Starting phenix.real_space_refine on Mon Jun 16 18:25:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y9x_33695/06_2025/7y9x_33695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9x_33695/06_2025/7y9x_33695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y9x_33695/06_2025/7y9x_33695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9x_33695/06_2025/7y9x_33695.map" model { file = "/net/cci-nas-00/data/ceres_data/7y9x_33695/06_2025/7y9x_33695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9x_33695/06_2025/7y9x_33695.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 37 5.49 5 S 82 5.16 5 C 11675 2.51 5 N 3279 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18662 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 6100 Classifications: {'peptide': 734} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 705} Chain breaks: 3 Chain: "A" Number of atoms: 11757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11757 Classifications: {'peptide': 1458} Link IDs: {'PTRANS': 80, 'TRANS': 1377} Chain breaks: 7 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9480 SG CYS A 463 53.234 47.188 50.151 1.00 30.75 S ATOM 9542 SG CYS A 472 52.720 46.575 46.490 1.00 20.27 S ATOM 9556 SG CYS A 474 55.530 44.820 48.140 1.00 18.75 S ATOM 9578 SG CYS A 477 51.964 43.813 49.066 1.00 22.67 S ATOM 11396 SG CYS A 706 59.788 61.985 74.738 1.00 26.90 S ATOM 11411 SG CYS A 708 62.693 60.033 76.135 1.00 26.45 S ATOM 11433 SG CYS A 711 59.555 58.181 74.794 1.00 27.20 S ATOM 13321 SG CYS A 965 57.303 59.788 113.258 1.00 4.19 S ATOM 15508 SG CYS A1312 56.557 62.405 110.592 1.00 0.00 S ATOM 15747 SG CYS A1342 60.130 61.592 111.411 1.00 11.80 S ATOM 15765 SG CYS A1345 58.132 59.188 109.443 1.00 12.63 S ATOM 6804 SG CYS A 86 37.102 32.582 23.551 1.00 54.96 S ATOM 7050 SG CYS A 115 33.948 31.679 22.886 1.00 51.87 S ATOM 7112 SG CYS A 123 36.120 29.686 25.705 1.00 42.82 S ATOM 7136 SG CYS A 126 34.260 32.609 26.602 1.00 45.37 S Time building chain proxies: 11.69, per 1000 atoms: 0.63 Number of scatterers: 18662 At special positions: 0 Unit cell: (100.43, 102.92, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 82 16.00 P 37 15.00 O 3585 8.00 N 3279 7.00 C 11675 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: 4.08 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 472 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 477 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 706 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 965 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 115 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " Number of angles added : 21 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4118 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 26 sheets defined 41.1% alpha, 20.7% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 7.24 Creating SS restraints... Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.733A pdb=" N THR B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.862A pdb=" N MET B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 92 through 113 removed outlier: 4.827A pdb=" N ASN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.797A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.785A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.607A pdb=" N LEU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 360 through 374 Processing helix chain 'B' and resid 376 through 393 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.549A pdb=" N ARG B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 419 " --> pdb=" O PHE B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.828A pdb=" N GLU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.533A pdb=" N LEU B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 595 through 605 removed outlier: 3.638A pdb=" N GLU B 605 " --> pdb=" O GLU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 625 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 675 through 682 Processing helix chain 'B' and resid 696 through 711 Processing helix chain 'B' and resid 712 through 732 removed outlier: 3.741A pdb=" N GLN B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 731 " --> pdb=" O ASN B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.707A pdb=" N PHE B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.768A pdb=" N ARG A 26 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.235A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 301' Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 344 through 367 removed outlier: 3.534A pdb=" N LYS A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 removed outlier: 3.510A pdb=" N ARG A 598 " --> pdb=" O TRP A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.652A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.791A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.649A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.630A pdb=" N GLU A1032 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1302 through 1305 removed outlier: 3.581A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1302 through 1305' Processing helix chain 'A' and resid 1321 through 1326 removed outlier: 3.575A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.650A pdb=" N ARG A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A1336 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 3.879A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 removed outlier: 3.607A pdb=" N GLY A1492 " --> pdb=" O LYS A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1539 through 1548 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.966A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1594 removed outlier: 3.578A pdb=" N LYS A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AA2, first strand: chain 'B' and resid 457 through 462 removed outlier: 6.459A pdb=" N ILE B 424 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 518 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 426 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 Processing sheet with id=AA4, first strand: chain 'B' and resid 589 through 590 removed outlier: 7.018A pdb=" N SER B 569 " --> pdb=" O GLU B 589 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 610 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY B 691 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 615 through 617 removed outlier: 4.060A pdb=" N HIS B 615 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.548A pdb=" N LYS A 6 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.835A pdb=" N TRP A 42 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 107 removed outlier: 5.892A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.759A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.759A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB4, first strand: chain 'A' and resid 497 through 504 removed outlier: 11.047A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.273A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.273A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 655 through 656 removed outlier: 7.128A pdb=" N VAL A 655 " --> pdb=" O SER A 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB9, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 4.537A pdb=" N ARG A1558 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 861 " --> pdb=" O TRP A1600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AC2, first strand: chain 'A' and resid 938 through 939 removed outlier: 6.542A pdb=" N ILE A 943 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 5.420A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.329A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 936 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 974 through 978 removed outlier: 5.501A pdb=" N LEU A 975 " --> pdb=" O ASP A1297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1128 through 1130 removed outlier: 3.800A pdb=" N LYS A1128 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 19.138A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.120A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A1217 " --> pdb=" O HIS A1149 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL A1284 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A1229 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASP A1286 " --> pdb=" O GLU A1229 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1156 through 1159 Processing sheet with id=AC8, first strand: chain 'A' and resid 1187 through 1190 removed outlier: 7.410A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 9.10 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5784 1.33 - 1.46: 3700 1.46 - 1.58: 9482 1.58 - 1.70: 74 1.70 - 1.82: 122 Bond restraints: 19162 Sorted by residual: bond pdb=" CB THR A 653 " pdb=" CG2 THR A 653 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" N PRO A 495 " pdb=" CA PRO A 495 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 9.46e-01 bond pdb=" CB VAL A 521 " pdb=" CG1 VAL A 521 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.09e-01 bond pdb=" CG1 ILE A 856 " pdb=" CD1 ILE A 856 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.78e-01 ... (remaining 19157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 24878 1.10 - 2.21: 890 2.21 - 3.31: 194 3.31 - 4.42: 27 4.42 - 5.52: 8 Bond angle restraints: 25997 Sorted by residual: angle pdb=" N ILE B 740 " pdb=" CA ILE B 740 " pdb=" C ILE B 740 " ideal model delta sigma weight residual 112.96 109.59 3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" N VAL A 907 " pdb=" CA VAL A 907 " pdb=" C VAL A 907 " ideal model delta sigma weight residual 108.15 105.61 2.54 9.90e-01 1.02e+00 6.57e+00 angle pdb=" C ASP B 39 " pdb=" N SER B 40 " pdb=" CA SER B 40 " ideal model delta sigma weight residual 122.21 118.74 3.47 1.48e+00 4.57e-01 5.50e+00 angle pdb=" CA ILE B 740 " pdb=" C ILE B 740 " pdb=" N ALA B 741 " ideal model delta sigma weight residual 118.65 116.27 2.38 1.07e+00 8.73e-01 4.96e+00 angle pdb=" CA ASN B 402 " pdb=" C ASN B 402 " pdb=" N PRO B 403 " ideal model delta sigma weight residual 117.69 119.68 -1.99 9.50e-01 1.11e+00 4.39e+00 ... (remaining 25992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.93: 11262 19.93 - 39.87: 318 39.87 - 59.80: 83 59.80 - 79.74: 35 79.74 - 99.67: 4 Dihedral angle restraints: 11702 sinusoidal: 5335 harmonic: 6367 Sorted by residual: dihedral pdb=" O4' A R 12 " pdb=" C1' A R 12 " pdb=" N9 A R 12 " pdb=" C4 A R 12 " ideal model delta sinusoidal sigma weight residual -106.00 -157.95 51.95 1 1.70e+01 3.46e-03 1.27e+01 dihedral pdb=" CA CYS A 86 " pdb=" C CYS A 86 " pdb=" N PRO A 87 " pdb=" CA PRO A 87 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A1299 " pdb=" C ARG A1299 " pdb=" N MET A1300 " pdb=" CA MET A1300 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1642 0.031 - 0.062: 783 0.062 - 0.093: 204 0.093 - 0.124: 95 0.124 - 0.154: 17 Chirality restraints: 2741 Sorted by residual: chirality pdb=" CA VAL B 142 " pdb=" N VAL B 142 " pdb=" C VAL B 142 " pdb=" CB VAL B 142 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA PRO A 864 " pdb=" N PRO A 864 " pdb=" C PRO A 864 " pdb=" CB PRO A 864 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C1' A R 13 " pdb=" O4' A R 13 " pdb=" C2' A R 13 " pdb=" N9 A R 13 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2738 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 904 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 864 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " 0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A 436 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.020 5.00e-02 4.00e+02 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 343 2.68 - 3.24: 17314 3.24 - 3.79: 29577 3.79 - 4.35: 43480 4.35 - 4.90: 67834 Nonbonded interactions: 158548 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" OD1 ASP B 210 " model vdw 2.130 3.040 nonbonded pdb=" OE2 GLU B 432 " pdb=" OG SER B 669 " model vdw 2.199 3.040 nonbonded pdb=" NH2 ARG A 689 " pdb=" OE2 GLU A1461 " model vdw 2.210 3.120 nonbonded pdb=" NH2 ARG A 227 " pdb=" OG1 THR A 484 " model vdw 2.225 3.120 nonbonded pdb=" O GLN B 721 " pdb=" OG1 THR B 725 " model vdw 2.232 3.040 ... (remaining 158543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 54.900 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.004 0.044 19178 Z= 0.160 Angle : 0.551 17.533 26018 Z= 0.279 Chirality : 0.040 0.154 2741 Planarity : 0.005 0.050 3260 Dihedral : 11.111 99.675 7584 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.31 % Allowed : 2.24 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2168 helix: -0.21 (0.17), residues: 754 sheet: 0.94 (0.27), residues: 346 loop : -0.25 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 326 HIS 0.007 0.001 HIS A 871 PHE 0.018 0.002 PHE A 187 TYR 0.014 0.002 TYR B 333 ARG 0.008 0.001 ARG A1346 Details of bonding type rmsd hydrogen bonds : bond 0.23182 ( 742) hydrogen bonds : angle 7.46100 ( 2160) metal coordination : bond 0.00942 ( 16) metal coordination : angle 6.83165 ( 21) covalent geometry : bond 0.00368 (19162) covalent geometry : angle 0.51608 (25997) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 329 time to evaluate : 1.924 Fit side-chains REVERT: B 32 LYS cc_start: 0.8049 (tttt) cc_final: 0.7818 (ttpp) REVERT: B 62 GLN cc_start: 0.7640 (mt0) cc_final: 0.7437 (mt0) REVERT: B 85 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7413 (mm-30) REVERT: B 198 TYR cc_start: 0.7237 (m-80) cc_final: 0.6778 (m-80) REVERT: B 400 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6601 (mtm-85) REVERT: B 541 GLU cc_start: 0.7490 (tt0) cc_final: 0.7265 (tp30) REVERT: B 668 PHE cc_start: 0.7965 (m-80) cc_final: 0.7703 (m-80) REVERT: B 722 MET cc_start: 0.7776 (mtp) cc_final: 0.7549 (mtp) REVERT: A 311 ASP cc_start: 0.6249 (t0) cc_final: 0.6037 (t0) REVERT: A 387 ASP cc_start: 0.7653 (t0) cc_final: 0.7325 (m-30) REVERT: A 426 LYS cc_start: 0.7957 (mttt) cc_final: 0.7743 (mmtt) REVERT: A 605 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6745 (mm-30) REVERT: A 816 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7417 (tp40) REVERT: A 1239 LYS cc_start: 0.7775 (tttt) cc_final: 0.7529 (tttp) REVERT: A 1358 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7200 (mtm-85) REVERT: A 1393 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.7237 (ptt-90) outliers start: 6 outliers final: 2 residues processed: 335 average time/residue: 1.8641 time to fit residues: 678.4058 Evaluate side-chains 203 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 0.0170 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 GLN B 59 GLN B 75 GLN B 235 GLN B 256 GLN B 329 GLN B 389 GLN A 170 GLN A 208 ASN A 276 ASN ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 883 HIS A 942 GLN A1246 ASN A1590 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.183831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.138516 restraints weight = 16387.813| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.65 r_work: 0.3288 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19178 Z= 0.141 Angle : 0.551 18.689 26018 Z= 0.280 Chirality : 0.041 0.202 2741 Planarity : 0.004 0.044 3260 Dihedral : 11.847 98.676 3004 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.34 % Allowed : 8.44 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2168 helix: 0.93 (0.18), residues: 772 sheet: 0.50 (0.26), residues: 375 loop : 0.01 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 474 HIS 0.004 0.001 HIS A 871 PHE 0.015 0.002 PHE A 187 TYR 0.010 0.001 TYR A 492 ARG 0.005 0.000 ARG A1358 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 742) hydrogen bonds : angle 5.16141 ( 2160) metal coordination : bond 0.00602 ( 16) metal coordination : angle 6.80656 ( 21) covalent geometry : bond 0.00302 (19162) covalent geometry : angle 0.51655 (25997) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6865 (ttp80) REVERT: B 16 LYS cc_start: 0.6463 (mmmt) cc_final: 0.6072 (mmmt) REVERT: B 32 LYS cc_start: 0.7953 (tttt) cc_final: 0.7332 (ttpp) REVERT: B 38 MET cc_start: 0.7937 (mtp) cc_final: 0.7734 (mtt) REVERT: B 85 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 198 TYR cc_start: 0.6672 (m-80) cc_final: 0.6336 (m-80) REVERT: B 265 GLU cc_start: 0.7400 (tt0) cc_final: 0.7160 (tt0) REVERT: B 362 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: B 389 GLN cc_start: 0.7831 (tt0) cc_final: 0.7212 (pt0) REVERT: B 400 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6476 (mtm-85) REVERT: B 483 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: B 541 GLU cc_start: 0.7536 (tt0) cc_final: 0.6942 (tp30) REVERT: B 629 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7893 (mmpt) REVERT: B 668 PHE cc_start: 0.7778 (m-80) cc_final: 0.7518 (m-80) REVERT: A 3 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8109 (p) REVERT: A 93 GLU cc_start: 0.6700 (pm20) cc_final: 0.6186 (mp0) REVERT: A 97 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6933 (ptt90) REVERT: A 311 ASP cc_start: 0.6395 (t0) cc_final: 0.5969 (t0) REVERT: A 387 ASP cc_start: 0.7914 (t0) cc_final: 0.7352 (m-30) REVERT: A 426 LYS cc_start: 0.8049 (mttt) cc_final: 0.7339 (mmtt) REVERT: A 559 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: A 605 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6698 (mm-30) REVERT: A 816 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7220 (tp40) REVERT: A 857 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: A 932 LYS cc_start: 0.7974 (mttp) cc_final: 0.7746 (mttt) REVERT: A 1151 VAL cc_start: 0.4406 (OUTLIER) cc_final: 0.4049 (t) REVERT: A 1239 LYS cc_start: 0.6693 (tttt) cc_final: 0.6323 (tttp) REVERT: A 1358 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7302 (mtm-85) REVERT: A 1501 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: A 1525 LYS cc_start: 0.7830 (mttt) cc_final: 0.6758 (tttt) REVERT: A 1588 ASP cc_start: 0.7041 (t0) cc_final: 0.6759 (t0) outliers start: 45 outliers final: 6 residues processed: 244 average time/residue: 1.7888 time to fit residues: 478.7617 Evaluate side-chains 209 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1501 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 14 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN A 276 ASN A 619 ASN A 626 HIS A 942 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.183123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137596 restraints weight = 16344.736| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.49 r_work: 0.3274 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19178 Z= 0.136 Angle : 0.528 17.901 26018 Z= 0.266 Chirality : 0.041 0.202 2741 Planarity : 0.004 0.046 3260 Dihedral : 11.763 97.981 3002 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.40 % Allowed : 9.64 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2168 helix: 1.32 (0.19), residues: 780 sheet: 0.50 (0.26), residues: 376 loop : -0.06 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 474 HIS 0.005 0.001 HIS A 871 PHE 0.015 0.002 PHE A 187 TYR 0.014 0.001 TYR B 31 ARG 0.007 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 742) hydrogen bonds : angle 4.87702 ( 2160) metal coordination : bond 0.00575 ( 16) metal coordination : angle 6.61652 ( 21) covalent geometry : bond 0.00300 (19162) covalent geometry : angle 0.49320 (25997) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: B 16 LYS cc_start: 0.6441 (mmmt) cc_final: 0.6063 (mmmt) REVERT: B 32 LYS cc_start: 0.7935 (tttt) cc_final: 0.7256 (ttpp) REVERT: B 38 MET cc_start: 0.7939 (mtp) cc_final: 0.7679 (mtm) REVERT: B 85 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 198 TYR cc_start: 0.6618 (m-80) cc_final: 0.6328 (m-80) REVERT: B 233 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 265 GLU cc_start: 0.7438 (tt0) cc_final: 0.7171 (tt0) REVERT: B 362 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.5984 (tm-30) REVERT: B 389 GLN cc_start: 0.7841 (tt0) cc_final: 0.7159 (pt0) REVERT: B 400 ARG cc_start: 0.7362 (mtp180) cc_final: 0.6437 (mtm-85) REVERT: B 500 MET cc_start: 0.8608 (mtt) cc_final: 0.8355 (mtt) REVERT: B 541 GLU cc_start: 0.7499 (tt0) cc_final: 0.6936 (tp30) REVERT: B 629 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7782 (mmpt) REVERT: A 3 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 97 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6923 (ptt90) REVERT: A 311 ASP cc_start: 0.6429 (t0) cc_final: 0.5960 (t0) REVERT: A 338 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6853 (t0) REVERT: A 426 LYS cc_start: 0.8072 (mttt) cc_final: 0.7349 (mmtt) REVERT: A 559 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: A 605 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6634 (mm-30) REVERT: A 816 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7178 (tp40) REVERT: A 857 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: A 1239 LYS cc_start: 0.6721 (tttt) cc_final: 0.6316 (tttp) REVERT: A 1358 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7269 (mtm-85) REVERT: A 1525 LYS cc_start: 0.7791 (mttt) cc_final: 0.6734 (tttm) REVERT: A 1588 ASP cc_start: 0.7094 (t0) cc_final: 0.6811 (t0) outliers start: 46 outliers final: 11 residues processed: 236 average time/residue: 1.7149 time to fit residues: 445.3532 Evaluate side-chains 214 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN A 260 ASN A 276 ASN A 619 ASN A 942 GLN A1590 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134153 restraints weight = 16532.454| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.54 r_work: 0.3230 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19178 Z= 0.220 Angle : 0.620 18.961 26018 Z= 0.313 Chirality : 0.045 0.224 2741 Planarity : 0.005 0.067 3260 Dihedral : 11.968 101.164 3002 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.86 % Allowed : 9.53 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2168 helix: 1.14 (0.19), residues: 779 sheet: 0.40 (0.26), residues: 373 loop : -0.24 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 474 HIS 0.006 0.001 HIS A 871 PHE 0.017 0.002 PHE A1361 TYR 0.013 0.002 TYR A 804 ARG 0.008 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 742) hydrogen bonds : angle 5.00543 ( 2160) metal coordination : bond 0.01017 ( 16) metal coordination : angle 7.16089 ( 21) covalent geometry : bond 0.00506 (19162) covalent geometry : angle 0.58605 (25997) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 3.311 Fit side-chains REVERT: B 16 LYS cc_start: 0.6628 (mmmt) cc_final: 0.6225 (mmmt) REVERT: B 24 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6539 (mmm) REVERT: B 32 LYS cc_start: 0.7953 (tttt) cc_final: 0.7181 (ttpp) REVERT: B 38 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7757 (mtm) REVERT: B 85 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 198 TYR cc_start: 0.6740 (m-80) cc_final: 0.6526 (m-80) REVERT: B 265 GLU cc_start: 0.7431 (tt0) cc_final: 0.7190 (tt0) REVERT: B 362 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.5887 (tm-30) REVERT: B 368 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7388 (ttm110) REVERT: B 400 ARG cc_start: 0.7380 (mtp180) cc_final: 0.6411 (mtm-85) REVERT: B 483 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: B 500 MET cc_start: 0.8717 (mtt) cc_final: 0.8473 (mtt) REVERT: B 541 GLU cc_start: 0.7516 (tt0) cc_final: 0.6937 (tp30) REVERT: B 629 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7804 (mmpt) REVERT: A 3 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 93 GLU cc_start: 0.6702 (pm20) cc_final: 0.6174 (mp0) REVERT: A 97 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6907 (ptt90) REVERT: A 283 ARG cc_start: 0.7647 (tpt-90) cc_final: 0.5943 (ttp-110) REVERT: A 311 ASP cc_start: 0.6504 (t0) cc_final: 0.5959 (t0) REVERT: A 338 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6954 (t0) REVERT: A 426 LYS cc_start: 0.8014 (mttt) cc_final: 0.7263 (mmtm) REVERT: A 605 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6620 (mm-30) REVERT: A 816 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7190 (tp40) REVERT: A 857 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: A 1239 LYS cc_start: 0.6674 (tttt) cc_final: 0.6264 (tttp) REVERT: A 1250 GLN cc_start: 0.6659 (mt0) cc_final: 0.6351 (mt0) REVERT: A 1358 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.7327 (mtm-85) REVERT: A 1393 ARG cc_start: 0.7625 (ptt-90) cc_final: 0.7424 (ptt-90) REVERT: A 1408 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7131 (mmpt) REVERT: A 1457 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7341 (pp20) REVERT: A 1525 LYS cc_start: 0.7743 (mttt) cc_final: 0.6615 (tttm) REVERT: A 1577 GLU cc_start: 0.7499 (tt0) cc_final: 0.7247 (tt0) REVERT: A 1588 ASP cc_start: 0.7176 (t0) cc_final: 0.6925 (t0) outliers start: 55 outliers final: 18 residues processed: 234 average time/residue: 2.1948 time to fit residues: 564.3222 Evaluate side-chains 225 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 46 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 619 ASN A 942 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.182766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137516 restraints weight = 16614.359| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.47 r_work: 0.3278 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19178 Z= 0.122 Angle : 0.518 18.194 26018 Z= 0.260 Chirality : 0.040 0.205 2741 Planarity : 0.004 0.046 3260 Dihedral : 11.783 98.570 3002 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.98 % Allowed : 10.89 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2168 helix: 1.45 (0.19), residues: 779 sheet: 0.44 (0.26), residues: 376 loop : -0.14 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 474 HIS 0.005 0.001 HIS A1483 PHE 0.016 0.001 PHE A 776 TYR 0.010 0.001 TYR A 492 ARG 0.008 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 742) hydrogen bonds : angle 4.73103 ( 2160) metal coordination : bond 0.00709 ( 16) metal coordination : angle 6.65672 ( 21) covalent geometry : bond 0.00269 (19162) covalent geometry : angle 0.48244 (25997) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.969 Fit side-chains REVERT: B 6 ARG cc_start: 0.7140 (ttm110) cc_final: 0.6938 (ttp80) REVERT: B 16 LYS cc_start: 0.6585 (mmmt) cc_final: 0.6164 (mmmt) REVERT: B 32 LYS cc_start: 0.7917 (tttt) cc_final: 0.7173 (ttpp) REVERT: B 38 MET cc_start: 0.8010 (mtp) cc_final: 0.7737 (mtm) REVERT: B 85 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7359 (mm-30) REVERT: B 233 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: B 265 GLU cc_start: 0.7427 (tt0) cc_final: 0.7188 (tt0) REVERT: B 362 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: B 368 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7420 (ttm110) REVERT: B 388 GLU cc_start: 0.7767 (mt-10) cc_final: 0.6878 (mm-30) REVERT: B 400 ARG cc_start: 0.7301 (mtp180) cc_final: 0.6380 (mtm-85) REVERT: B 541 GLU cc_start: 0.7480 (tt0) cc_final: 0.6913 (tp30) REVERT: B 629 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7880 (mmpt) REVERT: A 3 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 97 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6806 (ptt180) REVERT: A 283 ARG cc_start: 0.7599 (tpt-90) cc_final: 0.5922 (ttp-110) REVERT: A 311 ASP cc_start: 0.6489 (t0) cc_final: 0.5942 (t0) REVERT: A 338 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6888 (t0) REVERT: A 426 LYS cc_start: 0.8040 (mttt) cc_final: 0.7318 (mmtm) REVERT: A 559 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: A 605 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6627 (mm-30) REVERT: A 816 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7163 (tp40) REVERT: A 857 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: A 1037 MET cc_start: 0.6113 (mpt) cc_final: 0.5536 (mpt) REVERT: A 1239 LYS cc_start: 0.6685 (tttt) cc_final: 0.6281 (tttp) REVERT: A 1250 GLN cc_start: 0.6657 (mt0) cc_final: 0.6424 (mt0) REVERT: A 1286 ASP cc_start: 0.6367 (t0) cc_final: 0.5574 (m-30) REVERT: A 1358 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7283 (mtm-85) REVERT: A 1408 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7047 (mmpt) REVERT: A 1457 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: A 1525 LYS cc_start: 0.7699 (mttt) cc_final: 0.6672 (tttt) REVERT: A 1577 GLU cc_start: 0.7498 (tt0) cc_final: 0.7226 (tt0) REVERT: A 1588 ASP cc_start: 0.7141 (t0) cc_final: 0.6895 (t0) outliers start: 38 outliers final: 14 residues processed: 227 average time/residue: 1.7557 time to fit residues: 437.2767 Evaluate side-chains 225 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1583 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 161 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 112 optimal weight: 0.0170 chunk 177 optimal weight: 8.9990 chunk 191 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 619 ASN A 942 GLN A1590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.182564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137040 restraints weight = 16579.002| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.50 r_work: 0.3260 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19178 Z= 0.130 Angle : 0.519 17.646 26018 Z= 0.261 Chirality : 0.041 0.206 2741 Planarity : 0.004 0.045 3260 Dihedral : 11.737 97.645 3002 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.24 % Allowed : 11.20 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2168 helix: 1.54 (0.19), residues: 779 sheet: 0.41 (0.26), residues: 377 loop : -0.12 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 474 HIS 0.004 0.001 HIS A1483 PHE 0.015 0.001 PHE A 776 TYR 0.010 0.001 TYR A 492 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 742) hydrogen bonds : angle 4.64196 ( 2160) metal coordination : bond 0.00725 ( 16) metal coordination : angle 6.54736 ( 21) covalent geometry : bond 0.00291 (19162) covalent geometry : angle 0.48483 (25997) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 2.400 Fit side-chains REVERT: B 16 LYS cc_start: 0.6481 (mmmt) cc_final: 0.6084 (mmmt) REVERT: B 32 LYS cc_start: 0.7913 (tttt) cc_final: 0.7153 (ttpp) REVERT: B 38 MET cc_start: 0.8001 (mtp) cc_final: 0.7723 (mtm) REVERT: B 85 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 233 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: B 362 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6065 (tm-30) REVERT: B 368 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7419 (ttm110) REVERT: B 388 GLU cc_start: 0.7737 (mt-10) cc_final: 0.6851 (mm-30) REVERT: B 400 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6371 (mtm-85) REVERT: B 483 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: B 500 MET cc_start: 0.8609 (mtt) cc_final: 0.8359 (mtt) REVERT: B 541 GLU cc_start: 0.7484 (tt0) cc_final: 0.6889 (tp30) REVERT: B 629 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7827 (mmpt) REVERT: A 3 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.7979 (p) REVERT: A 97 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6923 (ptt180) REVERT: A 283 ARG cc_start: 0.7613 (tpt-90) cc_final: 0.5844 (ttp-110) REVERT: A 311 ASP cc_start: 0.6438 (t0) cc_final: 0.6058 (t0) REVERT: A 338 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6862 (t0) REVERT: A 361 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 426 LYS cc_start: 0.8032 (mttt) cc_final: 0.7292 (mmtm) REVERT: A 559 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: A 605 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6642 (mm-30) REVERT: A 816 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7144 (tp40) REVERT: A 857 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 1037 MET cc_start: 0.6086 (mpt) cc_final: 0.5172 (ptp) REVERT: A 1239 LYS cc_start: 0.6717 (tttt) cc_final: 0.6314 (tttp) REVERT: A 1250 GLN cc_start: 0.6700 (mt0) cc_final: 0.6460 (mt0) REVERT: A 1286 ASP cc_start: 0.6312 (t0) cc_final: 0.5508 (m-30) REVERT: A 1358 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7293 (mtm-85) REVERT: A 1366 ASN cc_start: 0.6456 (p0) cc_final: 0.5505 (m110) REVERT: A 1408 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6994 (mmpt) REVERT: A 1457 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7262 (pp20) REVERT: A 1525 LYS cc_start: 0.7702 (mttt) cc_final: 0.6661 (tttt) REVERT: A 1577 GLU cc_start: 0.7441 (tt0) cc_final: 0.7194 (tt0) REVERT: A 1590 GLN cc_start: 0.8183 (mt0) cc_final: 0.7959 (mt0) outliers start: 43 outliers final: 17 residues processed: 228 average time/residue: 1.9384 time to fit residues: 487.4715 Evaluate side-chains 228 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1408 LYS Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1583 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 169 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 619 ASN A 626 HIS A 942 GLN A1127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132810 restraints weight = 16426.529| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.53 r_work: 0.3187 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 19178 Z= 0.295 Angle : 0.704 19.094 26018 Z= 0.355 Chirality : 0.049 0.242 2741 Planarity : 0.006 0.082 3260 Dihedral : 12.137 103.648 3002 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.55 % Allowed : 11.46 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2168 helix: 0.90 (0.18), residues: 779 sheet: 0.29 (0.26), residues: 363 loop : -0.40 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 474 HIS 0.007 0.002 HIS A 871 PHE 0.019 0.003 PHE A1361 TYR 0.017 0.002 TYR A 804 ARG 0.008 0.001 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.05671 ( 742) hydrogen bonds : angle 5.10628 ( 2160) metal coordination : bond 0.01419 ( 16) metal coordination : angle 7.46222 ( 21) covalent geometry : bond 0.00688 (19162) covalent geometry : angle 0.67121 (25997) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 2.162 Fit side-chains REVERT: B 16 LYS cc_start: 0.6558 (mmmt) cc_final: 0.6148 (mmmt) REVERT: B 24 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6548 (mmm) REVERT: B 32 LYS cc_start: 0.7933 (tttt) cc_final: 0.7157 (ttpp) REVERT: B 38 MET cc_start: 0.8115 (mtp) cc_final: 0.7796 (mtt) REVERT: B 233 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 362 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.5941 (tm-30) REVERT: B 368 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7413 (ttm110) REVERT: B 400 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6421 (mtm-85) REVERT: B 483 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 500 MET cc_start: 0.8770 (mtt) cc_final: 0.8527 (mtt) REVERT: B 541 GLU cc_start: 0.7568 (tt0) cc_final: 0.6942 (tp30) REVERT: B 629 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: A 3 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.7877 (p) REVERT: A 93 GLU cc_start: 0.6649 (pm20) cc_final: 0.5971 (mp0) REVERT: A 97 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6838 (ptt180) REVERT: A 283 ARG cc_start: 0.7683 (tpt-90) cc_final: 0.5978 (ttp-110) REVERT: A 311 ASP cc_start: 0.6515 (t0) cc_final: 0.6131 (t70) REVERT: A 338 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6887 (t0) REVERT: A 361 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7043 (mp) REVERT: A 373 THR cc_start: 0.7530 (m) cc_final: 0.6930 (t) REVERT: A 426 LYS cc_start: 0.8022 (mttt) cc_final: 0.7313 (mmtm) REVERT: A 559 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: A 605 GLU cc_start: 0.7582 (mt-10) cc_final: 0.6684 (mm-30) REVERT: A 816 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7350 (tp40) REVERT: A 857 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: A 1037 MET cc_start: 0.6246 (mpt) cc_final: 0.5805 (mpt) REVERT: A 1239 LYS cc_start: 0.6779 (tttt) cc_final: 0.6357 (tttp) REVERT: A 1250 GLN cc_start: 0.6675 (mt0) cc_final: 0.6409 (mt0) REVERT: A 1358 ARG cc_start: 0.8435 (mtm-85) cc_final: 0.7391 (mtm-85) REVERT: A 1457 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7373 (pp20) REVERT: A 1577 GLU cc_start: 0.7433 (tt0) cc_final: 0.7206 (tt0) outliers start: 49 outliers final: 16 residues processed: 219 average time/residue: 2.3061 time to fit residues: 556.2618 Evaluate side-chains 215 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 199 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 165 optimal weight: 0.0980 chunk 219 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 619 ASN A 942 GLN A1127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.183030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138608 restraints weight = 16495.879| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.50 r_work: 0.3279 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19178 Z= 0.108 Angle : 0.514 18.470 26018 Z= 0.258 Chirality : 0.040 0.206 2741 Planarity : 0.004 0.046 3260 Dihedral : 11.778 98.401 3002 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.72 % Allowed : 12.24 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2168 helix: 1.47 (0.19), residues: 779 sheet: 0.32 (0.26), residues: 378 loop : -0.19 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 474 HIS 0.005 0.001 HIS A1483 PHE 0.019 0.001 PHE A 776 TYR 0.010 0.001 TYR B 578 ARG 0.005 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 742) hydrogen bonds : angle 4.63037 ( 2160) metal coordination : bond 0.00834 ( 16) metal coordination : angle 6.66543 ( 21) covalent geometry : bond 0.00238 (19162) covalent geometry : angle 0.47851 (25997) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: B 16 LYS cc_start: 0.6532 (mmmt) cc_final: 0.6141 (mmmt) REVERT: B 24 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6409 (mmm) REVERT: B 32 LYS cc_start: 0.7874 (tttt) cc_final: 0.7131 (ttpp) REVERT: B 38 MET cc_start: 0.7946 (mtp) cc_final: 0.7639 (mtm) REVERT: B 78 LYS cc_start: 0.6761 (mtpp) cc_final: 0.6422 (ttmm) REVERT: B 109 ASN cc_start: 0.6374 (t160) cc_final: 0.5994 (m-40) REVERT: B 233 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: B 362 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6075 (tm-30) REVERT: B 368 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7367 (ttm110) REVERT: B 388 GLU cc_start: 0.7701 (mt-10) cc_final: 0.6811 (mm-30) REVERT: B 400 ARG cc_start: 0.7276 (mtp180) cc_final: 0.6383 (mtm-85) REVERT: B 541 GLU cc_start: 0.7439 (tt0) cc_final: 0.6857 (tp30) REVERT: B 629 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7846 (mmpt) REVERT: A 3 THR cc_start: 0.8549 (m) cc_final: 0.8009 (p) REVERT: A 24 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7422 (t) REVERT: A 93 GLU cc_start: 0.6497 (pm20) cc_final: 0.6071 (mp0) REVERT: A 97 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6968 (ptt180) REVERT: A 283 ARG cc_start: 0.7610 (tpt-90) cc_final: 0.5926 (ttp-110) REVERT: A 311 ASP cc_start: 0.6434 (t0) cc_final: 0.6071 (t70) REVERT: A 338 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6647 (p0) REVERT: A 426 LYS cc_start: 0.8045 (mttt) cc_final: 0.7344 (mmtm) REVERT: A 559 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8030 (mmm) REVERT: A 605 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6631 (mm-30) REVERT: A 786 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 816 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7046 (tp40) REVERT: A 857 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: A 1037 MET cc_start: 0.6107 (mpt) cc_final: 0.5645 (mpt) REVERT: A 1239 LYS cc_start: 0.6688 (tttt) cc_final: 0.6279 (tttp) REVERT: A 1250 GLN cc_start: 0.6660 (mt0) cc_final: 0.6453 (mt0) REVERT: A 1286 ASP cc_start: 0.6408 (t0) cc_final: 0.5544 (m-30) REVERT: A 1358 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7278 (mtm-85) REVERT: A 1457 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7302 (pp20) REVERT: A 1577 GLU cc_start: 0.7443 (tt0) cc_final: 0.7174 (tt0) REVERT: A 1588 ASP cc_start: 0.7148 (t0) cc_final: 0.6882 (t0) outliers start: 33 outliers final: 12 residues processed: 219 average time/residue: 1.8435 time to fit residues: 446.1534 Evaluate side-chains 211 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 104 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 500 HIS A 942 GLN A1590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.180173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136735 restraints weight = 16480.551| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.25 r_work: 0.3232 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19178 Z= 0.203 Angle : 0.605 18.323 26018 Z= 0.304 Chirality : 0.044 0.224 2741 Planarity : 0.005 0.054 3260 Dihedral : 11.931 100.384 3002 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2168 helix: 1.25 (0.19), residues: 779 sheet: 0.29 (0.26), residues: 368 loop : -0.29 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1509 HIS 0.006 0.001 HIS A 871 PHE 0.016 0.002 PHE A 776 TYR 0.020 0.002 TYR B 31 ARG 0.006 0.001 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 742) hydrogen bonds : angle 4.82837 ( 2160) metal coordination : bond 0.01054 ( 16) metal coordination : angle 7.03580 ( 21) covalent geometry : bond 0.00470 (19162) covalent geometry : angle 0.57102 (25997) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 2.202 Fit side-chains REVERT: B 16 LYS cc_start: 0.6761 (mmmt) cc_final: 0.6335 (mmmt) REVERT: B 24 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6636 (mmm) REVERT: B 32 LYS cc_start: 0.7996 (tttt) cc_final: 0.7292 (ttpp) REVERT: B 38 MET cc_start: 0.8161 (mtp) cc_final: 0.7862 (mtm) REVERT: B 109 ASN cc_start: 0.6505 (t160) cc_final: 0.6046 (m110) REVERT: B 233 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: B 362 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6085 (tm-30) REVERT: B 368 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7497 (ttm110) REVERT: B 400 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6506 (mtm-85) REVERT: B 483 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: B 500 MET cc_start: 0.8751 (mtt) cc_final: 0.8521 (mtt) REVERT: B 541 GLU cc_start: 0.7544 (tt0) cc_final: 0.7001 (tp30) REVERT: B 629 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7825 (mmpt) REVERT: A 3 THR cc_start: 0.8544 (m) cc_final: 0.8012 (p) REVERT: A 93 GLU cc_start: 0.6701 (pm20) cc_final: 0.6153 (mp0) REVERT: A 97 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6923 (ptt180) REVERT: A 283 ARG cc_start: 0.7750 (tpt-90) cc_final: 0.6157 (ttp-110) REVERT: A 311 ASP cc_start: 0.6674 (t0) cc_final: 0.6284 (t70) REVERT: A 338 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6913 (t0) REVERT: A 373 THR cc_start: 0.7616 (m) cc_final: 0.7225 (t) REVERT: A 426 LYS cc_start: 0.8111 (mttt) cc_final: 0.7459 (mmtm) REVERT: A 605 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6801 (mm-30) REVERT: A 786 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 816 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7317 (tp40) REVERT: A 857 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: A 1037 MET cc_start: 0.6230 (mpt) cc_final: 0.5758 (mpt) REVERT: A 1239 LYS cc_start: 0.6813 (tttt) cc_final: 0.6396 (tttp) REVERT: A 1250 GLN cc_start: 0.6767 (mt0) cc_final: 0.6537 (mt0) REVERT: A 1286 ASP cc_start: 0.6355 (t0) cc_final: 0.5533 (m-30) REVERT: A 1358 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.7384 (mtm-85) REVERT: A 1457 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: A 1577 GLU cc_start: 0.7542 (tt0) cc_final: 0.7313 (tt0) REVERT: A 1590 GLN cc_start: 0.8272 (mt0) cc_final: 0.8050 (mt0) outliers start: 30 outliers final: 14 residues processed: 207 average time/residue: 1.7623 time to fit residues: 400.9525 Evaluate side-chains 209 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 114 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 173 optimal weight: 0.0040 overall best weight: 0.7552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138219 restraints weight = 16456.250| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.45 r_work: 0.3286 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19178 Z= 0.114 Angle : 0.521 18.085 26018 Z= 0.260 Chirality : 0.040 0.205 2741 Planarity : 0.004 0.046 3260 Dihedral : 11.746 97.708 3002 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.46 % Allowed : 12.81 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2168 helix: 1.55 (0.19), residues: 780 sheet: 0.36 (0.26), residues: 377 loop : -0.14 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1509 HIS 0.005 0.001 HIS B 436 PHE 0.017 0.001 PHE A 776 TYR 0.021 0.001 TYR B 31 ARG 0.005 0.000 ARG A 780 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 742) hydrogen bonds : angle 4.58611 ( 2160) metal coordination : bond 0.00780 ( 16) metal coordination : angle 6.55777 ( 21) covalent geometry : bond 0.00255 (19162) covalent geometry : angle 0.48630 (25997) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.906 Fit side-chains REVERT: B 16 LYS cc_start: 0.6682 (mmmt) cc_final: 0.6192 (mmmt) REVERT: B 24 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6457 (mmm) REVERT: B 32 LYS cc_start: 0.7870 (tttt) cc_final: 0.7120 (ttpp) REVERT: B 38 MET cc_start: 0.8003 (mtp) cc_final: 0.7705 (mtm) REVERT: B 109 ASN cc_start: 0.6425 (t160) cc_final: 0.6084 (m110) REVERT: B 148 GLU cc_start: 0.6753 (mm-30) cc_final: 0.5449 (pt0) REVERT: B 233 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: B 362 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6085 (tm-30) REVERT: B 368 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7396 (ttm110) REVERT: B 388 GLU cc_start: 0.7712 (mt-10) cc_final: 0.6825 (mm-30) REVERT: B 400 ARG cc_start: 0.7270 (mtp180) cc_final: 0.6390 (mtm-85) REVERT: B 483 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7177 (mt-10) REVERT: B 541 GLU cc_start: 0.7446 (tt0) cc_final: 0.6880 (tp30) REVERT: B 629 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (mmpt) REVERT: A 3 THR cc_start: 0.8561 (m) cc_final: 0.8038 (p) REVERT: A 97 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6820 (ptt180) REVERT: A 283 ARG cc_start: 0.7616 (tpt-90) cc_final: 0.5938 (ttp-110) REVERT: A 311 ASP cc_start: 0.6484 (t0) cc_final: 0.6085 (t70) REVERT: A 338 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6631 (p0) REVERT: A 426 LYS cc_start: 0.8015 (mttt) cc_final: 0.7340 (mmtm) REVERT: A 559 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8018 (mmm) REVERT: A 605 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6578 (mm-30) REVERT: A 609 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7260 (mtp-110) REVERT: A 786 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 816 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7155 (tp40) REVERT: A 857 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 973 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (ttmt) REVERT: A 1037 MET cc_start: 0.6177 (mpt) cc_final: 0.5708 (mpt) REVERT: A 1239 LYS cc_start: 0.6662 (tttt) cc_final: 0.6259 (tttp) REVERT: A 1250 GLN cc_start: 0.6659 (mt0) cc_final: 0.6456 (mt0) REVERT: A 1286 ASP cc_start: 0.6320 (t0) cc_final: 0.5527 (m-30) REVERT: A 1358 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7270 (mtm-85) REVERT: A 1366 ASN cc_start: 0.6296 (p0) cc_final: 0.5356 (m110) REVERT: A 1457 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: A 1577 GLU cc_start: 0.7485 (tt0) cc_final: 0.7234 (tt0) outliers start: 28 outliers final: 12 residues processed: 208 average time/residue: 1.7331 time to fit residues: 396.0877 Evaluate side-chains 213 residues out of total 1920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 973 LYS Chi-restraints excluded: chain A residue 1455 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 118 optimal weight: 0.8980 chunk 211 optimal weight: 0.2980 chunk 206 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 276 ASN A 942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139031 restraints weight = 16522.785| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.57 r_work: 0.3307 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19178 Z= 0.109 Angle : 0.506 16.828 26018 Z= 0.253 Chirality : 0.040 0.202 2741 Planarity : 0.004 0.045 3260 Dihedral : 11.639 95.895 3002 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.35 % Allowed : 12.97 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2168 helix: 1.68 (0.19), residues: 781 sheet: 0.47 (0.26), residues: 369 loop : -0.08 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1509 HIS 0.005 0.001 HIS A1483 PHE 0.016 0.001 PHE A 776 TYR 0.017 0.001 TYR A 577 ARG 0.004 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 742) hydrogen bonds : angle 4.47421 ( 2160) metal coordination : bond 0.00661 ( 16) metal coordination : angle 6.18455 ( 21) covalent geometry : bond 0.00243 (19162) covalent geometry : angle 0.47430 (25997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18786.44 seconds wall clock time: 328 minutes 13.77 seconds (19693.77 seconds total)