Starting phenix.real_space_refine on Fri Aug 7 01:10:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lov_63261/08_2026/9lov_63261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lov_63261/08_2026/9lov_63261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lov_63261/08_2026/9lov_63261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lov_63261/08_2026/9lov_63261.map" model { file = "/net/cci-nas-00/data/ceres_data/9lov_63261/08_2026/9lov_63261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lov_63261/08_2026/9lov_63261.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 96 5.49 5 Mg 3 5.21 5 S 108 5.16 5 C 10995 2.51 5 N 3179 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17978 Number of models: 1 Model: "" Number of chains: 8 Chain: "Y" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 945 Classifications: {'RNA': 45} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 27} Link IDs: {'rna3p': 44} Chain: "X" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 967 Classifications: {'RNA': 45} Modifications used: {'rna3p_pur': 27, 'rna3p_pyr': 18} Link IDs: {'rna3p': 44} Chain: "A" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5220 Classifications: {'peptide': 658} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 634} Chain breaks: 1 Chain: "B" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5454 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 24, 'TRANS': 650} Chain breaks: 3 Chain: "C" Number of atoms: 5305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5305 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 23, 'TRANS': 633} Chain breaks: 4 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6206 SG CYS A 556 74.268 47.147 38.660 1.00176.53 S ATOM 6228 SG CYS A 559 78.004 46.567 38.529 1.00177.72 S ATOM 6642 SG CYS A 612 76.385 46.987 41.944 1.00170.78 S ATOM 6667 SG CYS A 615 76.506 49.954 39.686 1.00174.13 S ATOM 11702 SG CYS B 907 65.942 76.677 76.973 1.00142.84 S ATOM 11725 SG CYS B 910 67.680 80.028 76.560 1.00153.98 S ATOM 12143 SG CYS B 962 66.900 78.691 80.107 1.00149.09 S ATOM 12158 SG CYS B 964 64.191 79.967 77.804 1.00145.21 S ATOM 17132 SG CYS C 907 41.325 80.609 119.730 1.00191.28 S ATOM 17155 SG CYS C 910 38.427 83.057 119.817 1.00203.16 S ATOM 17474 SG CYS C 962 40.384 82.451 122.999 1.00211.90 S ATOM 17489 SG CYS C 964 38.135 79.735 121.619 1.00195.70 S Time building chain proxies: 4.18, per 1000 atoms: 0.23 Number of scatterers: 17978 At special positions: 0 Unit cell: (114.54, 103.335, 156.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 108 16.00 P 96 15.00 Mg 3 11.99 O 3594 8.00 N 3179 7.00 C 10995 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 775.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 615 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 556 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 612 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 559 " pdb=" ZN B1102 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 964 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 910 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 907 " pdb="ZN ZN B1102 " - pdb=" SG CYS B 962 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 910 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 964 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 962 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 907 " Number of angles added : 18 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 15 sheets defined 55.5% alpha, 12.2% beta 45 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 removed outlier: 3.566A pdb=" N ILE A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.690A pdb=" N GLU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 45 Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.802A pdb=" N VAL A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.515A pdb=" N THR A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 140 through 155 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.604A pdb=" N HIS A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 274 through 297 removed outlier: 3.779A pdb=" N ARG A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.678A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.657A pdb=" N ARG A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 3.508A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 removed outlier: 3.609A pdb=" N SER A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.598A pdb=" N GLN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.754A pdb=" N VAL A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.562A pdb=" N GLU A 442 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 443 " --> pdb=" O VAL A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 443' Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.554A pdb=" N ARG A 471 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 removed outlier: 3.553A pdb=" N LYS A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 540 removed outlier: 3.722A pdb=" N ALA A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 583 through 587 removed outlier: 3.958A pdb=" N TYR A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 587' Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.518A pdb=" N VAL A 655 " --> pdb=" O TRP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'B' and resid 309 through 321 removed outlier: 3.619A pdb=" N VAL B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Proline residue: B 318 - end of helix removed outlier: 3.602A pdb=" N GLU B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 365 through 376 removed outlier: 3.803A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.516A pdb=" N PHE B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.910A pdb=" N LYS B 397 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 398 " --> pdb=" O GLN B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 394 through 398' Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 414 through 423 removed outlier: 4.002A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 452 through 474 removed outlier: 3.646A pdb=" N HIS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 473 " --> pdb=" O ASN B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 513 Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.761A pdb=" N ASN B 530 " --> pdb=" O ASP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 566 Processing helix chain 'B' and resid 575 through 593 Processing helix chain 'B' and resid 594 through 617 Processing helix chain 'B' and resid 618 through 638 removed outlier: 3.609A pdb=" N ALA B 622 " --> pdb=" O ARG B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 683 removed outlier: 3.780A pdb=" N ASN B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 698 through 715 removed outlier: 4.258A pdb=" N THR B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 741 removed outlier: 3.596A pdb=" N ASN B 741 " --> pdb=" O TRP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 747 removed outlier: 4.008A pdb=" N ALA B 745 " --> pdb=" O ASN B 741 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 780 Processing helix chain 'B' and resid 790 through 794 removed outlier: 3.933A pdb=" N GLU B 794 " --> pdb=" O VAL B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 822 removed outlier: 3.518A pdb=" N ARG B 822 " --> pdb=" O GLN B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 863 Processing helix chain 'B' and resid 865 through 891 Processing helix chain 'B' and resid 899 through 901 No H-bonds generated for 'chain 'B' and resid 899 through 901' Processing helix chain 'B' and resid 932 through 937 removed outlier: 3.632A pdb=" N LYS B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 937 " --> pdb=" O PRO B 933 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 932 through 937' Processing helix chain 'B' and resid 944 through 951 Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.540A pdb=" N VAL C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Proline residue: C 318 - end of helix removed outlier: 3.599A pdb=" N GLU C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 365 through 376 removed outlier: 3.852A pdb=" N VAL C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.813A pdb=" N PHE C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 398 removed outlier: 4.004A pdb=" N LYS C 397 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 398 " --> pdb=" O GLN C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 398' Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 433 through 437 removed outlier: 3.534A pdb=" N PHE C 437 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.774A pdb=" N HIS C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 474 removed outlier: 3.588A pdb=" N HIS C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 473 " --> pdb=" O ASN C 469 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 548 through 565 Processing helix chain 'C' and resid 575 through 593 Processing helix chain 'C' and resid 594 through 617 Processing helix chain 'C' and resid 618 through 637 removed outlier: 3.864A pdb=" N ALA C 622 " --> pdb=" O ARG C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 682 Processing helix chain 'C' and resid 683 through 693 Processing helix chain 'C' and resid 698 through 715 removed outlier: 3.715A pdb=" N THR C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 741 removed outlier: 3.549A pdb=" N ASN C 741 " --> pdb=" O TRP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 747 removed outlier: 3.928A pdb=" N ALA C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 790 through 794 removed outlier: 4.013A pdb=" N GLU C 794 " --> pdb=" O VAL C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 823 removed outlier: 4.033A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 863 removed outlier: 3.533A pdb=" N ARG C 843 " --> pdb=" O GLY C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 891 Processing helix chain 'C' and resid 932 through 939 removed outlier: 3.690A pdb=" N LYS C 936 " --> pdb=" O THR C 932 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU C 937 " --> pdb=" O PRO C 933 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 938 " --> pdb=" O GLU C 934 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 939 " --> pdb=" O PHE C 935 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 932 through 939' Processing helix chain 'C' and resid 1002 through 1006 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.459A pdb=" N THR A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR A 103 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU A 80 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 50 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N CYS A 102 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL A 52 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 20 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 21 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.631A pdb=" N CYS A 215 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE A 481 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 217 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 371 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N TYR A 456 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 373 " --> pdb=" O TYR A 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.507A pdb=" N LEU A 554 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 572 Processing sheet with id=AA5, first strand: chain 'A' and resid 588 through 591 removed outlier: 6.504A pdb=" N CYS A 612 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 618 " --> pdb=" O CYS A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 387 through 390 removed outlier: 3.717A pdb=" N THR B 413 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 325 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR B 488 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE B 327 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 326 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 536 through 542 removed outlier: 6.002A pdb=" N CYS B 536 " --> pdb=" O TYR B 830 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU B 832 " --> pdb=" O CYS B 536 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 538 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA B 834 " --> pdb=" O LYS B 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 540 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 804 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 833 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG B 806 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N HIS B 835 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE B 722 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N TYR B 807 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE B 724 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 721 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA B 788 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE B 723 " --> pdb=" O ALA B 788 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 916 removed outlier: 7.069A pdb=" N PHE B 905 " --> pdb=" O ALA B 914 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER B 916 " --> pdb=" O ILE B 903 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE B 903 " --> pdb=" O SER B 916 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 920 through 923 Processing sheet with id=AB1, first strand: chain 'B' and resid 939 through 941 removed outlier: 6.700A pdb=" N ILE B 960 " --> pdb=" O TRP B 968 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 387 through 390 removed outlier: 3.686A pdb=" N THR C 413 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 359 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER C 412 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL C 361 " --> pdb=" O SER C 412 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 325 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE C 326 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 536 through 542 removed outlier: 3.578A pdb=" N LEU C 832 " --> pdb=" O LYS C 538 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL C 804 " --> pdb=" O VAL C 831 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL C 833 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG C 806 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS C 835 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE C 722 " --> pdb=" O ILE C 805 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR C 807 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE C 724 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY C 721 " --> pdb=" O LEU C 786 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA C 788 " --> pdb=" O GLY C 721 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE C 723 " --> pdb=" O ALA C 788 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 913 through 916 removed outlier: 7.044A pdb=" N PHE C 905 " --> pdb=" O ALA C 914 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SER C 916 " --> pdb=" O ILE C 903 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 903 " --> pdb=" O SER C 916 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 920 through 923 Processing sheet with id=AB6, first strand: chain 'C' and resid 940 through 941 removed outlier: 6.655A pdb=" N ILE C 960 " --> pdb=" O TRP C 968 " (cutoff:3.500A) 831 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5405 1.34 - 1.45: 2809 1.45 - 1.57: 9905 1.57 - 1.69: 187 1.69 - 1.81: 171 Bond restraints: 18477 Sorted by residual: bond pdb=" N PRO B1007 " pdb=" CA PRO B1007 " ideal model delta sigma weight residual 1.469 1.480 -0.011 7.40e-03 1.83e+04 2.39e+00 bond pdb=" C GLN C 378 " pdb=" N PRO C 379 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.37e+00 bond pdb=" N SER C 568 " pdb=" CA SER C 568 " ideal model delta sigma weight residual 1.463 1.450 0.014 1.08e-02 8.57e+03 1.57e+00 bond pdb=" CB PRO B 569 " pdb=" CG PRO B 569 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.28e+00 bond pdb=" C4 ADP B1101 " pdb=" C5 ADP B1101 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.07e+00 ... (remaining 18472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 24523 1.34 - 2.68: 626 2.68 - 4.02: 164 4.02 - 5.36: 29 5.36 - 6.70: 8 Bond angle restraints: 25350 Sorted by residual: angle pdb=" O5' U Y 21 " pdb=" C5' U Y 21 " pdb=" C4' U Y 21 " ideal model delta sigma weight residual 109.40 112.22 -2.82 8.00e-01 1.56e+00 1.24e+01 angle pdb=" O5' C Y 22 " pdb=" C5' C Y 22 " pdb=" C4' C Y 22 " ideal model delta sigma weight residual 109.40 112.16 -2.76 8.00e-01 1.56e+00 1.19e+01 angle pdb=" O5' C Y 8 " pdb=" C5' C Y 8 " pdb=" C4' C Y 8 " ideal model delta sigma weight residual 109.40 112.15 -2.75 8.00e-01 1.56e+00 1.18e+01 angle pdb=" O5' U Y 35 " pdb=" C5' U Y 35 " pdb=" C4' U Y 35 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" O5' U X 27 " pdb=" C5' U X 27 " pdb=" C4' U X 27 " ideal model delta sigma weight residual 109.40 112.10 -2.70 8.00e-01 1.56e+00 1.14e+01 ... (remaining 25345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.19: 11098 32.19 - 64.38: 334 64.38 - 96.57: 37 96.57 - 128.75: 0 128.75 - 160.94: 2 Dihedral angle restraints: 11471 sinusoidal: 5637 harmonic: 5834 Sorted by residual: dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 -134.92 74.92 1 2.00e+01 2.50e-03 1.78e+01 dihedral pdb=" C4' U X 5 " pdb=" C3' U X 5 " pdb=" O3' U X 5 " pdb=" P G X 6 " ideal model delta sinusoidal sigma weight residual 220.00 59.06 160.94 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' G X 2 " pdb=" C3' G X 2 " pdb=" O3' G X 2 " pdb=" P A X 3 " ideal model delta sinusoidal sigma weight residual 220.00 74.62 145.38 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 11468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2108 0.034 - 0.067: 485 0.067 - 0.101: 182 0.101 - 0.134: 105 0.134 - 0.168: 51 Chirality restraints: 2931 Sorted by residual: chirality pdb=" C3' G X 2 " pdb=" C4' G X 2 " pdb=" O3' G X 2 " pdb=" C2' G X 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" C3' U X 5 " pdb=" C4' U X 5 " pdb=" O3' U X 5 " pdb=" C2' U X 5 " both_signs ideal model delta sigma weight residual False -2.48 -2.32 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" C2' U X 9 " pdb=" C3' U X 9 " pdb=" O2' U X 9 " pdb=" C1' U X 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2928 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 642 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO A 643 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 643 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 643 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 400 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 401 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 401 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 401 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 693 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 694 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " 0.026 5.00e-02 4.00e+02 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 86 2.58 - 3.16: 14255 3.16 - 3.74: 28366 3.74 - 4.32: 40596 4.32 - 4.90: 63885 Nonbonded interactions: 147188 Sorted by model distance: nonbonded pdb=" O2B ADP B1101 " pdb="MG MG B1103 " model vdw 1.999 2.170 nonbonded pdb=" O3B ADP A 701 " pdb="MG MG A 703 " model vdw 2.062 2.170 nonbonded pdb=" O THR A 296 " pdb=" OH TYR A 456 " model vdw 2.149 3.040 nonbonded pdb=" O2' U X 5 " pdb=" O5' G X 6 " model vdw 2.253 3.040 nonbonded pdb=" OD1 ASP B 348 " pdb=" OH TYR B 385 " model vdw 2.285 3.040 ... (remaining 147183 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 'B' and (resid 305 through 898 or resid 900 through 943 or resid 956 thro \ ugh 1013 or resid 1101 through 1103)) selection = chain 'C' } 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: 0.660 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: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 23.610 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 18489 Z= 0.138 Angle : 0.556 6.699 25368 Z= 0.339 Chirality : 0.043 0.168 2931 Planarity : 0.004 0.053 2896 Dihedral : 14.599 160.944 7671 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.28 % Allowed : 5.85 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 1968 helix: 2.09 (0.17), residues: 975 sheet: -0.11 (0.30), residues: 311 loop : -0.33 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 374 TYR 0.010 0.001 TYR A 588 PHE 0.009 0.001 PHE B 373 TRP 0.022 0.001 TRP A 386 HIS 0.003 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (18477) covalent geometry : angle 0.55275 / 0.34 (25350) hydrogen bonds : bond 0.25061 / 26.39 ( 941) hydrogen bonds : angle 7.39331 / 9.39 ( 2656) metal coordination : bond 0.00268 / 0.21 ( 12) metal coordination : angle 2.19159 / 3.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 392 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.6271 (tp30) cc_final: 0.5825 (tp30) REVERT: A 124 VAL cc_start: 0.8166 (p) cc_final: 0.7943 (m) REVERT: A 132 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6682 (mt-10) REVERT: A 222 HIS cc_start: 0.7486 (m-70) cc_final: 0.7122 (m90) REVERT: A 249 LEU cc_start: 0.5652 (pp) cc_final: 0.5393 (mp) REVERT: A 257 MET cc_start: 0.8078 (mtt) cc_final: 0.7532 (tmm) REVERT: A 267 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6621 (tp30) REVERT: A 353 MET cc_start: 0.7489 (tpp) cc_final: 0.7130 (tpp) REVERT: A 449 HIS cc_start: 0.7638 (m-70) cc_final: 0.7234 (m90) REVERT: A 473 ARG cc_start: 0.6412 (ttt-90) cc_final: 0.5620 (tpt170) REVERT: A 519 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7405 (mt0) REVERT: A 551 HIS cc_start: 0.7077 (m-70) cc_final: 0.6454 (m90) REVERT: A 552 VAL cc_start: 0.8327 (t) cc_final: 0.8072 (m) REVERT: A 555 LEU cc_start: 0.6058 (pp) cc_final: 0.5822 (mp) REVERT: A 568 ASP cc_start: 0.6519 (m-30) cc_final: 0.6300 (m-30) REVERT: A 575 THR cc_start: 0.6859 (p) cc_final: 0.6645 (p) REVERT: A 583 ASN cc_start: 0.8322 (m-40) cc_final: 0.7975 (t0) REVERT: A 644 GLN cc_start: 0.7765 (mt0) cc_final: 0.7473 (mm110) REVERT: A 663 ASP cc_start: 0.6647 (t0) cc_final: 0.6017 (m-30) REVERT: B 307 GLN cc_start: 0.7186 (tp40) cc_final: 0.6760 (pt0) REVERT: B 374 ARG cc_start: 0.7273 (ttp80) cc_final: 0.6477 (mpt-90) REVERT: B 402 GLU cc_start: 0.5857 (tp30) cc_final: 0.5340 (tp30) REVERT: B 522 LYS cc_start: 0.7041 (tttt) cc_final: 0.6230 (mttm) REVERT: B 533 GLN cc_start: 0.6294 (mm110) cc_final: 0.5757 (mm-40) REVERT: B 547 GLU cc_start: 0.7405 (tp30) cc_final: 0.6493 (tm-30) REVERT: B 710 GLU cc_start: 0.7280 (tt0) cc_final: 0.6898 (tp30) REVERT: B 726 LYS cc_start: 0.7536 (tttt) cc_final: 0.6315 (tptt) REVERT: B 742 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6470 (pt0) REVERT: B 743 LYS cc_start: 0.6634 (mttt) cc_final: 0.5978 (pttp) REVERT: B 766 MET cc_start: 0.7242 (ttt) cc_final: 0.6529 (ttp) REVERT: B 776 SER cc_start: 0.7415 (t) cc_final: 0.6962 (m) REVERT: B 852 LYS cc_start: 0.6868 (ptpt) cc_final: 0.6537 (ptmt) REVERT: B 860 CYS cc_start: 0.7100 (t) cc_final: 0.6879 (t) REVERT: B 865 LYS cc_start: 0.6692 (mtmt) cc_final: 0.6019 (mmtp) REVERT: B 918 GLU cc_start: 0.7231 (pt0) cc_final: 0.6826 (pm20) REVERT: B 1001 LYS cc_start: 0.7536 (tttt) cc_final: 0.7080 (ptmm) REVERT: B 1002 LYS cc_start: 0.7247 (mtmt) cc_final: 0.7010 (mtmm) REVERT: C 323 LYS cc_start: 0.7628 (mttm) cc_final: 0.7113 (mmtm) REVERT: C 359 VAL cc_start: 0.8645 (t) cc_final: 0.8432 (m) REVERT: C 374 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7426 (ttp80) REVERT: C 388 ILE cc_start: 0.7309 (tp) cc_final: 0.6953 (pt) REVERT: C 501 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6143 (mtpt) REVERT: C 533 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6321 (mm-40) REVERT: C 538 LYS cc_start: 0.6889 (mttt) cc_final: 0.6587 (mtpt) REVERT: C 548 ASP cc_start: 0.6339 (t0) cc_final: 0.5563 (t0) REVERT: C 565 CYS cc_start: 0.5570 (p) cc_final: 0.5183 (p) REVERT: C 567 MET cc_start: 0.6561 (mtt) cc_final: 0.6270 (mtm) REVERT: C 570 MET cc_start: 0.7696 (mmm) cc_final: 0.7055 (mmp) REVERT: C 632 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6879 (tp30) REVERT: C 667 LEU cc_start: 0.6877 (mt) cc_final: 0.6500 (mp) REVERT: C 670 ASP cc_start: 0.6549 (t0) cc_final: 0.5643 (m-30) REVERT: C 671 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6904 (tm-30) REVERT: C 685 LYS cc_start: 0.6849 (mttt) cc_final: 0.6578 (pttt) REVERT: C 720 ARG cc_start: 0.6376 (mmt90) cc_final: 0.5673 (mmm160) REVERT: C 726 LYS cc_start: 0.8261 (ttpt) cc_final: 0.7208 (tptt) REVERT: C 741 ASN cc_start: 0.7238 (t0) cc_final: 0.6612 (m-40) REVERT: C 743 LYS cc_start: 0.7343 (mtmt) cc_final: 0.6766 (ttpt) REVERT: C 762 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7811 (mm-30) REVERT: C 764 LYS cc_start: 0.7506 (pttt) cc_final: 0.6680 (pptt) REVERT: C 869 TYR cc_start: 0.6852 (t80) cc_final: 0.6435 (t80) REVERT: C 882 MET cc_start: 0.6551 (tpt) cc_final: 0.6349 (tpp) REVERT: C 902 LEU cc_start: 0.7329 (mt) cc_final: 0.6926 (tp) REVERT: C 926 MET cc_start: 0.5998 (mtt) cc_final: 0.5744 (mtm) REVERT: C 971 MET cc_start: 0.6461 (mmm) cc_final: 0.6148 (mmm) outliers start: 5 outliers final: 0 residues processed: 394 average time/residue: 0.1648 time to fit residues: 93.1063 Evaluate side-chains 243 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 501 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 137 HIS A 183 ASN A 277 GLN A 311 HIS A 314 HIS A 340 HIS A 344 HIS A 401 GLN A 411 GLN A 451 ASN A 545 GLN A 558 ASN A 581 ASN A 598 ASN A 648 GLN B 346 HIS B 395 GLN B 423 ASN B 460 HIS B 499 GLN B 533 GLN B 562 GLN B 576 GLN B 580 GLN B 584 GLN B 736 GLN B 769 ASN C 307 GLN C 576 GLN C 899 ASN C 957 ASN C 994 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125400 restraints weight = 20625.931| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.60 r_work: 0.3058 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18489 Z= 0.185 Angle : 0.585 6.566 25368 Z= 0.314 Chirality : 0.045 0.278 2931 Planarity : 0.004 0.051 2896 Dihedral : 14.725 164.342 3559 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.42 % Allowed : 8.17 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1968 helix: 2.28 (0.16), residues: 991 sheet: -0.33 (0.29), residues: 320 loop : -0.41 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 843 TYR 0.019 0.002 TYR C 630 PHE 0.018 0.002 PHE C 680 TRP 0.021 0.001 TRP A 604 HIS 0.006 0.001 HIS B 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (18477) covalent geometry : angle 0.58233 / 0.31 (25350) hydrogen bonds : bond 0.06895 / 7.52 ( 941) hydrogen bonds : angle 4.49444 / 5.89 ( 2656) metal coordination : bond 0.00267 / 0.23 ( 12) metal coordination : angle 2.28941 / 3.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7323 (mtp-110) REVERT: A 132 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7960 (mt-10) REVERT: A 154 LEU cc_start: 0.8370 (mm) cc_final: 0.8010 (mm) REVERT: A 169 SER cc_start: 0.9351 (t) cc_final: 0.8944 (p) REVERT: A 222 HIS cc_start: 0.7247 (m-70) cc_final: 0.7008 (m90) REVERT: A 353 MET cc_start: 0.8283 (tpp) cc_final: 0.8059 (tpp) REVERT: A 449 HIS cc_start: 0.7969 (m-70) cc_final: 0.7627 (m90) REVERT: A 473 ARG cc_start: 0.6913 (ttt-90) cc_final: 0.6313 (tpt170) REVERT: A 555 LEU cc_start: 0.8164 (pp) cc_final: 0.7656 (mp) REVERT: A 568 ASP cc_start: 0.7358 (m-30) cc_final: 0.6937 (m-30) REVERT: A 581 ASN cc_start: 0.6999 (m-40) cc_final: 0.6109 (m-40) REVERT: B 402 GLU cc_start: 0.7386 (tp30) cc_final: 0.7108 (tp30) REVERT: B 522 LYS cc_start: 0.7969 (tttt) cc_final: 0.7488 (mttt) REVERT: B 531 GLN cc_start: 0.8250 (mm-40) cc_final: 0.8044 (mm-40) REVERT: B 684 ASN cc_start: 0.8069 (t0) cc_final: 0.7826 (t0) REVERT: B 743 LYS cc_start: 0.8427 (mttt) cc_final: 0.8138 (pttp) REVERT: B 797 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7350 (p0) REVERT: B 865 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7952 (mmtp) REVERT: B 992 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7758 (ttpt) REVERT: B 994 ASN cc_start: 0.7636 (t0) cc_final: 0.7434 (t0) REVERT: C 323 LYS cc_start: 0.8363 (mttm) cc_final: 0.8060 (mmtm) REVERT: C 463 MET cc_start: 0.8328 (ttt) cc_final: 0.8092 (mtp) REVERT: C 501 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: C 533 GLN cc_start: 0.8267 (mm-40) cc_final: 0.8058 (mm-40) REVERT: C 570 MET cc_start: 0.8477 (mmm) cc_final: 0.7692 (mmp) REVERT: C 720 ARG cc_start: 0.8188 (mmt90) cc_final: 0.7762 (mmm160) REVERT: C 726 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8450 (tptt) REVERT: C 764 LYS cc_start: 0.8294 (pttt) cc_final: 0.7806 (pptt) REVERT: C 777 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7981 (mtmt) REVERT: C 879 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: C 882 MET cc_start: 0.7452 (tpt) cc_final: 0.7155 (tpp) REVERT: C 883 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: C 886 MET cc_start: 0.8065 (mmm) cc_final: 0.7791 (mmm) REVERT: C 902 LEU cc_start: 0.7937 (mt) cc_final: 0.7492 (tt) outliers start: 25 outliers final: 9 residues processed: 267 average time/residue: 0.1605 time to fit residues: 62.4019 Evaluate side-chains 209 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 883 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 52 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 311 HIS A 314 HIS A 344 HIS A 411 GLN A 551 HIS A 576 HIS C 530 ASN C 576 GLN C 863 ASN C 957 ASN C 986 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120660 restraints weight = 20994.255| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.42 r_work: 0.2980 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 18489 Z= 0.348 Angle : 0.732 8.072 25368 Z= 0.376 Chirality : 0.052 0.351 2931 Planarity : 0.005 0.053 2896 Dihedral : 14.664 159.030 3559 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.95 % Allowed : 8.91 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1968 helix: 1.92 (0.16), residues: 991 sheet: -0.81 (0.29), residues: 310 loop : -0.76 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 843 TYR 0.023 0.002 TYR C 630 PHE 0.026 0.003 PHE C 849 TRP 0.015 0.002 TRP A 386 HIS 0.010 0.002 HIS C 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.35 (18477) covalent geometry : angle 0.72584 / 0.38 (25350) hydrogen bonds : bond 0.07054 / 7.50 ( 941) hydrogen bonds : angle 4.41291 / 5.78 ( 2656) metal coordination : bond 0.00536 / 0.48 ( 12) metal coordination : angle 3.51846 / 4.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7291 (mtp-110) REVERT: A 123 THR cc_start: 0.8768 (m) cc_final: 0.8431 (p) REVERT: A 132 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8086 (mt-10) REVERT: A 169 SER cc_start: 0.9391 (t) cc_final: 0.8986 (p) REVERT: A 222 HIS cc_start: 0.7363 (m-70) cc_final: 0.7108 (m90) REVERT: A 378 GLN cc_start: 0.7748 (tp40) cc_final: 0.7515 (mm-40) REVERT: A 449 HIS cc_start: 0.8047 (m-70) cc_final: 0.7714 (m90) REVERT: A 473 ARG cc_start: 0.6860 (ttt-90) cc_final: 0.6328 (tpt170) REVERT: A 551 HIS cc_start: 0.7358 (m90) cc_final: 0.6736 (m90) REVERT: A 568 ASP cc_start: 0.7756 (m-30) cc_final: 0.7236 (m-30) REVERT: A 581 ASN cc_start: 0.7438 (m-40) cc_final: 0.7045 (m-40) REVERT: B 324 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7551 (m-40) REVERT: B 355 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: B 402 GLU cc_start: 0.7687 (tp30) cc_final: 0.7374 (tp30) REVERT: B 498 LYS cc_start: 0.8145 (mttm) cc_final: 0.7903 (mtpt) REVERT: B 522 LYS cc_start: 0.7916 (tttt) cc_final: 0.7608 (mttt) REVERT: B 552 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7521 (mt-10) REVERT: B 743 LYS cc_start: 0.8535 (mttt) cc_final: 0.8157 (pttp) REVERT: B 797 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7353 (p0) REVERT: B 865 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7972 (mmtp) REVERT: B 992 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7942 (ttpt) REVERT: C 306 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6682 (pp) REVERT: C 323 LYS cc_start: 0.8378 (mttm) cc_final: 0.7963 (mmtm) REVERT: C 390 LEU cc_start: 0.8972 (mt) cc_final: 0.8756 (mt) REVERT: C 463 MET cc_start: 0.8415 (ttt) cc_final: 0.8212 (mtp) REVERT: C 501 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7814 (mtpt) REVERT: C 720 ARG cc_start: 0.8292 (mmt90) cc_final: 0.7904 (mmm160) REVERT: C 726 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8561 (tptt) REVERT: C 764 LYS cc_start: 0.8301 (pttt) cc_final: 0.7805 (pptt) REVERT: C 777 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7928 (mtmt) REVERT: C 835 HIS cc_start: 0.7455 (m-70) cc_final: 0.7241 (t70) REVERT: C 879 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: C 882 MET cc_start: 0.7622 (tpt) cc_final: 0.7253 (tpp) REVERT: C 886 MET cc_start: 0.8242 (mmm) cc_final: 0.7939 (mmm) REVERT: C 902 LEU cc_start: 0.8014 (mt) cc_final: 0.7740 (tp) REVERT: C 926 MET cc_start: 0.7644 (mtm) cc_final: 0.7321 (mtp) outliers start: 52 outliers final: 25 residues processed: 233 average time/residue: 0.1485 time to fit residues: 50.7600 Evaluate side-chains 215 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 845 THR Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 119 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS A 344 HIS C 307 GLN C 576 GLN C 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123417 restraints weight = 20857.415| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.45 r_work: 0.3026 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18489 Z= 0.169 Angle : 0.552 6.763 25368 Z= 0.288 Chirality : 0.042 0.313 2931 Planarity : 0.004 0.047 2896 Dihedral : 14.744 161.898 3559 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.27 % Allowed : 9.99 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1968 helix: 2.21 (0.16), residues: 995 sheet: -0.79 (0.29), residues: 300 loop : -0.73 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 843 TYR 0.016 0.001 TYR A 588 PHE 0.014 0.001 PHE C 680 TRP 0.011 0.001 TRP A 386 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (18477) covalent geometry : angle 0.54774 / 0.29 (25350) hydrogen bonds : bond 0.05301 / 5.70 ( 941) hydrogen bonds : angle 4.05340 / 5.33 ( 2656) metal coordination : bond 0.00294 / 0.23 ( 12) metal coordination : angle 2.65128 / 3.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.689 Fit side-chains REVERT: A 87 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7422 (mtp-110) REVERT: A 123 THR cc_start: 0.8750 (m) cc_final: 0.8401 (p) REVERT: A 132 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8109 (mt-10) REVERT: A 169 SER cc_start: 0.9334 (t) cc_final: 0.8887 (p) REVERT: A 222 HIS cc_start: 0.7435 (m-70) cc_final: 0.7222 (m90) REVERT: A 313 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: A 449 HIS cc_start: 0.8019 (m-70) cc_final: 0.7681 (m90) REVERT: A 473 ARG cc_start: 0.6877 (ttt-90) cc_final: 0.6309 (tpt170) REVERT: A 551 HIS cc_start: 0.7319 (m90) cc_final: 0.6671 (m90) REVERT: A 568 ASP cc_start: 0.7669 (m-30) cc_final: 0.7131 (m-30) REVERT: A 581 ASN cc_start: 0.7381 (m-40) cc_final: 0.6956 (m-40) REVERT: B 402 GLU cc_start: 0.7579 (tp30) cc_final: 0.7089 (tp30) REVERT: B 498 LYS cc_start: 0.8145 (mttm) cc_final: 0.7865 (mtpt) REVERT: B 570 MET cc_start: 0.8461 (mmt) cc_final: 0.8035 (mmp) REVERT: B 687 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8560 (mt) REVERT: B 743 LYS cc_start: 0.8504 (mttt) cc_final: 0.8124 (pttp) REVERT: B 797 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7437 (p0) REVERT: B 865 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7850 (mmtp) REVERT: B 992 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7930 (mttt) REVERT: C 306 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6787 (pp) REVERT: C 323 LYS cc_start: 0.8358 (mttm) cc_final: 0.7917 (mmtm) REVERT: C 463 MET cc_start: 0.8379 (ttt) cc_final: 0.8173 (mtp) REVERT: C 501 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7817 (mtpt) REVERT: C 570 MET cc_start: 0.8306 (mmp) cc_final: 0.7616 (mmp) REVERT: C 635 ASP cc_start: 0.7750 (m-30) cc_final: 0.7385 (m-30) REVERT: C 696 TYR cc_start: 0.7465 (m-80) cc_final: 0.7255 (m-80) REVERT: C 720 ARG cc_start: 0.8312 (mmt90) cc_final: 0.7945 (mmm160) REVERT: C 726 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8518 (tptt) REVERT: C 764 LYS cc_start: 0.8287 (pttt) cc_final: 0.7765 (pptt) REVERT: C 777 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7930 (mtmt) REVERT: C 835 HIS cc_start: 0.7473 (m-70) cc_final: 0.7237 (t70) REVERT: C 882 MET cc_start: 0.7543 (tpt) cc_final: 0.7200 (tpp) REVERT: C 886 MET cc_start: 0.8156 (mmm) cc_final: 0.7822 (mmm) REVERT: C 902 LEU cc_start: 0.8001 (mt) cc_final: 0.7727 (tp) REVERT: C 926 MET cc_start: 0.7583 (mtm) cc_final: 0.7258 (mtp) outliers start: 40 outliers final: 22 residues processed: 215 average time/residue: 0.1392 time to fit residues: 44.8815 Evaluate side-chains 202 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 929 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 62 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 178 optimal weight: 0.0970 chunk 128 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS A 344 HIS A 411 GLN C 307 GLN C 576 GLN C 957 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129000 restraints weight = 20828.843| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.06 r_work: 0.2993 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18489 Z= 0.166 Angle : 0.543 9.207 25368 Z= 0.281 Chirality : 0.042 0.295 2931 Planarity : 0.004 0.045 2896 Dihedral : 14.676 160.997 3559 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.33 % Allowed : 10.84 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 1968 helix: 2.36 (0.16), residues: 990 sheet: -0.86 (0.29), residues: 298 loop : -0.73 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 843 TYR 0.015 0.001 TYR A 588 PHE 0.014 0.001 PHE C 680 TRP 0.011 0.001 TRP A 386 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (18477) covalent geometry : angle 0.53930 / 0.28 (25350) hydrogen bonds : bond 0.04949 / 5.30 ( 941) hydrogen bonds : angle 3.91476 / 5.15 ( 2656) metal coordination : bond 0.00290 / 0.22 ( 12) metal coordination : angle 2.55126 / 3.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7438 (mtp-110) REVERT: A 123 THR cc_start: 0.8797 (m) cc_final: 0.8426 (p) REVERT: A 132 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8219 (mt-10) REVERT: A 169 SER cc_start: 0.9342 (t) cc_final: 0.8898 (p) REVERT: A 222 HIS cc_start: 0.7377 (m-70) cc_final: 0.7162 (m90) REVERT: A 449 HIS cc_start: 0.8101 (m-70) cc_final: 0.7761 (m90) REVERT: A 473 ARG cc_start: 0.6833 (ttt-90) cc_final: 0.6335 (tpt170) REVERT: A 551 HIS cc_start: 0.7344 (m90) cc_final: 0.6831 (m-70) REVERT: A 568 ASP cc_start: 0.7733 (m-30) cc_final: 0.7214 (m-30) REVERT: A 581 ASN cc_start: 0.7358 (m-40) cc_final: 0.6837 (m110) REVERT: B 355 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: B 402 GLU cc_start: 0.7660 (tp30) cc_final: 0.7156 (tp30) REVERT: B 498 LYS cc_start: 0.8184 (mttm) cc_final: 0.7910 (mtpt) REVERT: B 687 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (mt) REVERT: B 743 LYS cc_start: 0.8531 (mttt) cc_final: 0.8160 (pttp) REVERT: B 797 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7438 (p0) REVERT: B 865 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7694 (mmtp) REVERT: B 992 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7999 (mttm) REVERT: C 306 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6835 (pp) REVERT: C 323 LYS cc_start: 0.8392 (mttm) cc_final: 0.7970 (mmtm) REVERT: C 501 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7891 (mtpt) REVERT: C 635 ASP cc_start: 0.7747 (m-30) cc_final: 0.7403 (m-30) REVERT: C 709 MET cc_start: 0.8649 (mmm) cc_final: 0.8430 (mmm) REVERT: C 720 ARG cc_start: 0.8439 (mmt90) cc_final: 0.8096 (mmm160) REVERT: C 726 LYS cc_start: 0.8835 (ttpt) cc_final: 0.8547 (tptt) REVERT: C 764 LYS cc_start: 0.8347 (pttt) cc_final: 0.7824 (pptt) REVERT: C 777 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7920 (mtmt) REVERT: C 835 HIS cc_start: 0.7613 (m-70) cc_final: 0.7339 (t70) REVERT: C 882 MET cc_start: 0.7655 (tpt) cc_final: 0.7328 (tpp) REVERT: C 886 MET cc_start: 0.8234 (mmm) cc_final: 0.7887 (mmm) REVERT: C 902 LEU cc_start: 0.7926 (mt) cc_final: 0.7662 (tp) REVERT: C 926 MET cc_start: 0.7616 (mtm) cc_final: 0.7286 (mtp) outliers start: 41 outliers final: 27 residues processed: 209 average time/residue: 0.1407 time to fit residues: 44.3420 Evaluate side-chains 205 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 978 ASP Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 929 VAL Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 38 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 198 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS A 344 HIS B 684 ASN C 307 GLN C 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120222 restraints weight = 20413.496| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.23 r_work: 0.3049 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18489 Z= 0.104 Angle : 0.483 6.222 25368 Z= 0.250 Chirality : 0.039 0.260 2931 Planarity : 0.003 0.043 2896 Dihedral : 14.718 161.602 3559 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.93 % Allowed : 11.69 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 1968 helix: 2.57 (0.16), residues: 992 sheet: -0.71 (0.29), residues: 296 loop : -0.69 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.015 0.001 TYR C 623 PHE 0.014 0.001 PHE C 680 TRP 0.010 0.001 TRP A 386 HIS 0.005 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (18477) covalent geometry : angle 0.47951 / 0.25 (25350) hydrogen bonds : bond 0.04243 / 4.55 ( 941) hydrogen bonds : angle 3.73289 / 4.91 ( 2656) metal coordination : bond 0.00231 / 0.20 ( 12) metal coordination : angle 2.08987 / 2.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7452 (mtp-110) REVERT: A 100 LEU cc_start: 0.8946 (tt) cc_final: 0.8508 (tp) REVERT: A 123 THR cc_start: 0.8804 (m) cc_final: 0.8444 (p) REVERT: A 131 ASP cc_start: 0.8091 (m-30) cc_final: 0.7731 (m-30) REVERT: A 132 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7854 (mt-10) REVERT: A 169 SER cc_start: 0.9209 (t) cc_final: 0.8594 (p) REVERT: A 222 HIS cc_start: 0.7623 (m-70) cc_final: 0.7338 (m90) REVERT: A 313 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7255 (tt0) REVERT: A 449 HIS cc_start: 0.7981 (m-70) cc_final: 0.7618 (m90) REVERT: A 473 ARG cc_start: 0.6831 (ttt-90) cc_final: 0.6152 (tpt170) REVERT: A 551 HIS cc_start: 0.7253 (m90) cc_final: 0.6527 (m90) REVERT: A 568 ASP cc_start: 0.7618 (m-30) cc_final: 0.7123 (m-30) REVERT: A 581 ASN cc_start: 0.7133 (m-40) cc_final: 0.6611 (m110) REVERT: A 604 TRP cc_start: 0.5516 (OUTLIER) cc_final: 0.5146 (t-100) REVERT: B 355 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: B 402 GLU cc_start: 0.7423 (tp30) cc_final: 0.6939 (tp30) REVERT: B 498 LYS cc_start: 0.7791 (mttm) cc_final: 0.7267 (mtpt) REVERT: B 570 MET cc_start: 0.8559 (mmp) cc_final: 0.8140 (mmp) REVERT: B 687 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8391 (mt) REVERT: B 743 LYS cc_start: 0.8374 (mttt) cc_final: 0.7732 (pttp) REVERT: B 797 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7280 (p0) REVERT: B 865 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7214 (mmtp) REVERT: B 992 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7917 (mttt) REVERT: C 306 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6552 (pp) REVERT: C 323 LYS cc_start: 0.8245 (mttm) cc_final: 0.7693 (mmtm) REVERT: C 501 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7388 (mtpt) REVERT: C 552 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7277 (mp0) REVERT: C 635 ASP cc_start: 0.7708 (m-30) cc_final: 0.7275 (m-30) REVERT: C 709 MET cc_start: 0.8435 (mmm) cc_final: 0.8156 (mmm) REVERT: C 720 ARG cc_start: 0.7988 (mmt90) cc_final: 0.7473 (mmm160) REVERT: C 726 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8234 (tptt) REVERT: C 777 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7253 (mtmt) REVERT: C 835 HIS cc_start: 0.7263 (m-70) cc_final: 0.6812 (t70) REVERT: C 882 MET cc_start: 0.7188 (tpt) cc_final: 0.6822 (tpp) REVERT: C 886 MET cc_start: 0.7821 (mmm) cc_final: 0.7421 (mmm) REVERT: C 902 LEU cc_start: 0.7739 (mt) cc_final: 0.7439 (tt) REVERT: C 926 MET cc_start: 0.7143 (mtm) cc_final: 0.6822 (mtp) outliers start: 34 outliers final: 19 residues processed: 213 average time/residue: 0.1278 time to fit residues: 41.4947 Evaluate side-chains 204 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 152 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 200 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS A 344 HIS C 307 GLN C 957 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119722 restraints weight = 20627.720| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.31 r_work: 0.3015 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18489 Z= 0.122 Angle : 0.491 6.328 25368 Z= 0.253 Chirality : 0.040 0.247 2931 Planarity : 0.003 0.043 2896 Dihedral : 14.652 160.461 3559 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.16 % Allowed : 11.35 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.19), residues: 1968 helix: 2.64 (0.16), residues: 992 sheet: -0.71 (0.29), residues: 294 loop : -0.67 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.014 0.001 TYR A 588 PHE 0.014 0.001 PHE C 680 TRP 0.013 0.001 TRP A 195 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (18477) covalent geometry : angle 0.48805 / 0.25 (25350) hydrogen bonds : bond 0.04212 / 4.50 ( 941) hydrogen bonds : angle 3.66589 / 4.82 ( 2656) metal coordination : bond 0.00241 / 0.20 ( 12) metal coordination : angle 2.12353 / 3.04 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.8814 (m) cc_final: 0.8451 (p) REVERT: A 132 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7880 (mt-10) REVERT: A 169 SER cc_start: 0.9218 (t) cc_final: 0.8603 (p) REVERT: A 222 HIS cc_start: 0.7639 (m-70) cc_final: 0.7358 (m90) REVERT: A 313 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 353 MET cc_start: 0.7642 (ttm) cc_final: 0.7419 (ttm) REVERT: A 449 HIS cc_start: 0.7992 (m-70) cc_final: 0.7643 (m90) REVERT: A 473 ARG cc_start: 0.6841 (ttt-90) cc_final: 0.6147 (tpt170) REVERT: A 551 HIS cc_start: 0.7263 (m90) cc_final: 0.6536 (m90) REVERT: A 568 ASP cc_start: 0.7656 (m-30) cc_final: 0.7167 (m-30) REVERT: A 581 ASN cc_start: 0.7134 (m-40) cc_final: 0.6621 (m110) REVERT: A 604 TRP cc_start: 0.5252 (OUTLIER) cc_final: 0.4935 (t-100) REVERT: B 355 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: B 402 GLU cc_start: 0.7453 (tp30) cc_final: 0.6960 (tp30) REVERT: B 498 LYS cc_start: 0.7799 (mttm) cc_final: 0.7285 (mtpt) REVERT: B 570 MET cc_start: 0.8593 (mmp) cc_final: 0.8156 (mmp) REVERT: B 687 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 743 LYS cc_start: 0.8357 (mttt) cc_final: 0.7665 (ptmm) REVERT: B 797 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7321 (p0) REVERT: B 865 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7370 (mmtp) REVERT: B 992 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7949 (mttt) REVERT: C 501 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7422 (mtpt) REVERT: C 552 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7300 (mp0) REVERT: C 635 ASP cc_start: 0.7641 (m-30) cc_final: 0.7210 (m-30) REVERT: C 709 MET cc_start: 0.8491 (mmm) cc_final: 0.8207 (mmm) REVERT: C 720 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7476 (mmm160) REVERT: C 726 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8246 (tptt) REVERT: C 777 LYS cc_start: 0.7617 (mtmt) cc_final: 0.7280 (mtmt) REVERT: C 835 HIS cc_start: 0.7303 (m-70) cc_final: 0.6839 (t70) REVERT: C 882 MET cc_start: 0.7230 (tpt) cc_final: 0.6849 (tpp) REVERT: C 886 MET cc_start: 0.7950 (mmm) cc_final: 0.7596 (mmm) REVERT: C 902 LEU cc_start: 0.7711 (mt) cc_final: 0.7410 (tt) outliers start: 38 outliers final: 22 residues processed: 206 average time/residue: 0.1351 time to fit residues: 42.4642 Evaluate side-chains 204 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 48 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 200 optimal weight: 20.0000 chunk 60 optimal weight: 0.0030 chunk 28 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS A 344 HIS B 684 ASN C 307 GLN C 957 ASN C 986 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120910 restraints weight = 20485.977| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.13 r_work: 0.3071 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18489 Z= 0.101 Angle : 0.471 8.829 25368 Z= 0.242 Chirality : 0.039 0.239 2931 Planarity : 0.003 0.042 2896 Dihedral : 14.672 160.401 3559 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.82 % Allowed : 11.69 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.19), residues: 1968 helix: 2.76 (0.16), residues: 984 sheet: -0.77 (0.29), residues: 298 loop : -0.65 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.016 0.001 TYR C 623 PHE 0.014 0.001 PHE C 680 TRP 0.017 0.001 TRP A 195 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (18477) covalent geometry : angle 0.46802 / 0.24 (25350) hydrogen bonds : bond 0.03864 / 4.12 ( 941) hydrogen bonds : angle 3.56749 / 4.68 ( 2656) metal coordination : bond 0.00242 / 0.21 ( 12) metal coordination : angle 1.92935 / 2.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 123 THR cc_start: 0.8813 (m) cc_final: 0.8449 (p) REVERT: A 132 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7838 (mt-10) REVERT: A 169 SER cc_start: 0.9211 (t) cc_final: 0.8565 (p) REVERT: A 222 HIS cc_start: 0.7599 (m-70) cc_final: 0.7329 (m90) REVERT: A 313 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: A 449 HIS cc_start: 0.7932 (m-70) cc_final: 0.7617 (m90) REVERT: A 473 ARG cc_start: 0.6865 (ttt-90) cc_final: 0.6227 (tpt170) REVERT: A 551 HIS cc_start: 0.7330 (m90) cc_final: 0.6724 (m-70) REVERT: A 568 ASP cc_start: 0.7594 (m-30) cc_final: 0.7028 (m-30) REVERT: A 581 ASN cc_start: 0.7179 (m-40) cc_final: 0.6680 (m110) REVERT: B 355 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7265 (pt0) REVERT: B 402 GLU cc_start: 0.7363 (tp30) cc_final: 0.6669 (tp30) REVERT: B 498 LYS cc_start: 0.7748 (mttm) cc_final: 0.7230 (mtpt) REVERT: B 532 ILE cc_start: 0.7033 (pp) cc_final: 0.6674 (tp) REVERT: B 567 MET cc_start: 0.8060 (mtp) cc_final: 0.7753 (mtt) REVERT: B 570 MET cc_start: 0.8535 (mmp) cc_final: 0.8111 (mmp) REVERT: B 585 MET cc_start: 0.8371 (tpt) cc_final: 0.8081 (mmm) REVERT: B 687 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 743 LYS cc_start: 0.8349 (mttt) cc_final: 0.7663 (ptmm) REVERT: B 797 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7301 (p0) REVERT: B 992 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7946 (mttt) REVERT: C 501 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7368 (mtpt) REVERT: C 552 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7255 (mp0) REVERT: C 635 ASP cc_start: 0.7541 (m-30) cc_final: 0.7114 (m-30) REVERT: C 709 MET cc_start: 0.8479 (mmm) cc_final: 0.8166 (mmm) REVERT: C 720 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7426 (mmm160) REVERT: C 726 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8206 (tptt) REVERT: C 777 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7362 (mtmt) REVERT: C 882 MET cc_start: 0.7385 (tpt) cc_final: 0.7038 (tpp) REVERT: C 886 MET cc_start: 0.7943 (mmm) cc_final: 0.7729 (mmm) REVERT: C 902 LEU cc_start: 0.7746 (mt) cc_final: 0.7475 (tt) REVERT: C 939 TYR cc_start: 0.7935 (p90) cc_final: 0.7643 (p90) outliers start: 32 outliers final: 21 residues processed: 199 average time/residue: 0.1353 time to fit residues: 41.4116 Evaluate side-chains 199 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 138 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS A 344 HIS B 684 ASN C 307 GLN C 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120409 restraints weight = 20497.293| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.25 r_work: 0.3051 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18489 Z= 0.120 Angle : 0.485 11.507 25368 Z= 0.248 Chirality : 0.040 0.243 2931 Planarity : 0.003 0.043 2896 Dihedral : 14.608 159.664 3559 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.65 % Allowed : 11.98 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 1968 helix: 2.73 (0.16), residues: 990 sheet: -0.70 (0.29), residues: 294 loop : -0.64 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.014 0.001 TYR C 623 PHE 0.013 0.001 PHE C 680 TRP 0.030 0.001 TRP A 604 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (18477) covalent geometry : angle 0.48251 / 0.25 (25350) hydrogen bonds : bond 0.03965 / 4.22 ( 941) hydrogen bonds : angle 3.56512 / 4.66 ( 2656) metal coordination : bond 0.00246 / 0.20 ( 12) metal coordination : angle 2.07166 / 2.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.654 Fit side-chains REVERT: A 12 MET cc_start: 0.7453 (mmm) cc_final: 0.7192 (mmm) REVERT: A 123 THR cc_start: 0.8932 (m) cc_final: 0.8572 (p) REVERT: A 132 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7859 (mt-10) REVERT: A 169 SER cc_start: 0.9215 (t) cc_final: 0.8574 (p) REVERT: A 222 HIS cc_start: 0.7587 (m-70) cc_final: 0.7314 (m90) REVERT: A 313 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: A 449 HIS cc_start: 0.7946 (m-70) cc_final: 0.7634 (m90) REVERT: A 473 ARG cc_start: 0.6867 (ttt-90) cc_final: 0.6192 (tpt170) REVERT: A 551 HIS cc_start: 0.7332 (m90) cc_final: 0.6752 (m-70) REVERT: A 568 ASP cc_start: 0.7625 (m-30) cc_final: 0.7091 (m-30) REVERT: A 581 ASN cc_start: 0.7106 (m-40) cc_final: 0.6600 (m110) REVERT: B 355 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: B 402 GLU cc_start: 0.7406 (tp30) cc_final: 0.6701 (tp30) REVERT: B 532 ILE cc_start: 0.7036 (pp) cc_final: 0.6677 (tp) REVERT: B 570 MET cc_start: 0.8585 (mmp) cc_final: 0.8193 (mmp) REVERT: B 585 MET cc_start: 0.8414 (tpt) cc_final: 0.8158 (mmm) REVERT: B 687 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 743 LYS cc_start: 0.8345 (mttt) cc_final: 0.7658 (ptmm) REVERT: B 797 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7393 (p0) REVERT: B 992 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7973 (mttt) REVERT: C 501 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7395 (mtpt) REVERT: C 552 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7272 (mp0) REVERT: C 635 ASP cc_start: 0.7548 (m-30) cc_final: 0.7112 (m-30) REVERT: C 720 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7355 (mmm160) REVERT: C 726 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8199 (tptt) REVERT: C 777 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7350 (mtmt) REVERT: C 882 MET cc_start: 0.7403 (tpt) cc_final: 0.7041 (tpp) REVERT: C 886 MET cc_start: 0.7951 (mmm) cc_final: 0.7730 (mmm) REVERT: C 902 LEU cc_start: 0.7766 (mt) cc_final: 0.7515 (tt) REVERT: C 939 TYR cc_start: 0.7920 (p90) cc_final: 0.7625 (p90) outliers start: 29 outliers final: 22 residues processed: 194 average time/residue: 0.1359 time to fit residues: 39.9572 Evaluate side-chains 201 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.0030 chunk 130 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 66 optimal weight: 0.0020 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN A 311 HIS A 314 HIS B 684 ASN C 307 GLN C 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121369 restraints weight = 20385.217| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.20 r_work: 0.3026 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18489 Z= 0.103 Angle : 0.478 12.896 25368 Z= 0.243 Chirality : 0.039 0.239 2931 Planarity : 0.003 0.042 2896 Dihedral : 14.619 159.812 3559 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.65 % Allowed : 12.03 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 1968 helix: 2.81 (0.16), residues: 983 sheet: -0.71 (0.29), residues: 298 loop : -0.64 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.015 0.001 TYR C 623 PHE 0.013 0.001 PHE C 680 TRP 0.034 0.001 TRP A 604 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (18477) covalent geometry : angle 0.47526 / 0.24 (25350) hydrogen bonds : bond 0.03784 / 4.03 ( 941) hydrogen bonds : angle 3.53193 / 4.62 ( 2656) metal coordination : bond 0.00240 / 0.21 ( 12) metal coordination : angle 1.93022 / 2.72 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.390 Fit side-chains REVERT: A 12 MET cc_start: 0.7446 (mmm) cc_final: 0.7167 (mmm) REVERT: A 123 THR cc_start: 0.8921 (m) cc_final: 0.8554 (p) REVERT: A 132 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7827 (mt-10) REVERT: A 169 SER cc_start: 0.9204 (t) cc_final: 0.8543 (p) REVERT: A 222 HIS cc_start: 0.7601 (m-70) cc_final: 0.7324 (m90) REVERT: A 313 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: A 449 HIS cc_start: 0.7879 (m-70) cc_final: 0.7592 (m90) REVERT: A 473 ARG cc_start: 0.6850 (ttt-90) cc_final: 0.6169 (tpt170) REVERT: A 551 HIS cc_start: 0.7449 (m90) cc_final: 0.6871 (m-70) REVERT: A 555 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 568 ASP cc_start: 0.7587 (m-30) cc_final: 0.7067 (m-30) REVERT: A 581 ASN cc_start: 0.7158 (m-40) cc_final: 0.6657 (m110) REVERT: B 402 GLU cc_start: 0.7369 (tp30) cc_final: 0.6672 (tp30) REVERT: B 532 ILE cc_start: 0.6940 (pp) cc_final: 0.6616 (tp) REVERT: B 570 MET cc_start: 0.8559 (mmp) cc_final: 0.8161 (mmp) REVERT: B 687 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8344 (mt) REVERT: B 743 LYS cc_start: 0.8325 (mttt) cc_final: 0.7613 (ptmm) REVERT: B 797 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7368 (p0) REVERT: B 992 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (mttt) REVERT: C 501 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7327 (mtpt) REVERT: C 552 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7218 (mp0) REVERT: C 635 ASP cc_start: 0.7612 (m-30) cc_final: 0.7169 (m-30) REVERT: C 720 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7272 (mmm160) REVERT: C 726 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8169 (tptt) REVERT: C 777 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7274 (mtmt) REVERT: C 882 MET cc_start: 0.7394 (tpt) cc_final: 0.6995 (tpp) REVERT: C 886 MET cc_start: 0.7866 (mmm) cc_final: 0.7654 (mmm) REVERT: C 902 LEU cc_start: 0.7960 (mt) cc_final: 0.7669 (tt) REVERT: C 939 TYR cc_start: 0.7869 (p90) cc_final: 0.7582 (p90) outliers start: 29 outliers final: 22 residues processed: 199 average time/residue: 0.1340 time to fit residues: 40.2680 Evaluate side-chains 196 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 HIS A 314 HIS B 684 ASN C 307 GLN C 957 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117301 restraints weight = 20589.927| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.28 r_work: 0.3008 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18489 Z= 0.199 Angle : 0.552 12.502 25368 Z= 0.280 Chirality : 0.043 0.255 2931 Planarity : 0.004 0.044 2896 Dihedral : 14.545 159.212 3559 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.65 % Allowed : 12.37 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.19), residues: 1968 helix: 2.65 (0.16), residues: 989 sheet: -0.88 (0.29), residues: 298 loop : -0.57 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 689 TYR 0.016 0.002 TYR B 311 PHE 0.012 0.002 PHE C 680 TRP 0.034 0.002 TRP A 604 HIS 0.006 0.001 HIS B 625 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (18477) covalent geometry : angle 0.54793 / 0.28 (25350) hydrogen bonds : bond 0.04545 / 4.83 ( 941) hydrogen bonds : angle 3.65723 / 4.79 ( 2656) metal coordination : bond 0.00374 / 0.29 ( 12) metal coordination : angle 2.63428 / 3.67 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3564.10 seconds wall clock time: 62 minutes 1.82 seconds (3721.82 seconds total)