Starting phenix.real_space_refine on Sun Jun 15 04:44:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmc_37649/06_2025/8wmc_37649.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmc_37649/06_2025/8wmc_37649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmc_37649/06_2025/8wmc_37649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmc_37649/06_2025/8wmc_37649.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmc_37649/06_2025/8wmc_37649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmc_37649/06_2025/8wmc_37649.cif" } resolution = 2.9 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= 0.041 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 75 5.16 5 C 10574 2.51 5 N 2982 2.21 5 O 3257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16929 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: {'PTRANS': 28, 'TRANS': 705} Chain breaks: 3 Chain: "A" Number of atoms: 10024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1249, 10024 Classifications: {'peptide': 1249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 69, 'TRANS': 1179} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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 9483 SG CYS A 463 41.138 48.304 52.348 1.00 67.66 S ATOM 9545 SG CYS A 472 41.211 49.211 48.693 1.00 56.85 S ATOM 9559 SG CYS A 474 37.862 48.869 50.447 1.00 54.69 S ATOM 9581 SG CYS A 477 39.928 51.836 51.198 1.00 48.17 S ATOM 11402 SG CYS A 706 48.213 32.538 77.785 1.00 75.16 S ATOM 11417 SG CYS A 708 44.842 32.617 79.503 1.00 62.30 S ATOM 11439 SG CYS A 711 46.273 35.796 78.048 1.00 59.36 S ATOM 13327 SG CYS A 965 53.998 37.341 116.916 1.00 51.96 S ATOM 13787 SG CYS A1312 55.837 36.299 113.552 1.00 53.87 S ATOM 14026 SG CYS A1342 52.994 34.240 115.261 1.00 48.21 S ATOM 14044 SG CYS A1345 52.230 37.325 113.386 1.00 43.09 S ATOM 7112 SG CYS A 123 42.070 72.923 25.592 1.00 77.33 S ATOM 7136 SG CYS A 126 44.927 71.978 26.346 1.00 74.46 S Time building chain proxies: 9.96, per 1000 atoms: 0.59 Number of scatterers: 16929 At special positions: 0 Unit cell: (102, 103.7, 169.15, 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 75 16.00 P 37 15.00 O 3257 8.00 N 2982 7.00 C 10574 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: 4.19 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 472 " 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 708 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " 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 A 965 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1312 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " Number of angles added : 15 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 43.7% alpha, 15.1% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.642A pdb=" N THR B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.655A pdb=" N THR B 44 " --> pdb=" O SER B 41 " (cutoff:3.500A) 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: 4.957A pdb=" N ASN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.817A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.869A 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 removed outlier: 3.652A pdb=" N GLY B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.852A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 5.165A 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: 3.752A pdb=" N LEU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 277 through 293 removed outlier: 4.528A pdb=" N ASP B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) 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 removed outlier: 4.313A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.554A pdb=" N ARG B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.633A 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 482 Processing helix chain 'B' and resid 485 through 500 Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.722A pdb=" N LYS B 505 " --> pdb=" O PHE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.780A pdb=" N LEU B 523 " --> pdb=" O HIS B 520 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 524 " --> pdb=" O GLY B 521 " (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 removed outlier: 3.634A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 595 through 606 removed outlier: 3.725A pdb=" N ASN B 606 " --> pdb=" O ALA B 602 " (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 683 removed outlier: 3.650A pdb=" N HIS B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 710 Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.619A pdb=" N ASN B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.638A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.004A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) 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 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 300 removed outlier: 5.707A pdb=" N SER A 296 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.143A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (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 555 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.431A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (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 708 through 715 Processing helix chain 'A' and resid 780 through 785 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 removed outlier: 3.823A pdb=" N LEU A 832 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 963 removed outlier: 3.938A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.559A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1242 " --> pdb=" O TYR A1238 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG A1243 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.046A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 removed outlier: 3.575A pdb=" N ARG A1310 " --> pdb=" O ALA A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1327 removed outlier: 4.206A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A1326 " --> pdb=" O SER A1323 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA A1327 " --> pdb=" O ALA A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.614A pdb=" N LYS A1331 " --> pdb=" O TYR A1328 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1333 " --> pdb=" O GLU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1420 through 1426 removed outlier: 3.648A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1539 through 1548 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 4.395A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.564A pdb=" N LYS A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1595 " --> pdb=" O LYS A1591 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 314 through 315 removed outlier: 6.763A pdb=" N TYR B 321 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU B 359 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER B 323 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 457 through 462 removed outlier: 3.523A pdb=" N GLN B 458 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 428 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 removed outlier: 4.009A pdb=" N GLU B 541 " --> pdb=" O LYS B 533 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 569 through 573 removed outlier: 6.761A pdb=" N THR B 570 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU B 613 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 572 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 615 through 617 removed outlier: 4.247A pdb=" N HIS B 615 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 633 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 150 removed outlier: 4.038A pdb=" N LYS A 6 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 238 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.501A pdb=" N MET A 17 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.040A 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: 4.976A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 557 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.976A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.796A 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 removed outlier: 3.936A pdb=" N ALA A 488 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 497 through 504 removed outlier: 11.065A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.450A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.678A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.050A 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 663 removed outlier: 7.779A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.403A 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 663 removed outlier: 7.779A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB8, first strand: chain 'A' and resid 739 through 740 Processing sheet with id=AB9, first strand: chain 'A' and resid 861 through 862 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 1357 through 1359 removed outlier: 5.979A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A1502 " --> pdb=" O ARG A 896 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AC4, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.240A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.729A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1941 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: 6.40 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2798 1.32 - 1.44: 4826 1.44 - 1.57: 9574 1.57 - 1.69: 74 1.69 - 1.82: 112 Bond restraints: 17384 Sorted by residual: bond pdb=" C PRO A 198 " pdb=" O PRO A 198 " ideal model delta sigma weight residual 1.239 1.193 0.046 1.22e-02 6.72e+03 1.45e+01 bond pdb=" C PHE B 197 " pdb=" O PHE B 197 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.22e-02 6.72e+03 1.34e+01 bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.24e-02 6.50e+03 1.26e+01 bond pdb=" N ASP B 448 " pdb=" CA ASP B 448 " ideal model delta sigma weight residual 1.462 1.492 -0.031 9.30e-03 1.16e+04 1.08e+01 bond pdb=" N ARG A 199 " pdb=" CA ARG A 199 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.79e+00 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 22886 1.68 - 3.35: 528 3.35 - 5.03: 166 5.03 - 6.71: 16 6.71 - 8.38: 4 Bond angle restraints: 23600 Sorted by residual: angle pdb=" N PRO B 449 " pdb=" CA PRO B 449 " pdb=" C PRO B 449 " ideal model delta sigma weight residual 113.84 122.22 -8.38 1.30e+00 5.92e-01 4.16e+01 angle pdb=" CA ASP A 162 " pdb=" C ASP A 162 " pdb=" O ASP A 162 " ideal model delta sigma weight residual 120.55 114.00 6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" CA PHE A 200 " pdb=" C PHE A 200 " pdb=" O PHE A 200 " ideal model delta sigma weight residual 121.44 114.71 6.73 1.17e+00 7.31e-01 3.30e+01 angle pdb=" C PRO B 449 " pdb=" CA PRO B 449 " pdb=" CB PRO B 449 " ideal model delta sigma weight residual 111.85 104.60 7.25 1.42e+00 4.96e-01 2.61e+01 angle pdb=" CA ILE B 446 " pdb=" C ILE B 446 " pdb=" O ILE B 446 " ideal model delta sigma weight residual 121.93 116.46 5.47 1.12e+00 7.97e-01 2.39e+01 ... (remaining 23595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.79: 9569 18.79 - 37.57: 850 37.57 - 56.36: 127 56.36 - 75.14: 63 75.14 - 93.93: 15 Dihedral angle restraints: 10624 sinusoidal: 4873 harmonic: 5751 Sorted by residual: dihedral pdb=" CA TYR B 447 " pdb=" C TYR B 447 " pdb=" N ASP B 448 " pdb=" CA ASP B 448 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP A1404 " pdb=" CB ASP A1404 " pdb=" CG ASP A1404 " pdb=" OD1 ASP A1404 " ideal model delta sinusoidal sigma weight residual -30.00 -89.69 59.69 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA TYR B 209 " pdb=" C TYR B 209 " pdb=" N ASP B 210 " pdb=" CA ASP B 210 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 10621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1930 0.042 - 0.085: 416 0.085 - 0.127: 118 0.127 - 0.170: 33 0.170 - 0.212: 4 Chirality restraints: 2501 Sorted by residual: chirality pdb=" CA GLU A 857 " pdb=" N GLU A 857 " pdb=" C GLU A 857 " pdb=" CB GLU A 857 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE B 446 " pdb=" N ILE B 446 " pdb=" C ILE B 446 " pdb=" CB ILE B 446 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA ILE B 205 " pdb=" N ILE B 205 " pdb=" C ILE B 205 " pdb=" CB ILE B 205 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 2498 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 420 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ALA A 420 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA A 420 " 0.017 2.00e-02 2.50e+03 pdb=" N ILE A 421 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 904 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1376 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A1377 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " 0.030 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 227 2.67 - 3.23: 14718 3.23 - 3.78: 23795 3.78 - 4.34: 33413 4.34 - 4.90: 57427 Nonbonded interactions: 129580 Sorted by model distance: nonbonded pdb=" O2' G R 33 " pdb=" O4' G R 34 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR A 435 " pdb=" OD1 ASP A 437 " model vdw 2.234 3.040 nonbonded pdb=" NZ LYS A1580 " pdb=" OP2 C R 30 " model vdw 2.239 3.120 nonbonded pdb=" NH2 ARG A 876 " pdb=" O ASP A1308 " model vdw 2.242 3.120 nonbonded pdb=" O GLU B 344 " pdb=" OG1 THR B 347 " model vdw 2.255 3.040 ... (remaining 129575 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 46.200 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 0.055 17398 Z= 0.212 Angle : 0.682 8.383 23615 Z= 0.394 Chirality : 0.042 0.212 2501 Planarity : 0.004 0.058 2941 Dihedral : 14.804 93.927 6904 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1959 helix: 1.56 (0.19), residues: 765 sheet: -0.30 (0.30), residues: 277 loop : -1.37 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 457 HIS 0.009 0.001 HIS B 253 PHE 0.023 0.001 PHE A 197 TYR 0.031 0.001 TYR B 209 ARG 0.009 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.17304 ( 669) hydrogen bonds : angle 6.10985 ( 1941) metal coordination : bond 0.01786 ( 14) metal coordination : angle 3.77492 ( 15) covalent geometry : bond 0.00381 (17384) covalent geometry : angle 0.67578 (23600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.808 Fit side-chains REVERT: B 232 GLN cc_start: 0.8095 (mm110) cc_final: 0.7488 (tt0) REVERT: A 664 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6278 (pt0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 1.5869 time to fit residues: 392.8855 Evaluate side-chains 137 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 0.4980 chunk 181 optimal weight: 10.0000 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1366 ASN A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.147272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110329 restraints weight = 22261.960| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.34 r_work: 0.3155 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17398 Z= 0.113 Angle : 0.500 7.232 23615 Z= 0.257 Chirality : 0.039 0.185 2501 Planarity : 0.004 0.043 2941 Dihedral : 11.512 90.363 2772 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.02 % Allowed : 8.26 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1959 helix: 1.96 (0.19), residues: 765 sheet: -0.12 (0.29), residues: 275 loop : -1.27 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 544 HIS 0.005 0.001 HIS A1483 PHE 0.012 0.001 PHE A1456 TYR 0.012 0.001 TYR B 188 ARG 0.008 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 669) hydrogen bonds : angle 4.40808 ( 1941) metal coordination : bond 0.00368 ( 14) metal coordination : angle 3.32959 ( 15) covalent geometry : bond 0.00257 (17384) covalent geometry : angle 0.49275 (23600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 2.141 Fit side-chains REVERT: B 24 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6069 (mpp) REVERT: B 34 GLU cc_start: 0.7421 (tp30) cc_final: 0.7022 (mt-10) REVERT: B 150 MET cc_start: 0.7815 (mmt) cc_final: 0.7208 (mmt) REVERT: B 377 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.6133 (mmp80) REVERT: B 378 ARG cc_start: 0.5270 (tmt170) cc_final: 0.4984 (tpt90) REVERT: B 481 ASN cc_start: 0.6949 (OUTLIER) cc_final: 0.6613 (p0) REVERT: B 559 ASP cc_start: 0.7279 (p0) cc_final: 0.7046 (p0) REVERT: B 667 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6586 (tm-30) REVERT: A 199 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8348 (ttt180) REVERT: A 361 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6962 (mp) REVERT: A 422 ASP cc_start: 0.7637 (t0) cc_final: 0.7391 (t0) REVERT: A 491 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: A 513 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: A 816 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8034 (mm-40) REVERT: A 1299 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6763 (ptt90) REVERT: A 1321 ASP cc_start: 0.7995 (p0) cc_final: 0.7777 (p0) REVERT: A 1395 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.6722 (mmm160) REVERT: A 1513 ARG cc_start: 0.7875 (ptm160) cc_final: 0.7674 (ptm160) outliers start: 35 outliers final: 11 residues processed: 162 average time/residue: 1.8969 time to fit residues: 337.4061 Evaluate side-chains 147 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 376 ASN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1395 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 166 optimal weight: 0.0070 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104407 restraints weight = 22384.713| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.34 r_work: 0.3072 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17398 Z= 0.204 Angle : 0.580 7.525 23615 Z= 0.303 Chirality : 0.043 0.170 2501 Planarity : 0.004 0.049 2941 Dihedral : 11.671 94.174 2772 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.43 % Allowed : 9.94 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 1959 helix: 1.72 (0.19), residues: 762 sheet: -0.20 (0.30), residues: 265 loop : -1.44 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1466 HIS 0.007 0.001 HIS A1483 PHE 0.017 0.002 PHE A1456 TYR 0.015 0.002 TYR B 551 ARG 0.007 0.001 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.05953 ( 669) hydrogen bonds : angle 4.48709 ( 1941) metal coordination : bond 0.00688 ( 14) metal coordination : angle 3.45119 ( 15) covalent geometry : bond 0.00496 (17384) covalent geometry : angle 0.57381 (23600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.806 Fit side-chains REVERT: B 24 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6082 (mpp) REVERT: B 34 GLU cc_start: 0.7730 (tp30) cc_final: 0.7474 (tp30) REVERT: B 145 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7076 (mtt90) REVERT: B 229 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6636 (ptm) REVERT: B 232 GLN cc_start: 0.8374 (mm110) cc_final: 0.7206 (tt0) REVERT: B 377 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.6204 (mmt-90) REVERT: B 542 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7790 (mm) REVERT: B 667 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6846 (tm-30) REVERT: A 199 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (ttt180) REVERT: A 267 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: A 290 ARG cc_start: 0.7222 (tmm160) cc_final: 0.6985 (tmm160) REVERT: A 361 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 422 ASP cc_start: 0.8045 (t0) cc_final: 0.7836 (t0) REVERT: A 491 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: A 513 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: A 664 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 816 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8139 (mm-40) REVERT: A 1299 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7047 (ptt90) REVERT: A 1321 ASP cc_start: 0.8007 (p0) cc_final: 0.7645 (p0) REVERT: A 1395 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7347 (mmt90) REVERT: A 1578 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7587 (pp20) outliers start: 42 outliers final: 16 residues processed: 175 average time/residue: 1.6786 time to fit residues: 321.4920 Evaluate side-chains 156 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1565 ARG Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105260 restraints weight = 22282.087| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.22 r_work: 0.3095 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17398 Z= 0.170 Angle : 0.537 8.459 23615 Z= 0.280 Chirality : 0.041 0.177 2501 Planarity : 0.004 0.054 2941 Dihedral : 11.642 94.798 2772 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.77 % Allowed : 10.57 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 1959 helix: 1.82 (0.19), residues: 754 sheet: -0.14 (0.30), residues: 267 loop : -1.47 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1466 HIS 0.006 0.001 HIS B 427 PHE 0.013 0.002 PHE A 776 TYR 0.013 0.001 TYR A 492 ARG 0.005 0.000 ARG A 645 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 669) hydrogen bonds : angle 4.29828 ( 1941) metal coordination : bond 0.00617 ( 14) metal coordination : angle 3.30254 ( 15) covalent geometry : bond 0.00414 (17384) covalent geometry : angle 0.53033 (23600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 1.825 Fit side-chains REVERT: B 24 MET cc_start: 0.6563 (OUTLIER) cc_final: 0.6083 (mpp) REVERT: B 34 GLU cc_start: 0.7740 (tp30) cc_final: 0.7161 (mt-10) REVERT: B 38 MET cc_start: 0.7403 (tpp) cc_final: 0.7083 (tpp) REVERT: B 145 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: B 166 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: B 229 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6702 (ptm) REVERT: B 232 GLN cc_start: 0.8487 (mm110) cc_final: 0.7244 (tt0) REVERT: B 481 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.6944 (p0) REVERT: B 542 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7865 (mm) REVERT: A 199 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8452 (ttt180) REVERT: A 290 ARG cc_start: 0.7213 (tmm160) cc_final: 0.6953 (tmm160) REVERT: A 361 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6983 (mp) REVERT: A 422 ASP cc_start: 0.8120 (t0) cc_final: 0.7874 (t0) REVERT: A 491 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8090 (mm-30) REVERT: A 513 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7197 (tm-30) REVERT: A 740 ASP cc_start: 0.8410 (p0) cc_final: 0.8133 (p0) REVERT: A 816 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8164 (mm-40) REVERT: A 1299 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7109 (ptt90) REVERT: A 1321 ASP cc_start: 0.7965 (p0) cc_final: 0.7571 (p0) REVERT: A 1395 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7310 (mmt90) REVERT: A 1578 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7644 (pp20) outliers start: 48 outliers final: 18 residues processed: 175 average time/residue: 2.1674 time to fit residues: 418.0513 Evaluate side-chains 166 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 70 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.0770 chunk 165 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 123 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105683 restraints weight = 22461.603| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17398 Z= 0.156 Angle : 0.518 7.602 23615 Z= 0.271 Chirality : 0.041 0.174 2501 Planarity : 0.004 0.054 2941 Dihedral : 11.625 95.011 2772 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.77 % Allowed : 11.55 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1959 helix: 1.90 (0.19), residues: 753 sheet: -0.06 (0.30), residues: 269 loop : -1.49 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1466 HIS 0.005 0.001 HIS B 427 PHE 0.013 0.001 PHE A 776 TYR 0.012 0.001 TYR A 492 ARG 0.006 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 669) hydrogen bonds : angle 4.21814 ( 1941) metal coordination : bond 0.00622 ( 14) metal coordination : angle 3.26554 ( 15) covalent geometry : bond 0.00377 (17384) covalent geometry : angle 0.51120 (23600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 1.875 Fit side-chains REVERT: B 24 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6075 (mpp) REVERT: B 34 GLU cc_start: 0.7742 (tp30) cc_final: 0.7157 (mt-10) REVERT: B 118 ASP cc_start: 0.7628 (m-30) cc_final: 0.7150 (t0) REVERT: B 145 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7103 (mtt90) REVERT: B 166 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: B 229 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6733 (ptm) REVERT: B 232 GLN cc_start: 0.8476 (mm110) cc_final: 0.7228 (tt0) REVERT: B 481 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6888 (p0) REVERT: B 542 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7868 (mm) REVERT: B 632 ASN cc_start: 0.7802 (t0) cc_final: 0.7590 (t0) REVERT: A 267 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 290 ARG cc_start: 0.7264 (tmm160) cc_final: 0.6991 (tmm160) REVERT: A 361 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6956 (mp) REVERT: A 422 ASP cc_start: 0.8099 (t0) cc_final: 0.7807 (t0) REVERT: A 491 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: A 513 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 740 ASP cc_start: 0.8406 (p0) cc_final: 0.8150 (p0) REVERT: A 816 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8150 (mm-40) REVERT: A 1299 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7077 (ptt90) REVERT: A 1321 ASP cc_start: 0.7975 (p0) cc_final: 0.7568 (p0) REVERT: A 1365 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7466 (mm-30) REVERT: A 1395 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7275 (mmt90) REVERT: A 1578 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7644 (pp20) outliers start: 48 outliers final: 21 residues processed: 174 average time/residue: 1.5862 time to fit residues: 304.1654 Evaluate side-chains 166 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 126 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106358 restraints weight = 22357.906| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.40 r_work: 0.3101 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17398 Z= 0.133 Angle : 0.494 7.481 23615 Z= 0.258 Chirality : 0.040 0.168 2501 Planarity : 0.004 0.052 2941 Dihedral : 11.585 94.995 2772 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.72 % Allowed : 12.36 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1959 helix: 1.95 (0.19), residues: 758 sheet: 0.02 (0.30), residues: 272 loop : -1.51 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1466 HIS 0.004 0.001 HIS B 427 PHE 0.013 0.001 PHE A 776 TYR 0.012 0.001 TYR A 492 ARG 0.004 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 669) hydrogen bonds : angle 4.12228 ( 1941) metal coordination : bond 0.00516 ( 14) metal coordination : angle 3.22490 ( 15) covalent geometry : bond 0.00316 (17384) covalent geometry : angle 0.48700 (23600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 1.775 Fit side-chains REVERT: B 24 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.6056 (mpp) REVERT: B 34 GLU cc_start: 0.7737 (tp30) cc_final: 0.7129 (mt-10) REVERT: B 38 MET cc_start: 0.7345 (tpp) cc_final: 0.7022 (tpp) REVERT: B 118 ASP cc_start: 0.7620 (m-30) cc_final: 0.7142 (t0) REVERT: B 145 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7064 (mtt90) REVERT: B 166 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: B 229 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6726 (ptm) REVERT: B 481 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6823 (p0) REVERT: B 542 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7845 (mm) REVERT: B 632 ASN cc_start: 0.7789 (t0) cc_final: 0.7557 (t0) REVERT: A 267 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: A 290 ARG cc_start: 0.7259 (tmm160) cc_final: 0.6985 (tmm160) REVERT: A 343 LYS cc_start: 0.7862 (tptp) cc_final: 0.7566 (tppp) REVERT: A 422 ASP cc_start: 0.8078 (t0) cc_final: 0.7777 (t0) REVERT: A 491 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: A 513 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: A 740 ASP cc_start: 0.8350 (p0) cc_final: 0.8111 (p0) REVERT: A 1299 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7123 (ptt90) REVERT: A 1321 ASP cc_start: 0.7947 (p0) cc_final: 0.7525 (p0) REVERT: A 1365 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7406 (mm-30) REVERT: A 1395 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7257 (mmt90) outliers start: 47 outliers final: 21 residues processed: 176 average time/residue: 1.5708 time to fit residues: 306.8973 Evaluate side-chains 163 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 108 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 177 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104485 restraints weight = 22349.309| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.28 r_work: 0.3078 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17398 Z= 0.199 Angle : 0.561 7.881 23615 Z= 0.292 Chirality : 0.042 0.191 2501 Planarity : 0.004 0.055 2941 Dihedral : 11.631 96.011 2772 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.89 % Allowed : 13.00 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1959 helix: 1.83 (0.19), residues: 753 sheet: -0.06 (0.30), residues: 271 loop : -1.58 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 693 HIS 0.006 0.001 HIS B 427 PHE 0.014 0.002 PHE A 776 TYR 0.013 0.001 TYR B 478 ARG 0.005 0.000 ARG A1294 Details of bonding type rmsd hydrogen bonds : bond 0.05487 ( 669) hydrogen bonds : angle 4.28320 ( 1941) metal coordination : bond 0.00868 ( 14) metal coordination : angle 3.27170 ( 15) covalent geometry : bond 0.00486 (17384) covalent geometry : angle 0.55461 (23600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 1.781 Fit side-chains REVERT: B 24 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6058 (mpp) REVERT: B 34 GLU cc_start: 0.7791 (tp30) cc_final: 0.7198 (mt-10) REVERT: B 118 ASP cc_start: 0.7626 (m-30) cc_final: 0.7151 (t0) REVERT: B 145 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7168 (mtt90) REVERT: B 166 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6504 (pm20) REVERT: B 229 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6745 (ptm) REVERT: B 542 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7899 (mm) REVERT: B 632 ASN cc_start: 0.7801 (t0) cc_final: 0.7568 (t0) REVERT: B 736 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7762 (tt) REVERT: A 199 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8428 (ttt180) REVERT: A 267 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: A 290 ARG cc_start: 0.7327 (tmm160) cc_final: 0.7055 (tmm160) REVERT: A 343 LYS cc_start: 0.7893 (tptp) cc_final: 0.7622 (tppp) REVERT: A 361 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7188 (mp) REVERT: A 422 ASP cc_start: 0.8116 (t0) cc_final: 0.7810 (t0) REVERT: A 426 LYS cc_start: 0.8119 (mttt) cc_final: 0.7723 (mtmp) REVERT: A 491 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: A 513 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: A 740 ASP cc_start: 0.8369 (p0) cc_final: 0.8101 (p0) REVERT: A 816 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8178 (mm-40) REVERT: A 1299 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7165 (ptt90) REVERT: A 1321 ASP cc_start: 0.7927 (p0) cc_final: 0.7500 (p0) REVERT: A 1395 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7287 (mmt90) outliers start: 50 outliers final: 25 residues processed: 168 average time/residue: 1.5079 time to fit residues: 279.5815 Evaluate side-chains 164 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1393 ARG Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106369 restraints weight = 22257.360| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.22 r_work: 0.3109 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17398 Z= 0.131 Angle : 0.504 7.334 23615 Z= 0.262 Chirality : 0.040 0.193 2501 Planarity : 0.004 0.053 2941 Dihedral : 11.576 95.362 2772 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.25 % Allowed : 13.92 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1959 helix: 1.95 (0.19), residues: 758 sheet: 0.05 (0.30), residues: 274 loop : -1.54 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 693 HIS 0.004 0.001 HIS B 427 PHE 0.013 0.001 PHE A 776 TYR 0.012 0.001 TYR A 492 ARG 0.004 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 669) hydrogen bonds : angle 4.11440 ( 1941) metal coordination : bond 0.00527 ( 14) metal coordination : angle 3.15476 ( 15) covalent geometry : bond 0.00310 (17384) covalent geometry : angle 0.49760 (23600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 2.354 Fit side-chains REVERT: B 24 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6025 (mpp) REVERT: B 34 GLU cc_start: 0.7716 (tp30) cc_final: 0.7114 (mt-10) REVERT: B 118 ASP cc_start: 0.7594 (m-30) cc_final: 0.7120 (t0) REVERT: B 145 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7034 (mtt90) REVERT: B 166 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: B 229 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6817 (ptm) REVERT: B 232 GLN cc_start: 0.8381 (mm110) cc_final: 0.7137 (tt0) REVERT: B 481 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6807 (p0) REVERT: B 542 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7822 (mm) REVERT: B 632 ASN cc_start: 0.7799 (t0) cc_final: 0.7590 (t0) REVERT: B 736 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7725 (tt) REVERT: A 267 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7235 (tm-30) REVERT: A 290 ARG cc_start: 0.7254 (tmm160) cc_final: 0.6986 (tmm160) REVERT: A 343 LYS cc_start: 0.7863 (tptp) cc_final: 0.7600 (tppp) REVERT: A 361 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7108 (mp) REVERT: A 422 ASP cc_start: 0.7986 (t0) cc_final: 0.7672 (t0) REVERT: A 426 LYS cc_start: 0.8080 (mttt) cc_final: 0.7684 (mtmp) REVERT: A 491 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: A 513 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: A 740 ASP cc_start: 0.8260 (p0) cc_final: 0.7986 (p0) REVERT: A 1299 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7132 (ptt90) REVERT: A 1321 ASP cc_start: 0.7908 (p0) cc_final: 0.7473 (p0) REVERT: A 1365 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7397 (mm-30) REVERT: A 1395 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7242 (mmt90) outliers start: 39 outliers final: 21 residues processed: 166 average time/residue: 2.0158 time to fit residues: 372.5733 Evaluate side-chains 161 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 338 MET Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1299 ARG Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 28 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 chunk 151 optimal weight: 0.0010 chunk 198 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108985 restraints weight = 22329.998| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.27 r_work: 0.3151 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17398 Z= 0.096 Angle : 0.468 6.595 23615 Z= 0.242 Chirality : 0.038 0.202 2501 Planarity : 0.004 0.047 2941 Dihedral : 11.441 93.992 2772 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 14.50 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1959 helix: 2.10 (0.19), residues: 759 sheet: 0.16 (0.30), residues: 278 loop : -1.45 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 693 HIS 0.003 0.000 HIS A1483 PHE 0.012 0.001 PHE A 776 TYR 0.011 0.001 TYR A 492 ARG 0.007 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 669) hydrogen bonds : angle 3.90680 ( 1941) metal coordination : bond 0.00354 ( 14) metal coordination : angle 3.02132 ( 15) covalent geometry : bond 0.00219 (17384) covalent geometry : angle 0.46225 (23600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 2.018 Fit side-chains REVERT: B 24 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.5903 (mpp) REVERT: B 34 GLU cc_start: 0.7630 (tp30) cc_final: 0.6992 (mt-10) REVERT: B 118 ASP cc_start: 0.7574 (m-30) cc_final: 0.7083 (t0) REVERT: B 229 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6783 (ptm) REVERT: B 377 ARG cc_start: 0.6116 (mmp80) cc_final: 0.5768 (mmp80) REVERT: B 378 ARG cc_start: 0.5489 (tmt170) cc_final: 0.5243 (tpt90) REVERT: B 458 GLN cc_start: 0.8119 (mt0) cc_final: 0.7843 (tt0) REVERT: B 481 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6596 (p0) REVERT: B 542 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7782 (mm) REVERT: B 632 ASN cc_start: 0.7834 (t0) cc_final: 0.7630 (t0) REVERT: B 724 GLU cc_start: 0.6149 (mp0) cc_final: 0.5926 (mp0) REVERT: A 267 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: A 290 ARG cc_start: 0.7203 (tmm160) cc_final: 0.6931 (tmm160) REVERT: A 297 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7405 (ptmm) REVERT: A 343 LYS cc_start: 0.7790 (tptp) cc_final: 0.7554 (tppp) REVERT: A 422 ASP cc_start: 0.7924 (t0) cc_final: 0.7609 (t0) REVERT: A 426 LYS cc_start: 0.8092 (mttt) cc_final: 0.7668 (mtmt) REVERT: A 491 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7989 (mm-30) REVERT: A 740 ASP cc_start: 0.8159 (p0) cc_final: 0.7909 (p0) REVERT: A 1321 ASP cc_start: 0.7935 (p0) cc_final: 0.7502 (p0) REVERT: A 1365 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7408 (mm-30) REVERT: A 1395 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7185 (mmt90) REVERT: A 1497 GLU cc_start: 0.8048 (tt0) cc_final: 0.7793 (tt0) outliers start: 30 outliers final: 16 residues processed: 162 average time/residue: 1.6084 time to fit residues: 288.1836 Evaluate side-chains 153 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104217 restraints weight = 22399.905| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.28 r_work: 0.3073 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17398 Z= 0.222 Angle : 0.588 8.228 23615 Z= 0.305 Chirality : 0.043 0.227 2501 Planarity : 0.005 0.056 2941 Dihedral : 11.575 96.123 2772 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.50 % Allowed : 15.37 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1959 helix: 1.83 (0.19), residues: 761 sheet: 0.05 (0.30), residues: 271 loop : -1.57 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 693 HIS 0.008 0.001 HIS B 427 PHE 0.015 0.002 PHE A 776 TYR 0.014 0.002 TYR B 478 ARG 0.005 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.05679 ( 669) hydrogen bonds : angle 4.26898 ( 1941) metal coordination : bond 0.01005 ( 14) metal coordination : angle 3.32860 ( 15) covalent geometry : bond 0.00542 (17384) covalent geometry : angle 0.58176 (23600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3918 Ramachandran restraints generated. 1959 Oldfield, 0 Emsley, 1959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 2.048 Fit side-chains REVERT: B 24 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6043 (mpp) REVERT: B 34 GLU cc_start: 0.7799 (tp30) cc_final: 0.7206 (mt-10) REVERT: B 118 ASP cc_start: 0.7620 (m-30) cc_final: 0.7153 (t0) REVERT: B 190 GLU cc_start: 0.7834 (mp0) cc_final: 0.7611 (tp30) REVERT: B 229 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6848 (ptm) REVERT: B 542 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7769 (mm) REVERT: B 632 ASN cc_start: 0.7874 (t0) cc_final: 0.7661 (t0) REVERT: A 290 ARG cc_start: 0.7336 (tmm160) cc_final: 0.7056 (tmm160) REVERT: A 343 LYS cc_start: 0.7896 (tptp) cc_final: 0.7643 (tppp) REVERT: A 422 ASP cc_start: 0.8008 (t0) cc_final: 0.7692 (t0) REVERT: A 491 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: A 740 ASP cc_start: 0.8355 (p0) cc_final: 0.8069 (p0) REVERT: A 771 MET cc_start: 0.8501 (mmm) cc_final: 0.8299 (mmm) REVERT: A 1321 ASP cc_start: 0.7888 (p0) cc_final: 0.7433 (p0) REVERT: A 1395 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7317 (mmt90) outliers start: 26 outliers final: 15 residues processed: 145 average time/residue: 1.5335 time to fit residues: 246.2457 Evaluate side-chains 140 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 1395 ARG Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1581 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 156 optimal weight: 0.0010 chunk 145 optimal weight: 0.0060 chunk 154 optimal weight: 4.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 HIS ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.145605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108976 restraints weight = 22284.443| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.23 r_work: 0.3151 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17398 Z= 0.095 Angle : 0.480 7.060 23615 Z= 0.248 Chirality : 0.038 0.193 2501 Planarity : 0.004 0.049 2941 Dihedral : 11.474 94.602 2772 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.33 % Allowed : 15.66 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1959 helix: 2.06 (0.19), residues: 758 sheet: 0.15 (0.30), residues: 280 loop : -1.43 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 693 HIS 0.004 0.000 HIS A1483 PHE 0.011 0.001 PHE A 776 TYR 0.012 0.001 TYR A 492 ARG 0.007 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 669) hydrogen bonds : angle 3.92081 ( 1941) metal coordination : bond 0.00321 ( 14) metal coordination : angle 3.07467 ( 15) covalent geometry : bond 0.00214 (17384) covalent geometry : angle 0.47377 (23600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13329.06 seconds wall clock time: 234 minutes 55.88 seconds (14095.88 seconds total)