Starting phenix.real_space_refine on Thu Feb 5 15:11:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lov_63261/02_2026/9lov_63261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lov_63261/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lov_63261/02_2026/9lov_63261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lov_63261/02_2026/9lov_63261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lov_63261/02_2026/9lov_63261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lov_63261/02_2026/9lov_63261.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 3.84, per 1000 atoms: 0.21 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 800.3 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: 4.51 Time building geometry restraints manager: 2.20 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: 24791 1.34 - 2.68: 434 2.68 - 4.02: 88 4.02 - 5.36: 29 5.36 - 6.70: 8 Bond angle restraints: 25350 Sorted by residual: angle pdb=" O3' G X 2 " pdb=" C3' G X 2 " pdb=" C2' G X 2 " ideal model delta sigma weight residual 113.70 117.17 -3.47 1.50e+00 4.44e-01 5.34e+00 angle pdb=" C3' U X 5 " pdb=" O3' U X 5 " pdb=" P G X 6 " ideal model delta sigma weight residual 120.20 123.54 -3.34 1.50e+00 4.44e-01 4.96e+00 angle pdb=" C GLU C 924 " pdb=" N LYS C 925 " pdb=" CA LYS C 925 " ideal model delta sigma weight residual 123.05 126.52 -3.47 1.57e+00 4.06e-01 4.89e+00 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 110.62 108.45 2.17 1.02e+00 9.61e-01 4.54e+00 angle pdb=" C3' G X 2 " pdb=" O3' G X 2 " pdb=" P A X 3 " ideal model delta sigma weight residual 120.20 123.36 -3.16 1.50e+00 4.44e-01 4.44e+00 ... (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: 2200 0.034 - 0.067: 483 0.067 - 0.101: 182 0.101 - 0.134: 64 0.134 - 0.168: 2 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=" CA ILE B 722 " pdb=" N ILE B 722 " pdb=" C ILE B 722 " pdb=" CB ILE B 722 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-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: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.190 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 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= 0.118 Angle : 0.496 6.699 25368 Z= 0.278 Chirality : 0.036 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 covalent geometry : bond 0.00238 (18477) covalent geometry : angle 0.49318 (25350) hydrogen bonds : bond 0.25061 ( 941) hydrogen bonds : angle 7.39331 ( 2656) metal coordination : bond 0.00268 ( 12) metal coordination : angle 2.19159 ( 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 : 0.700 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: 0.6494 (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: 0.6218 (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: 0.5564 (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: 0.7810 (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: 0.5611 (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: 0.1811 time to fit residues: 100.8977 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 : 0.639 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 58 HIS 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 533 GLN B 562 GLN B 576 GLN B 580 GLN B 584 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127262 restraints weight = 20698.287| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.45 r_work: 0.3051 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2335 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= 0.174 Angle : 0.561 6.555 25368 Z= 0.289 Chirality : 0.043 0.217 2931 Planarity : 0.004 0.049 2896 Dihedral : 14.654 163.061 3559 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.59 % Allowed : 7.83 % Favored : 90.58 % 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: 2.33 (0.16), residues: 987 sheet: -0.32 (0.29), residues: 318 loop : -0.43 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 495 TYR 0.016 0.001 TYR C 630 PHE 0.017 0.001 PHE C 849 TRP 0.014 0.001 TRP A 386 HIS 0.007 0.001 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00392 (18477) covalent geometry : angle 0.55806 (25350) hydrogen bonds : bond 0.05145 ( 941) hydrogen bonds : angle 4.21332 ( 2656) metal coordination : bond 0.00246 ( 12) metal coordination : angle 2.32172 ( 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 288 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7189 (mtp-110) REVERT: A 123 THR cc_start: 0.8583 (m) cc_final: 0.8256 (p) REVERT: A 124 VAL cc_start: 0.8533 (p) cc_final: 0.8275 (m) REVERT: A 132 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7929 (mt-10) REVERT: A 169 SER cc_start: 0.9327 (t) cc_final: 0.8909 (p) REVERT: A 222 HIS cc_start: 0.7270 (m-70) cc_final: 0.7023 (m90) REVERT: A 357 ILE cc_start: 0.8127 (mt) cc_final: 0.7854 (mt) REVERT: A 449 HIS cc_start: 0.7971 (m-70) cc_final: 0.7667 (m90) REVERT: A 473 ARG cc_start: 0.6815 (ttt-90) cc_final: 0.6288 (tpt170) REVERT: A 555 LEU cc_start: 0.8218 (pp) cc_final: 0.7743 (mp) REVERT: A 568 ASP cc_start: 0.7415 (m-30) cc_final: 0.6900 (m-30) REVERT: A 581 ASN cc_start: 0.6925 (m-40) cc_final: 0.6047 (m-40) REVERT: B 522 LYS cc_start: 0.7882 (tttt) cc_final: 0.7526 (mttt) REVERT: B 743 LYS cc_start: 0.8447 (mttt) cc_final: 0.8130 (pttp) REVERT: B 797 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7440 (p0) REVERT: B 865 LYS cc_start: 0.8068 (mtmt) cc_final: 0.7692 (mmtp) REVERT: B 992 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7749 (ttpt) REVERT: C 463 MET cc_start: 0.8412 (ttt) cc_final: 0.8194 (mtp) REVERT: C 470 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7336 (ttp80) REVERT: C 501 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7684 (mtpt) REVERT: C 670 ASP cc_start: 0.7790 (t0) cc_final: 0.7401 (m-30) REVERT: C 685 LYS cc_start: 0.7775 (mttt) cc_final: 0.7544 (pttt) REVERT: C 720 ARG cc_start: 0.8194 (mmt90) cc_final: 0.7750 (mmm160) REVERT: C 726 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8487 (tptt) REVERT: C 764 LYS cc_start: 0.8233 (pttt) cc_final: 0.7730 (pptt) REVERT: C 777 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7816 (mtmt) REVERT: C 835 HIS cc_start: 0.7553 (m-70) cc_final: 0.7283 (t70) REVERT: C 882 MET cc_start: 0.7513 (tpt) cc_final: 0.7166 (tpp) REVERT: C 883 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: C 886 MET cc_start: 0.8149 (mmm) cc_final: 0.7832 (mmm) REVERT: C 902 LEU cc_start: 0.7944 (mt) cc_final: 0.7609 (tp) REVERT: C 926 MET cc_start: 0.7335 (mtt) cc_final: 0.7112 (mtm) outliers start: 28 outliers final: 10 residues processed: 276 average time/residue: 0.1598 time to fit residues: 63.8049 Evaluate side-chains 215 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU 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 497 THR 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 760 SER Chi-restraints excluded: chain C residue 883 GLU Chi-restraints excluded: chain C residue 990 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 314 HIS A 344 HIS A 411 GLN A 551 HIS ** C 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 GLN C 863 ASN C 957 ASN C 986 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115018 restraints weight = 20781.932| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.25 r_work: 0.2967 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18489 Z= 0.251 Angle : 0.618 6.993 25368 Z= 0.315 Chirality : 0.045 0.227 2931 Planarity : 0.004 0.047 2896 Dihedral : 14.703 161.659 3559 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.27 % Allowed : 9.08 % Favored : 88.65 % 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: 1.20 (0.19), residues: 1968 helix: 2.23 (0.16), residues: 989 sheet: -0.74 (0.29), residues: 315 loop : -0.57 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 843 TYR 0.018 0.002 TYR C 630 PHE 0.017 0.002 PHE C 849 TRP 0.014 0.001 TRP A 386 HIS 0.007 0.002 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00587 (18477) covalent geometry : angle 0.61333 (25350) hydrogen bonds : bond 0.05437 ( 941) hydrogen bonds : angle 4.03512 ( 2656) metal coordination : bond 0.00351 ( 12) metal coordination : angle 3.00484 ( 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 240 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7482 (mtm110) cc_final: 0.6989 (mtp-110) REVERT: A 100 LEU cc_start: 0.8977 (tt) cc_final: 0.8708 (tp) REVERT: A 118 GLU cc_start: 0.7406 (tp30) cc_final: 0.7199 (tp30) REVERT: A 123 THR cc_start: 0.8888 (m) cc_final: 0.8526 (p) REVERT: A 132 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7904 (mt-10) REVERT: A 169 SER cc_start: 0.9337 (t) cc_final: 0.8771 (p) REVERT: A 222 HIS cc_start: 0.7664 (m-70) cc_final: 0.7336 (m90) REVERT: A 332 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: A 449 HIS cc_start: 0.8002 (m-70) cc_final: 0.7665 (m90) REVERT: A 473 ARG cc_start: 0.6887 (ttt-90) cc_final: 0.6158 (tpt170) REVERT: A 551 HIS cc_start: 0.7194 (m90) cc_final: 0.6474 (m90) REVERT: A 568 ASP cc_start: 0.7711 (m-30) cc_final: 0.7281 (m-30) REVERT: A 581 ASN cc_start: 0.7168 (m-40) cc_final: 0.6778 (m-40) REVERT: B 355 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: B 402 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7260 (tp30) REVERT: B 498 LYS cc_start: 0.7992 (mttm) cc_final: 0.7511 (mtpt) REVERT: B 522 LYS cc_start: 0.7822 (tttt) cc_final: 0.7197 (mttt) REVERT: B 743 LYS cc_start: 0.8417 (mttt) cc_final: 0.7740 (pttp) REVERT: B 797 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7327 (p0) REVERT: B 865 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7526 (mmtp) REVERT: B 992 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7918 (mttm) REVERT: C 470 ARG cc_start: 0.6937 (ttp-170) cc_final: 0.6545 (ttp80) REVERT: C 501 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7461 (mtpt) REVERT: C 635 ASP cc_start: 0.7637 (m-30) cc_final: 0.7206 (m-30) REVERT: C 670 ASP cc_start: 0.7646 (t0) cc_final: 0.7302 (t0) REVERT: C 685 LYS cc_start: 0.7356 (mttt) cc_final: 0.7096 (pttt) REVERT: C 709 MET cc_start: 0.8381 (mmm) cc_final: 0.8157 (mmm) REVERT: C 720 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7370 (mmm160) REVERT: C 726 LYS cc_start: 0.8937 (ttpt) cc_final: 0.8222 (tptt) REVERT: C 764 LYS cc_start: 0.8174 (pttt) cc_final: 0.7434 (pptt) REVERT: C 777 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7438 (mtmt) REVERT: C 835 HIS cc_start: 0.7349 (m-70) cc_final: 0.6894 (t70) REVERT: C 882 MET cc_start: 0.7459 (tpt) cc_final: 0.7068 (tpp) REVERT: C 886 MET cc_start: 0.8003 (mmm) cc_final: 0.7654 (mmm) REVERT: C 902 LEU cc_start: 0.7821 (mt) cc_final: 0.7495 (tp) REVERT: C 926 MET cc_start: 0.7278 (mtt) cc_final: 0.6771 (mtm) REVERT: C 931 MET cc_start: 0.8312 (ptp) cc_final: 0.8006 (ptp) REVERT: C 971 MET cc_start: 0.7704 (mmm) cc_final: 0.6973 (mmm) outliers start: 40 outliers final: 21 residues processed: 229 average time/residue: 0.1650 time to fit residues: 55.2422 Evaluate side-chains 207 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 617 ILE 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 B residue 996 THR Chi-restraints excluded: chain C residue 349 LYS 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 829 THR 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: 7.9990 chunk 55 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 314 HIS A 344 HIS C 307 GLN C 562 GLN C 753 HIS C 957 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119816 restraints weight = 20594.649| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.22 r_work: 0.3047 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18489 Z= 0.117 Angle : 0.498 6.366 25368 Z= 0.250 Chirality : 0.039 0.212 2931 Planarity : 0.003 0.044 2896 Dihedral : 14.657 162.545 3559 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.76 % Allowed : 9.76 % Favored : 88.48 % 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: 1.49 (0.19), residues: 1968 helix: 2.53 (0.16), residues: 991 sheet: -0.54 (0.29), residues: 294 loop : -0.61 (0.23), residues: 683 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 0.012 0.001 PHE C 680 TRP 0.012 0.001 TRP A 386 HIS 0.005 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00252 (18477) covalent geometry : angle 0.49491 (25350) hydrogen bonds : bond 0.03920 ( 941) hydrogen bonds : angle 3.66347 ( 2656) metal coordination : bond 0.00234 ( 12) metal coordination : angle 2.25986 ( 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 216 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7396 (mtp-110) REVERT: A 100 LEU cc_start: 0.8937 (tt) cc_final: 0.8644 (tp) REVERT: A 118 GLU cc_start: 0.7362 (tp30) cc_final: 0.7111 (tp30) REVERT: A 123 THR cc_start: 0.8904 (m) cc_final: 0.8600 (p) REVERT: A 132 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7845 (mt-10) REVERT: A 169 SER cc_start: 0.9227 (t) cc_final: 0.8569 (p) REVERT: A 222 HIS cc_start: 0.7623 (m-70) cc_final: 0.7308 (m90) REVERT: A 449 HIS cc_start: 0.7980 (m-70) cc_final: 0.7705 (m90) REVERT: A 551 HIS cc_start: 0.7126 (m90) cc_final: 0.6534 (m-70) REVERT: A 555 LEU cc_start: 0.7608 (pp) cc_final: 0.7312 (mp) REVERT: A 568 ASP cc_start: 0.7496 (m-30) cc_final: 0.7037 (m-30) REVERT: A 581 ASN cc_start: 0.7064 (m-40) cc_final: 0.6602 (m110) REVERT: B 402 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7120 (tp30) REVERT: B 522 LYS cc_start: 0.7779 (tttt) cc_final: 0.7170 (mttt) REVERT: B 570 MET cc_start: 0.8647 (mmp) cc_final: 0.8178 (mmp) REVERT: B 743 LYS cc_start: 0.8396 (mttt) cc_final: 0.7718 (ptmt) REVERT: B 797 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7284 (p0) REVERT: B 865 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7269 (mmtp) REVERT: B 992 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7939 (mttm) REVERT: C 501 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7346 (mtpt) REVERT: C 552 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7290 (mp0) REVERT: C 635 ASP cc_start: 0.7597 (m-30) cc_final: 0.7171 (m-30) REVERT: C 670 ASP cc_start: 0.7712 (t0) cc_final: 0.7335 (t0) REVERT: C 685 LYS cc_start: 0.7511 (mttt) cc_final: 0.7205 (pttt) REVERT: C 709 MET cc_start: 0.8471 (mmm) cc_final: 0.8151 (mmm) REVERT: C 720 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7243 (mmm160) REVERT: C 726 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8182 (tptt) REVERT: C 777 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7327 (mtmt) REVERT: C 835 HIS cc_start: 0.7233 (m-70) cc_final: 0.6688 (t70) REVERT: C 882 MET cc_start: 0.7411 (tpt) cc_final: 0.7020 (tpp) REVERT: C 886 MET cc_start: 0.7986 (mmm) cc_final: 0.7747 (mmm) REVERT: C 902 LEU cc_start: 0.7771 (mt) cc_final: 0.7490 (tt) REVERT: C 925 LYS cc_start: 0.7647 (mttt) cc_final: 0.7373 (mttm) REVERT: C 926 MET cc_start: 0.6989 (mtt) cc_final: 0.6607 (mtm) REVERT: C 931 MET cc_start: 0.8276 (ptp) cc_final: 0.7965 (ptp) outliers start: 31 outliers final: 15 residues processed: 209 average time/residue: 0.1527 time to fit residues: 48.0159 Evaluate side-chains 187 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 484 THR 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 797 ASP Chi-restraints excluded: chain B residue 828 SER 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 B residue 996 THR Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 854 MET 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: 9.9990 chunk 166 optimal weight: 0.9990 chunk 185 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 314 HIS C 307 GLN C 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119227 restraints weight = 20558.750| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.20 r_work: 0.3046 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18489 Z= 0.131 Angle : 0.497 6.370 25368 Z= 0.249 Chirality : 0.040 0.213 2931 Planarity : 0.003 0.043 2896 Dihedral : 14.596 161.611 3559 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.93 % Allowed : 9.82 % Favored : 88.25 % 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: 1.55 (0.19), residues: 1968 helix: 2.60 (0.16), residues: 992 sheet: -0.62 (0.29), residues: 306 loop : -0.58 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 495 TYR 0.014 0.001 TYR A 588 PHE 0.012 0.001 PHE C 680 TRP 0.012 0.001 TRP A 195 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00294 (18477) covalent geometry : angle 0.49324 (25350) hydrogen bonds : bond 0.03946 ( 941) hydrogen bonds : angle 3.57881 ( 2656) metal coordination : bond 0.00244 ( 12) metal coordination : angle 2.25674 ( 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 215 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7638 (mtm110) cc_final: 0.7360 (mtp-110) REVERT: A 100 LEU cc_start: 0.8966 (tt) cc_final: 0.8670 (tp) REVERT: A 118 GLU cc_start: 0.7472 (tp30) cc_final: 0.7142 (tp30) REVERT: A 123 THR cc_start: 0.8866 (m) cc_final: 0.8552 (p) REVERT: A 132 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7871 (mt-10) REVERT: A 169 SER cc_start: 0.9225 (t) cc_final: 0.8572 (p) REVERT: A 222 HIS cc_start: 0.7619 (m-70) cc_final: 0.7312 (m90) REVERT: A 449 HIS cc_start: 0.7911 (m-70) cc_final: 0.7663 (m90) REVERT: A 551 HIS cc_start: 0.6972 (m90) cc_final: 0.6397 (m90) REVERT: A 555 LEU cc_start: 0.7665 (pp) cc_final: 0.7368 (mp) REVERT: A 568 ASP cc_start: 0.7551 (m-30) cc_final: 0.7100 (m-30) REVERT: A 581 ASN cc_start: 0.7048 (m-40) cc_final: 0.6528 (m110) REVERT: B 355 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7433 (pt0) REVERT: B 522 LYS cc_start: 0.7780 (tttt) cc_final: 0.7188 (mttt) REVERT: B 570 MET cc_start: 0.8657 (mmp) cc_final: 0.8185 (mmp) REVERT: B 743 LYS cc_start: 0.8377 (mttt) cc_final: 0.7701 (pttp) REVERT: B 797 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7302 (p0) REVERT: B 865 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7285 (mmtp) REVERT: B 992 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7961 (mttm) REVERT: C 501 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7383 (mtpt) REVERT: C 635 ASP cc_start: 0.7593 (m-30) cc_final: 0.7150 (m-30) REVERT: C 670 ASP cc_start: 0.7721 (t0) cc_final: 0.7332 (t0) REVERT: C 685 LYS cc_start: 0.7504 (mttt) cc_final: 0.7218 (pttt) REVERT: C 720 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7248 (mmm160) REVERT: C 726 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8211 (tptt) REVERT: C 777 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7361 (mtmt) REVERT: C 835 HIS cc_start: 0.7316 (m-70) cc_final: 0.6754 (t70) REVERT: C 882 MET cc_start: 0.7487 (tpt) cc_final: 0.7082 (tpp) REVERT: C 886 MET cc_start: 0.8002 (mmm) cc_final: 0.7753 (mmm) REVERT: C 925 LYS cc_start: 0.7638 (mttt) cc_final: 0.7374 (mttm) REVERT: C 926 MET cc_start: 0.6966 (mtt) cc_final: 0.6571 (mtm) REVERT: C 931 MET cc_start: 0.8126 (ptp) cc_final: 0.7812 (ptp) outliers start: 34 outliers final: 23 residues processed: 203 average time/residue: 0.1547 time to fit residues: 47.2543 Evaluate side-chains 197 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 484 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 522 ILE 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 497 THR Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 797 ASP Chi-restraints excluded: chain B residue 828 SER Chi-restraints excluded: chain B residue 881 ILE 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 349 LYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 854 MET 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: 30.0000 chunk 131 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS C 307 GLN C 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116941 restraints weight = 20490.814| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.17 r_work: 0.3013 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3361 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= 0.176 Angle : 0.533 6.612 25368 Z= 0.268 Chirality : 0.041 0.219 2931 Planarity : 0.004 0.044 2896 Dihedral : 14.554 161.140 3559 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.99 % Allowed : 10.50 % Favored : 87.51 % 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: 2.55 (0.16), residues: 992 sheet: -0.76 (0.29), residues: 298 loop : -0.60 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 418 TYR 0.015 0.001 TYR A 588 PHE 0.012 0.001 PHE C 680 TRP 0.010 0.001 TRP A 386 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00407 (18477) covalent geometry : angle 0.52846 (25350) hydrogen bonds : bond 0.04333 ( 941) hydrogen bonds : angle 3.63563 ( 2656) metal coordination : bond 0.00269 ( 12) metal coordination : angle 2.57079 ( 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 210 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8962 (tt) cc_final: 0.8539 (tp) REVERT: A 123 THR cc_start: 0.8909 (m) cc_final: 0.8594 (p) REVERT: A 132 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7904 (mt-10) REVERT: A 169 SER cc_start: 0.9200 (t) cc_final: 0.8564 (p) REVERT: A 222 HIS cc_start: 0.7655 (m-70) cc_final: 0.7348 (m90) REVERT: A 449 HIS cc_start: 0.7899 (m-70) cc_final: 0.7649 (m90) REVERT: A 568 ASP cc_start: 0.7655 (m-30) cc_final: 0.7159 (m-30) REVERT: A 581 ASN cc_start: 0.7045 (m-40) cc_final: 0.6505 (m110) REVERT: A 638 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7836 (mtp) REVERT: B 355 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7488 (pt0) REVERT: B 498 LYS cc_start: 0.7873 (mttm) cc_final: 0.7354 (mtpt) REVERT: B 522 LYS cc_start: 0.7855 (tttt) cc_final: 0.7227 (mttt) REVERT: B 570 MET cc_start: 0.8539 (mmp) cc_final: 0.7997 (mmp) REVERT: B 743 LYS cc_start: 0.8384 (mttt) cc_final: 0.7705 (pttp) REVERT: B 797 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7385 (p0) REVERT: B 865 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7305 (mmtp) REVERT: B 992 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7955 (mttm) REVERT: C 501 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7418 (mtpt) REVERT: C 570 MET cc_start: 0.8488 (tpp) cc_final: 0.8233 (mmp) REVERT: C 635 ASP cc_start: 0.7667 (m-30) cc_final: 0.7279 (m-30) REVERT: C 670 ASP cc_start: 0.7591 (t0) cc_final: 0.7177 (t0) REVERT: C 685 LYS cc_start: 0.7520 (mttt) cc_final: 0.7217 (pttt) REVERT: C 720 ARG cc_start: 0.7876 (mmt90) cc_final: 0.7285 (mmm160) REVERT: C 726 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8204 (tptt) REVERT: C 777 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7347 (mtmt) REVERT: C 835 HIS cc_start: 0.7374 (m-70) cc_final: 0.6870 (t70) REVERT: C 882 MET cc_start: 0.7478 (tpt) cc_final: 0.7037 (tpp) REVERT: C 885 LYS cc_start: 0.7641 (tttt) cc_final: 0.7085 (mttt) REVERT: C 886 MET cc_start: 0.8041 (mmm) cc_final: 0.7759 (mmm) REVERT: C 925 LYS cc_start: 0.7668 (mttt) cc_final: 0.7412 (mttm) REVERT: C 926 MET cc_start: 0.6939 (mtt) cc_final: 0.6602 (mtm) REVERT: C 931 MET cc_start: 0.8270 (ptp) cc_final: 0.7907 (ptp) outliers start: 35 outliers final: 24 residues processed: 198 average time/residue: 0.1575 time to fit residues: 46.5624 Evaluate side-chains 201 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 638 MET 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 497 THR Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 742 GLU 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 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 829 THR 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: 9.9990 chunk 145 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 693 ASN C 307 GLN C 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117869 restraints weight = 20647.079| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.33 r_work: 0.3001 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18489 Z= 0.165 Angle : 0.527 10.582 25368 Z= 0.264 Chirality : 0.041 0.218 2931 Planarity : 0.003 0.044 2896 Dihedral : 14.529 161.208 3559 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.99 % Allowed : 10.44 % Favored : 87.57 % 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: 1.45 (0.19), residues: 1968 helix: 2.57 (0.16), residues: 992 sheet: -0.82 (0.30), residues: 288 loop : -0.64 (0.23), residues: 688 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 0.012 0.001 PHE C 680 TRP 0.010 0.001 TRP A 604 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00379 (18477) covalent geometry : angle 0.52300 (25350) hydrogen bonds : bond 0.04220 ( 941) hydrogen bonds : angle 3.59348 ( 2656) metal coordination : bond 0.00273 ( 12) metal coordination : angle 2.52159 ( 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 216 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8955 (tt) cc_final: 0.8519 (tp) REVERT: A 123 THR cc_start: 0.8952 (m) cc_final: 0.8648 (p) REVERT: A 132 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7928 (mt-10) REVERT: A 169 SER cc_start: 0.9193 (t) cc_final: 0.8550 (p) REVERT: A 222 HIS cc_start: 0.7672 (m-70) cc_final: 0.7348 (m90) REVERT: A 449 HIS cc_start: 0.7922 (m-70) cc_final: 0.7666 (m90) REVERT: A 568 ASP cc_start: 0.7682 (m-30) cc_final: 0.7177 (m-30) REVERT: A 581 ASN cc_start: 0.7248 (m-40) cc_final: 0.6641 (m110) REVERT: A 638 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: B 355 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: B 498 LYS cc_start: 0.7881 (mttm) cc_final: 0.7353 (mtpt) REVERT: B 522 LYS cc_start: 0.7844 (tttt) cc_final: 0.7230 (mttt) REVERT: B 552 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7097 (mt-10) REVERT: B 570 MET cc_start: 0.8616 (mmp) cc_final: 0.8085 (mmp) REVERT: B 743 LYS cc_start: 0.8371 (mttt) cc_final: 0.7695 (pttp) REVERT: B 797 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7330 (p0) REVERT: B 865 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7307 (mmtp) REVERT: B 992 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7977 (mttm) REVERT: C 501 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7439 (mtpt) REVERT: C 570 MET cc_start: 0.8509 (tpp) cc_final: 0.8245 (mmp) REVERT: C 635 ASP cc_start: 0.7622 (m-30) cc_final: 0.7233 (m-30) REVERT: C 670 ASP cc_start: 0.7585 (t0) cc_final: 0.7151 (t0) REVERT: C 685 LYS cc_start: 0.7534 (mttt) cc_final: 0.7211 (pttt) REVERT: C 709 MET cc_start: 0.8303 (mmm) cc_final: 0.8005 (mmm) REVERT: C 720 ARG cc_start: 0.7861 (mmt90) cc_final: 0.7345 (mmm160) REVERT: C 726 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8142 (tptt) REVERT: C 835 HIS cc_start: 0.7439 (m-70) cc_final: 0.6908 (t70) REVERT: C 882 MET cc_start: 0.7442 (tpt) cc_final: 0.7091 (tpp) REVERT: C 885 LYS cc_start: 0.7716 (tttt) cc_final: 0.7124 (mttt) REVERT: C 886 MET cc_start: 0.8052 (mmm) cc_final: 0.7759 (mmm) REVERT: C 925 LYS cc_start: 0.7678 (mttt) cc_final: 0.7433 (mttm) REVERT: C 926 MET cc_start: 0.6954 (mtt) cc_final: 0.6625 (mtm) REVERT: C 931 MET cc_start: 0.8429 (ptp) cc_final: 0.8027 (ptp) outliers start: 35 outliers final: 24 residues processed: 204 average time/residue: 0.1568 time to fit residues: 47.8404 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 : 0.684 ------------------------------------------------------------------------------- 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 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 638 MET 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 478 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 742 GLU 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 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 829 THR 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: 4.9990 chunk 185 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 60 optimal weight: 0.0570 chunk 28 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 311 HIS C 307 GLN C 957 ASN C 986 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.157514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120154 restraints weight = 20502.178| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.25 r_work: 0.3050 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18489 Z= 0.112 Angle : 0.489 8.949 25368 Z= 0.243 Chirality : 0.039 0.211 2931 Planarity : 0.003 0.043 2896 Dihedral : 14.515 161.135 3559 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.65 % Allowed : 10.67 % Favored : 87.68 % 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: 1.62 (0.19), residues: 1968 helix: 2.73 (0.16), residues: 992 sheet: -0.73 (0.29), residues: 296 loop : -0.60 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 714 TYR 0.014 0.001 TYR C 623 PHE 0.013 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 covalent geometry : bond 0.00247 (18477) covalent geometry : angle 0.48537 (25350) hydrogen bonds : bond 0.03665 ( 941) hydrogen bonds : angle 3.44803 ( 2656) metal coordination : bond 0.00246 ( 12) metal coordination : angle 2.16988 ( 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 207 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8953 (tt) cc_final: 0.8518 (tp) REVERT: A 132 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7889 (mt-10) REVERT: A 169 SER cc_start: 0.9186 (t) cc_final: 0.8525 (p) REVERT: A 222 HIS cc_start: 0.7623 (m-70) cc_final: 0.7321 (m90) REVERT: A 449 HIS cc_start: 0.7886 (m-70) cc_final: 0.7637 (m90) REVERT: A 568 ASP cc_start: 0.7603 (m-30) cc_final: 0.7032 (m-30) REVERT: A 581 ASN cc_start: 0.7193 (m-40) cc_final: 0.6639 (m110) REVERT: A 638 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7795 (mtp) REVERT: B 522 LYS cc_start: 0.7870 (tttt) cc_final: 0.7243 (mttt) REVERT: B 570 MET cc_start: 0.8605 (mmp) cc_final: 0.8180 (mmp) REVERT: B 743 LYS cc_start: 0.8360 (mttt) cc_final: 0.7704 (pttp) REVERT: B 797 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7326 (p0) REVERT: B 992 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8012 (mttm) REVERT: C 501 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7360 (mtpt) REVERT: C 570 MET cc_start: 0.8506 (tpp) cc_final: 0.8217 (mmp) REVERT: C 635 ASP cc_start: 0.7650 (m-30) cc_final: 0.7267 (m-30) REVERT: C 670 ASP cc_start: 0.7511 (t0) cc_final: 0.7132 (t0) REVERT: C 685 LYS cc_start: 0.7581 (mttt) cc_final: 0.7262 (pttt) REVERT: C 720 ARG cc_start: 0.7811 (mmt90) cc_final: 0.7285 (mmm160) REVERT: C 726 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8155 (tptt) REVERT: C 835 HIS cc_start: 0.7377 (m-70) cc_final: 0.6789 (t70) REVERT: C 882 MET cc_start: 0.7394 (tpt) cc_final: 0.7046 (tpp) REVERT: C 885 LYS cc_start: 0.7553 (tttt) cc_final: 0.6943 (mttt) REVERT: C 886 MET cc_start: 0.7945 (mmm) cc_final: 0.7682 (mmm) REVERT: C 925 LYS cc_start: 0.7662 (mttt) cc_final: 0.7412 (mttm) REVERT: C 926 MET cc_start: 0.6749 (mtt) cc_final: 0.6462 (mtm) REVERT: C 931 MET cc_start: 0.8409 (ptp) cc_final: 0.8006 (ptp) outliers start: 29 outliers final: 19 residues processed: 199 average time/residue: 0.1474 time to fit residues: 44.0275 Evaluate side-chains 193 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 484 THR Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 638 MET 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 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 501 LYS Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 854 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 138 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 314 HIS C 307 GLN C 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117885 restraints weight = 20527.325| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.26 r_work: 0.3017 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18489 Z= 0.155 Angle : 0.520 9.792 25368 Z= 0.260 Chirality : 0.040 0.216 2931 Planarity : 0.003 0.043 2896 Dihedral : 14.493 161.238 3559 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.36 % Allowed : 10.84 % Favored : 87.80 % 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: 1.55 (0.19), residues: 1968 helix: 2.66 (0.16), residues: 992 sheet: -0.82 (0.30), residues: 288 loop : -0.58 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 714 TYR 0.014 0.001 TYR A 588 PHE 0.012 0.001 PHE C 680 TRP 0.012 0.001 TRP A 386 HIS 0.006 0.001 HIS C 625 Details of bonding type rmsd covalent geometry : bond 0.00356 (18477) covalent geometry : angle 0.51570 (25350) hydrogen bonds : bond 0.04065 ( 941) hydrogen bonds : angle 3.53425 ( 2656) metal coordination : bond 0.00270 ( 12) metal coordination : angle 2.41260 ( 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 197 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 100 LEU cc_start: 0.8968 (tt) cc_final: 0.8529 (tp) REVERT: A 132 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7917 (mt-10) REVERT: A 169 SER cc_start: 0.9168 (t) cc_final: 0.8474 (p) REVERT: A 222 HIS cc_start: 0.7623 (m-70) cc_final: 0.7314 (m90) REVERT: A 418 ARG cc_start: 0.7922 (mmt-90) cc_final: 0.7510 (mmt90) REVERT: A 449 HIS cc_start: 0.7920 (m-70) cc_final: 0.7655 (m90) REVERT: A 568 ASP cc_start: 0.7771 (m-30) cc_final: 0.7278 (m-30) REVERT: A 581 ASN cc_start: 0.7257 (m-40) cc_final: 0.6656 (m110) REVERT: A 638 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7861 (mtp) REVERT: B 498 LYS cc_start: 0.7818 (mttm) cc_final: 0.7241 (mtpt) REVERT: B 522 LYS cc_start: 0.7886 (tttt) cc_final: 0.7225 (mttt) REVERT: B 552 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7157 (mt-10) REVERT: B 570 MET cc_start: 0.8574 (mmp) cc_final: 0.8000 (mmp) REVERT: B 743 LYS cc_start: 0.8407 (mttt) cc_final: 0.7713 (pttp) REVERT: B 797 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7324 (p0) REVERT: B 865 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7307 (mmtp) REVERT: B 992 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8029 (mttm) REVERT: C 501 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7419 (mtpt) REVERT: C 570 MET cc_start: 0.8320 (tpp) cc_final: 0.8079 (mmp) REVERT: C 635 ASP cc_start: 0.7597 (m-30) cc_final: 0.7212 (m-30) REVERT: C 670 ASP cc_start: 0.7553 (t0) cc_final: 0.7107 (t0) REVERT: C 685 LYS cc_start: 0.7607 (mttt) cc_final: 0.7269 (pttt) REVERT: C 720 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7296 (mmm160) REVERT: C 726 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8163 (tptt) REVERT: C 777 LYS cc_start: 0.7657 (mtmt) cc_final: 0.7334 (mtmt) REVERT: C 835 HIS cc_start: 0.7446 (m-70) cc_final: 0.6918 (t70) REVERT: C 882 MET cc_start: 0.7408 (tpt) cc_final: 0.7070 (tpp) REVERT: C 885 LYS cc_start: 0.7556 (tttt) cc_final: 0.6986 (mttt) REVERT: C 886 MET cc_start: 0.7974 (mmm) cc_final: 0.7700 (mmm) REVERT: C 925 LYS cc_start: 0.7677 (mttt) cc_final: 0.7425 (mttm) REVERT: C 926 MET cc_start: 0.6811 (mtt) cc_final: 0.6495 (mtm) REVERT: C 931 MET cc_start: 0.8524 (ptp) cc_final: 0.8128 (ptp) outliers start: 24 outliers final: 19 residues processed: 190 average time/residue: 0.1597 time to fit residues: 45.0858 Evaluate side-chains 196 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 638 MET 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 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 742 GLU 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 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 854 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.4980 chunk 130 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS C 307 GLN C 957 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114504 restraints weight = 20552.245| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.27 r_work: 0.2962 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18489 Z= 0.267 Angle : 0.620 11.993 25368 Z= 0.312 Chirality : 0.045 0.229 2931 Planarity : 0.004 0.044 2896 Dihedral : 14.580 160.970 3559 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 11.12 % Favored : 87.46 % 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: 2.38 (0.16), residues: 990 sheet: -1.03 (0.29), residues: 300 loop : -0.67 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 714 TYR 0.019 0.002 TYR B 311 PHE 0.014 0.002 PHE B 681 TRP 0.013 0.001 TRP A 604 HIS 0.007 0.002 HIS B 446 Details of bonding type rmsd covalent geometry : bond 0.00628 (18477) covalent geometry : angle 0.61479 (25350) hydrogen bonds : bond 0.05099 ( 941) hydrogen bonds : angle 3.79424 ( 2656) metal coordination : bond 0.00387 ( 12) metal coordination : angle 3.08364 ( 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 196 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.495 Fit side-chains REVERT: A 12 MET cc_start: 0.7377 (mmm) cc_final: 0.6981 (mmm) REVERT: A 132 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8014 (mt-10) REVERT: A 169 SER cc_start: 0.9306 (t) cc_final: 0.8700 (p) REVERT: A 222 HIS cc_start: 0.7688 (m-70) cc_final: 0.7334 (m90) REVERT: A 449 HIS cc_start: 0.7908 (m-70) cc_final: 0.7583 (m90) REVERT: A 604 TRP cc_start: 0.5372 (OUTLIER) cc_final: 0.4817 (t-100) REVERT: A 638 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8314 (mmm) REVERT: B 498 LYS cc_start: 0.7924 (mttm) cc_final: 0.7398 (mtpt) REVERT: B 522 LYS cc_start: 0.7969 (tttt) cc_final: 0.7339 (mttt) REVERT: B 743 LYS cc_start: 0.8313 (mttt) cc_final: 0.7661 (pttp) REVERT: B 797 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7342 (p0) REVERT: B 865 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7179 (mmtp) REVERT: B 992 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7980 (mttm) REVERT: C 501 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7485 (mtpt) REVERT: C 570 MET cc_start: 0.8361 (tpp) cc_final: 0.8118 (mmp) REVERT: C 635 ASP cc_start: 0.7657 (m-30) cc_final: 0.7275 (m-30) REVERT: C 685 LYS cc_start: 0.7592 (mttt) cc_final: 0.7258 (pttt) REVERT: C 777 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7468 (mtmt) REVERT: C 885 LYS cc_start: 0.7719 (tttt) cc_final: 0.7144 (mttt) REVERT: C 886 MET cc_start: 0.8078 (mmm) cc_final: 0.7772 (mmm) REVERT: C 925 LYS cc_start: 0.7648 (mttt) cc_final: 0.7410 (mttm) REVERT: C 926 MET cc_start: 0.7298 (mtt) cc_final: 0.6884 (mtm) outliers start: 25 outliers final: 20 residues processed: 189 average time/residue: 0.1477 time to fit residues: 42.0499 Evaluate side-chains 185 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 484 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 604 TRP Chi-restraints excluded: chain A residue 638 MET 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 518 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 686 MET Chi-restraints excluded: chain B residue 742 GLU 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 934 GLU Chi-restraints excluded: chain B residue 992 LYS Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 760 SER Chi-restraints excluded: chain C residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 195 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 314 HIS C 307 GLN C 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117665 restraints weight = 20501.108| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.09 r_work: 0.3025 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18489 Z= 0.141 Angle : 0.520 9.259 25368 Z= 0.260 Chirality : 0.040 0.214 2931 Planarity : 0.004 0.044 2896 Dihedral : 14.527 161.864 3559 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.31 % Allowed : 11.35 % Favored : 87.34 % 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: 1.41 (0.19), residues: 1968 helix: 2.58 (0.16), residues: 991 sheet: -0.94 (0.29), residues: 288 loop : -0.67 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 714 TYR 0.014 0.001 TYR A 588 PHE 0.013 0.001 PHE C 680 TRP 0.012 0.001 TRP A 195 HIS 0.006 0.001 HIS B 835 Details of bonding type rmsd covalent geometry : bond 0.00320 (18477) covalent geometry : angle 0.51640 (25350) hydrogen bonds : bond 0.04033 ( 941) hydrogen bonds : angle 3.57032 ( 2656) metal coordination : bond 0.00270 ( 12) metal coordination : angle 2.50053 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.82 seconds wall clock time: 67 minutes 29.44 seconds (4049.44 seconds total)