: C 754 ASP cc_start: 0.8218 (m-30) cc_final: 0.7998 (m-30) REVERT: D 341 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: D 348 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8170 (mttp) REVERT: D 360 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8599 (m) REVERT: D 420 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8647 (t80) REVERT: D 465 ASP cc_start: 0.8692 (t70) cc_final: 0.8450 (t0) REVERT: E 263 MET cc_start: 0.8018 (mtp) cc_final: 0.7676 (mtp) REVERT: E 265 LYS cc_start: 0.7328 (mmmt) cc_final: 0.7032 (tptp) REVERT: E 284 MET cc_start: 0.5590 (tpp) cc_final: 0.5328 (tpp) REVERT: E 298 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7584 (tpp) REVERT: E 375 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8194 (mtp85) REVERT: E 380 MET cc_start: 0.8126 (ttt) cc_final: 0.7841 (ttm) REVERT: E 423 ASP cc_start: 0.7454 (t70) cc_final: 0.7156 (t70) REVERT: E 453 ASN cc_start: 0.8065 (p0) cc_final: 0.7848 (p0) REVERT: E 537 ARG cc_start: 0.7750 (tpm170) cc_final: 0.7357 (tpp-160) REVERT: E 605 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: E 651 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7754 (tmtm) REVERT: F 280 MET cc_start: 0.5276 (mpp) cc_final: 0.4566 (tpt) REVERT: F 449 ASN cc_start: 0.8036 (m-40) cc_final: 0.7522 (m110) REVERT: F 517 LYS cc_start: 0.8094 (pmtt) cc_final: 0.7738 (pmtt) outliers start: 91 outliers final: 44 residues processed: 456 average time/residue: 1.6652 time to fit residues: 857.6072 Evaluate side-chains 440 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 383 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 651 LYS Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 155 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 367 GLN A 639 GLN E 639 GLN E 727 HIS F 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095242 restraints weight = 37692.498| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.57 r_work: 0.3047 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24701 Z= 0.116 Angle : 0.566 9.069 33371 Z= 0.286 Chirality : 0.044 0.198 3863 Planarity : 0.004 0.054 4272 Dihedral : 7.669 88.098 3548 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.86 % Allowed : 17.68 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3112 helix: 1.07 (0.15), residues: 1405 sheet: -0.24 (0.24), residues: 467 loop : -0.93 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 603 HIS 0.003 0.001 HIS E 758 PHE 0.013 0.001 PHE A 420 TYR 0.009 0.001 TYR A 294 ARG 0.006 0.000 ARG B 392 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 1028) hydrogen bonds : angle 4.45155 ( 2949) covalent geometry : bond 0.00271 (24701) covalent geometry : angle 0.56640 (33371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 409 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ASP cc_start: 0.8131 (t0) cc_final: 0.7805 (t0) REVERT: A 425 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8486 (mm) REVERT: A 432 MET cc_start: 0.6589 (mpm) cc_final: 0.5828 (ttp) REVERT: A 435 ASP cc_start: 0.8011 (t0) cc_final: 0.7662 (t70) REVERT: A 512 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8290 (tm-30) REVERT: A 583 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8435 (mtmt) REVERT: A 592 GLU cc_start: 0.8204 (tt0) cc_final: 0.7933 (tt0) REVERT: A 660 GLU cc_start: 0.7079 (mp0) cc_final: 0.6252 (tt0) REVERT: A 661 LYS cc_start: 0.8782 (pptt) cc_final: 0.8363 (pptt) REVERT: A 739 ASP cc_start: 0.8246 (p0) cc_final: 0.7973 (m-30) REVERT: B 321 ASP cc_start: 0.8812 (m-30) cc_final: 0.8498 (m-30) REVERT: B 396 ARG cc_start: 0.8972 (ptt-90) cc_final: 0.8584 (ptt-90) REVERT: B 650 ASP cc_start: 0.8386 (t70) cc_final: 0.8151 (t0) REVERT: C 309 VAL cc_start: 0.9332 (t) cc_final: 0.9046 (m) REVERT: C 432 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.6037 (pp-130) REVERT: C 476 ASN cc_start: 0.8484 (t0) cc_final: 0.8192 (p0) REVERT: C 754 ASP cc_start: 0.8172 (m-30) cc_final: 0.7937 (m-30) REVERT: D 341 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: D 348 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7636 (ptmm) REVERT: D 465 ASP cc_start: 0.8693 (t70) cc_final: 0.8463 (t0) REVERT: D 679 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8836 (m) REVERT: E 284 MET cc_start: 0.5653 (tpp) cc_final: 0.5374 (tpp) REVERT: E 298 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7656 (tpp) REVERT: E 375 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8246 (mtp85) REVERT: E 386 ARG cc_start: 0.6736 (mpp-170) cc_final: 0.6360 (mtm110) REVERT: E 420 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: E 423 ASP cc_start: 0.7567 (t70) cc_final: 0.7294 (t70) REVERT: E 453 ASN cc_start: 0.8083 (p0) cc_final: 0.7632 (p0) REVERT: E 537 ARG cc_start: 0.7693 (tpm170) cc_final: 0.7295 (tpp-160) REVERT: E 605 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: F 280 MET cc_start: 0.5154 (mpp) cc_final: 0.4367 (tpt) REVERT: F 333 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7191 (tpt170) REVERT: F 402 MET cc_start: 0.5859 (mmm) cc_final: 0.5428 (ttm) REVERT: F 517 LYS cc_start: 0.7993 (pmtt) cc_final: 0.7686 (pmtt) outliers start: 75 outliers final: 33 residues processed: 457 average time/residue: 1.7820 time to fit residues: 914.7419 Evaluate side-chains 427 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 168 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN E 727 HIS F 449 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093026 restraints weight = 37750.888| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.62 r_work: 0.3009 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24701 Z= 0.190 Angle : 0.627 11.037 33371 Z= 0.315 Chirality : 0.047 0.209 3863 Planarity : 0.005 0.054 4272 Dihedral : 7.816 88.562 3548 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.74 % Allowed : 17.87 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3112 helix: 1.01 (0.14), residues: 1410 sheet: -0.21 (0.24), residues: 469 loop : -0.89 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 603 HIS 0.005 0.001 HIS B 667 PHE 0.027 0.002 PHE A 420 TYR 0.021 0.002 TYR A 294 ARG 0.006 0.001 ARG B 392 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1028) hydrogen bonds : angle 4.53854 ( 2949) covalent geometry : bond 0.00463 (24701) covalent geometry : angle 0.62704 (33371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 389 time to evaluate : 2.793 Fit side-chains REVERT: A 425 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8482 (mm) REVERT: A 432 MET cc_start: 0.6614 (mpm) cc_final: 0.5772 (ttp) REVERT: A 435 ASP cc_start: 0.8044 (t0) cc_final: 0.7738 (t70) REVERT: A 512 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 592 GLU cc_start: 0.8198 (tt0) cc_final: 0.7893 (tt0) REVERT: A 660 GLU cc_start: 0.7358 (mp0) cc_final: 0.6301 (tt0) REVERT: B 255 LYS cc_start: 0.7664 (pmtt) cc_final: 0.7446 (ttmm) REVERT: B 321 ASP cc_start: 0.8877 (m-30) cc_final: 0.8593 (m-30) REVERT: B 650 ASP cc_start: 0.8417 (t70) cc_final: 0.8192 (t0) REVERT: C 276 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7932 (tp40) REVERT: C 309 VAL cc_start: 0.9325 (t) cc_final: 0.9051 (m) REVERT: C 476 ASN cc_start: 0.8554 (t0) cc_final: 0.8219 (p0) REVERT: C 583 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8462 (mptp) REVERT: C 604 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8460 (t) REVERT: C 605 GLU cc_start: 0.8144 (tp30) cc_final: 0.7902 (tt0) REVERT: C 754 ASP cc_start: 0.8109 (m-30) cc_final: 0.7881 (m-30) REVERT: D 348 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7623 (ptmm) REVERT: D 465 ASP cc_start: 0.8700 (t70) cc_final: 0.8458 (t0) REVERT: E 265 LYS cc_start: 0.7034 (mmmt) cc_final: 0.6765 (tptp) REVERT: E 281 MET cc_start: 0.3970 (ptp) cc_final: 0.3664 (ptp) REVERT: E 284 MET cc_start: 0.5653 (tpp) cc_final: 0.5378 (tpp) REVERT: E 298 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7574 (tpp) REVERT: E 375 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7038 (mtp85) REVERT: E 380 MET cc_start: 0.7988 (ttt) cc_final: 0.7676 (ttm) REVERT: E 420 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: E 453 ASN cc_start: 0.8065 (p0) cc_final: 0.7835 (p0) REVERT: E 537 ARG cc_start: 0.7798 (tpm170) cc_final: 0.7314 (tpp-160) REVERT: E 568 ILE cc_start: 0.8453 (mt) cc_final: 0.8104 (mm) REVERT: E 605 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: F 280 MET cc_start: 0.5210 (mpp) cc_final: 0.4519 (tpt) REVERT: F 284 MET cc_start: 0.4813 (mtm) cc_final: 0.4126 (mtp) REVERT: F 402 MET cc_start: 0.5948 (mmm) cc_final: 0.5370 (ttp) REVERT: F 449 ASN cc_start: 0.8013 (m-40) cc_final: 0.7686 (m-40) REVERT: F 517 LYS cc_start: 0.8006 (pmtt) cc_final: 0.7764 (pmtt) outliers start: 72 outliers final: 43 residues processed: 433 average time/residue: 1.7134 time to fit residues: 833.9238 Evaluate side-chains 428 residues out of total 2624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 376 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 716 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 583 LYS Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 375 ARG Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 420 PHE Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 605 GLU Chi-restraints excluded: chain E residue 625 THR Chi-restraints excluded: chain F residue 428 MET Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 634 MET Chi-restraints excluded: chain F residue 739 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6356 > 50: distance: 70 - 76: 4.480 distance: 76 - 77: 3.259 distance: 77 - 78: 7.350 distance: 78 - 79: 11.000 distance: 78 - 80: 6.022 distance: 80 - 81: 6.932 distance: 81 - 82: 5.402 distance: 81 - 84: 8.568 distance: 82 - 83: 7.922 distance: 82 - 88: 3.287 distance: 84 - 85: 5.098 distance: 85 - 86: 5.773 distance: 85 - 87: 4.063 distance: 88 - 89: 5.708 distance: 89 - 90: 7.393 distance: 90 - 91: 7.208 distance: 90 - 96: 6.206 distance: 92 - 93: 4.082 distance: 93 - 94: 5.485 distance: 97 - 98: 7.426 distance: 97 - 100: 5.724 distance: 98 - 99: 4.628 distance: 98 - 104: 6.723 distance: 99 - 132: 10.266 distance: 100 - 101: 3.730 distance: 101 - 102: 7.532 distance: 101 - 103: 4.411 distance: 104 - 105: 8.571 distance: 105 - 106: 11.198 distance: 105 - 108: 4.323 distance: 106 - 107: 12.902 distance: 106 - 113: 16.777 distance: 107 - 140: 13.353 distance: 108 - 109: 4.258 distance: 109 - 110: 3.616 distance: 111 - 112: 10.713 distance: 113 - 114: 19.716 distance: 114 - 115: 19.973 distance: 114 - 117: 12.058 distance: 115 - 116: 14.304 distance: 115 - 121: 10.419 distance: 117 - 118: 9.756 distance: 118 - 119: 15.610 distance: 118 - 120: 10.380 distance: 121 - 122: 13.434 distance: 122 - 123: 5.098 distance: 122 - 125: 5.230 distance: 123 - 124: 3.062 distance: 123 - 132: 7.093 distance: 125 - 126: 5.553 distance: 126 - 127: 4.603 distance: 126 - 128: 4.184 distance: 127 - 129: 4.402 distance: 128 - 130: 5.262 distance: 129 - 131: 4.036 distance: 130 - 131: 6.320 distance: 132 - 133: 5.793 distance: 133 - 134: 6.588 distance: 133 - 136: 7.913 distance: 134 - 135: 4.662 distance: 134 - 140: 5.719 distance: 137 - 138: 9.004 distance: 137 - 139: 10.413 distance: 140 - 141: 7.135 distance: 141 - 142: 8.872 distance: 142 - 143: 16.108 distance: 142 - 144: 5.658 distance: 145 - 146: 3.127 distance: 145 - 148: 5.990 distance: 146 - 147: 7.434 distance: 148 - 149: 9.086 distance: 148 - 150: 5.597