Starting phenix.real_space_refine on Sat Feb 17 12:47:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9x_33695/02_2024/7y9x_33695.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9x_33695/02_2024/7y9x_33695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9x_33695/02_2024/7y9x_33695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9x_33695/02_2024/7y9x_33695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9x_33695/02_2024/7y9x_33695.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9x_33695/02_2024/7y9x_33695.pdb" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 37 5.49 5 S 82 5.16 5 C 11675 2.51 5 N 3279 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18662 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 6100 Classifications: {'peptide': 734} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 705} Chain breaks: 3 Chain: "A" Number of atoms: 11757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11757 Classifications: {'peptide': 1458} Link IDs: {'PTRANS': 80, 'TRANS': 1377} Chain breaks: 7 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9480 SG CYS A 463 53.234 47.188 50.151 1.00 30.75 S ATOM 9542 SG CYS A 472 52.720 46.575 46.490 1.00 20.27 S ATOM 9556 SG CYS A 474 55.530 44.820 48.140 1.00 18.75 S ATOM 9578 SG CYS A 477 51.964 43.813 49.066 1.00 22.67 S ATOM 11396 SG CYS A 706 59.788 61.985 74.738 1.00 26.90 S ATOM 11411 SG CYS A 708 62.693 60.033 76.135 1.00 26.45 S ATOM 11433 SG CYS A 711 59.555 58.181 74.794 1.00 27.20 S ATOM 13321 SG CYS A 965 57.303 59.788 113.258 1.00 4.19 S ATOM 15508 SG CYS A1312 56.557 62.405 110.592 1.00 0.00 S ATOM 15747 SG CYS A1342 60.130 61.592 111.411 1.00 11.80 S ATOM 15765 SG CYS A1345 58.132 59.188 109.443 1.00 12.63 S ATOM 6804 SG CYS A 86 37.102 32.582 23.551 1.00 54.96 S ATOM 7050 SG CYS A 115 33.948 31.679 22.886 1.00 51.87 S ATOM 7112 SG CYS A 123 36.120 29.686 25.705 1.00 42.82 S ATOM 7136 SG CYS A 126 34.260 32.609 26.602 1.00 45.37 S Time building chain proxies: 10.01, per 1000 atoms: 0.54 Number of scatterers: 18662 At special positions: 0 Unit cell: (100.43, 102.92, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 82 16.00 P 37 15.00 O 3585 8.00 N 3279 7.00 C 11675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 472 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 477 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 706 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 965 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 115 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " Number of angles added : 21 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4118 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 26 sheets defined 41.1% alpha, 20.7% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 6.72 Creating SS restraints... Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.733A pdb=" N THR B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 removed outlier: 3.862A pdb=" N MET B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 92 through 113 removed outlier: 4.827A pdb=" N ASN B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 110 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 143 through 164 removed outlier: 3.797A pdb=" N LYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.785A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.607A pdb=" N LEU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 278 through 293 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 360 through 374 Processing helix chain 'B' and resid 376 through 393 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.549A pdb=" N ARG B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 419 " --> pdb=" O PHE B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 419' Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 464 through 481 Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.828A pdb=" N GLU B 497 " --> pdb=" O CYS B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.533A pdb=" N LEU B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 595 through 605 removed outlier: 3.638A pdb=" N GLU B 605 " --> pdb=" O GLU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 625 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 675 through 682 Processing helix chain 'B' and resid 696 through 711 Processing helix chain 'B' and resid 712 through 732 removed outlier: 3.741A pdb=" N GLN B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 731 " --> pdb=" O ASN B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.707A pdb=" N PHE B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.768A pdb=" N ARG A 26 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.235A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 301' Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 344 through 367 removed outlier: 3.534A pdb=" N LYS A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 removed outlier: 3.510A pdb=" N ARG A 598 " --> pdb=" O TRP A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.652A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 608 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.791A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.649A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.630A pdb=" N GLU A1032 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1302 through 1305 removed outlier: 3.581A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1302 through 1305' Processing helix chain 'A' and resid 1321 through 1326 removed outlier: 3.575A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1336 removed outlier: 3.650A pdb=" N ARG A1332 " --> pdb=" O PRO A1329 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A1336 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 3.879A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 removed outlier: 3.607A pdb=" N GLY A1492 " --> pdb=" O LYS A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1539 through 1548 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.966A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1594 removed outlier: 3.578A pdb=" N LYS A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 314 through 315 Processing sheet with id=AA2, first strand: chain 'B' and resid 457 through 462 removed outlier: 6.459A pdb=" N ILE B 424 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 518 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 426 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 532 through 533 Processing sheet with id=AA4, first strand: chain 'B' and resid 589 through 590 removed outlier: 7.018A pdb=" N SER B 569 " --> pdb=" O GLU B 589 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 610 " --> pdb=" O LEU B 654 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY B 691 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 615 through 617 removed outlier: 4.060A pdb=" N HIS B 615 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 148 through 150 removed outlier: 3.548A pdb=" N LYS A 6 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.835A pdb=" N TRP A 42 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 107 removed outlier: 5.892A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.759A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.759A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AB4, first strand: chain 'A' and resid 497 through 504 removed outlier: 11.047A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.273A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.273A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 655 through 656 removed outlier: 7.128A pdb=" N VAL A 655 " --> pdb=" O SER A 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 692 through 693 Processing sheet with id=AB9, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 4.537A pdb=" N ARG A1558 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 861 " --> pdb=" O TRP A1600 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AC2, first strand: chain 'A' and resid 938 through 939 removed outlier: 6.542A pdb=" N ILE A 943 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 5.420A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.329A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 936 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 974 through 978 removed outlier: 5.501A pdb=" N LEU A 975 " --> pdb=" O ASP A1297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1128 through 1130 removed outlier: 3.800A pdb=" N LYS A1128 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 19.138A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.120A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A1217 " --> pdb=" O HIS A1149 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL A1284 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU A1229 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ASP A1286 " --> pdb=" O GLU A1229 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1156 through 1159 Processing sheet with id=AC8, first strand: chain 'A' and resid 1187 through 1190 removed outlier: 7.410A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 9.58 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5784 1.33 - 1.46: 3700 1.46 - 1.58: 9482 1.58 - 1.70: 74 1.70 - 1.82: 122 Bond restraints: 19162 Sorted by residual: bond pdb=" CB THR A 653 " pdb=" CG2 THR A 653 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" N PRO A 495 " pdb=" CA PRO A 495 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 9.46e-01 bond pdb=" CB VAL A 521 " pdb=" CG1 VAL A 521 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.09e-01 bond pdb=" CG1 ILE A 856 " pdb=" CD1 ILE A 856 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.78e-01 ... (remaining 19157 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.01: 615 106.01 - 113.01: 10089 113.01 - 120.02: 6620 120.02 - 127.03: 8357 127.03 - 134.04: 316 Bond angle restraints: 25997 Sorted by residual: angle pdb=" N ILE B 740 " pdb=" CA ILE B 740 " pdb=" C ILE B 740 " ideal model delta sigma weight residual 112.96 109.59 3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" N VAL A 907 " pdb=" CA VAL A 907 " pdb=" C VAL A 907 " ideal model delta sigma weight residual 108.15 105.61 2.54 9.90e-01 1.02e+00 6.57e+00 angle pdb=" C ASP B 39 " pdb=" N SER B 40 " pdb=" CA SER B 40 " ideal model delta sigma weight residual 122.21 118.74 3.47 1.48e+00 4.57e-01 5.50e+00 angle pdb=" CA ILE B 740 " pdb=" C ILE B 740 " pdb=" N ALA B 741 " ideal model delta sigma weight residual 118.65 116.27 2.38 1.07e+00 8.73e-01 4.96e+00 angle pdb=" CA ASN B 402 " pdb=" C ASN B 402 " pdb=" N PRO B 403 " ideal model delta sigma weight residual 117.69 119.68 -1.99 9.50e-01 1.11e+00 4.39e+00 ... (remaining 25992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.93: 11262 19.93 - 39.87: 318 39.87 - 59.80: 83 59.80 - 79.74: 35 79.74 - 99.67: 4 Dihedral angle restraints: 11702 sinusoidal: 5335 harmonic: 6367 Sorted by residual: dihedral pdb=" O4' A R 12 " pdb=" C1' A R 12 " pdb=" N9 A R 12 " pdb=" C4 A R 12 " ideal model delta sinusoidal sigma weight residual -106.00 -157.95 51.95 1 1.70e+01 3.46e-03 1.27e+01 dihedral pdb=" CA CYS A 86 " pdb=" C CYS A 86 " pdb=" N PRO A 87 " pdb=" CA PRO A 87 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG A1299 " pdb=" C ARG A1299 " pdb=" N MET A1300 " pdb=" CA MET A1300 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1642 0.031 - 0.062: 783 0.062 - 0.093: 204 0.093 - 0.124: 95 0.124 - 0.154: 17 Chirality restraints: 2741 Sorted by residual: chirality pdb=" CA VAL B 142 " pdb=" N VAL B 142 " pdb=" C VAL B 142 " pdb=" CB VAL B 142 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA PRO A 864 " pdb=" N PRO A 864 " pdb=" C PRO A 864 " pdb=" CB PRO A 864 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C1' A R 13 " pdb=" O4' A R 13 " pdb=" C2' A R 13 " pdb=" N9 A R 13 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 2738 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 904 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 864 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " 0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A 436 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.020 5.00e-02 4.00e+02 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 343 2.68 - 3.24: 17314 3.24 - 3.79: 29577 3.79 - 4.35: 43480 4.35 - 4.90: 67834 Nonbonded interactions: 158548 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" OD1 ASP B 210 " model vdw 2.130 2.440 nonbonded pdb=" OE2 GLU B 432 " pdb=" OG SER B 669 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG A 689 " pdb=" OE2 GLU A1461 " model vdw 2.210 2.520 nonbonded pdb=" NH2 ARG A 227 " pdb=" OG1 THR A 484 " model vdw 2.225 2.520 nonbonded pdb=" O GLN B 721 " pdb=" OG1 THR B 725 " model vdw 2.232 2.440 ... (remaining 158543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 9.470 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: 0.000 Extract box with map and model: 13.770 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 59.040 Find NCS groups from input model: 0.490 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: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19162 Z= 0.237 Angle : 0.516 5.521 25997 Z= 0.277 Chirality : 0.040 0.154 2741 Planarity : 0.005 0.050 3260 Dihedral : 11.111 99.675 7584 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.31 % Allowed : 2.24 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2168 helix: -0.21 (0.17), residues: 754 sheet: 0.94 (0.27), residues: 346 loop : -0.25 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 326 HIS 0.007 0.001 HIS A 871 PHE 0.018 0.002 PHE A 187 TYR 0.014 0.002 TYR B 333 ARG 0.008 0.001 ARG A1346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 329 time to evaluate : 2.057 Fit side-chains REVERT: B 32 LYS cc_start: 0.8049 (tttt) cc_final: 0.7818 (ttpp) REVERT: B 62 GLN cc_start: 0.7640 (mt0) cc_final: 0.7437 (mt0) REVERT: B 85 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7413 (mm-30) REVERT: B 198 TYR cc_start: 0.7237 (m-80) cc_final: 0.6778 (m-80) REVERT: B 400 ARG cc_start: 0.7000 (mtp180) cc_final: 0.6601 (mtm-85) REVERT: B 541 GLU cc_start: 0.7490 (tt0) cc_final: 0.7265 (tp30) REVERT: B 668 PHE cc_start: 0.7965 (m-80) cc_final: 0.7703 (m-80) REVERT: B 722 MET cc_start: 0.7776 (mtp) cc_final: 0.7549 (mtp) REVERT: A 311 ASP cc_start: 0.6249 (t0) cc_final: 0.6037 (t0) REVERT: A 387 ASP cc_start: 0.7653 (t0) cc_final: 0.7325 (m-30) REVERT: A 426 LYS cc_start: 0.7957 (mttt) cc_final: 0.7743 (mmtt) REVERT: A 605 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6745 (mm-30) REVERT: A 816 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7417 (tp40) REVERT: A 1239 LYS cc_start: 0.7775 (tttt) cc_final: 0.7529 (tttp) REVERT: A 1358 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7200 (mtm-85) REVERT: A 1393 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.7237 (ptt-90) outliers start: 6 outliers final: 2 residues processed: 335 average time/residue: 1.8533 time to fit residues: 677.8434 Evaluate side-chains 203 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 36 GLN B 75 GLN B 235 GLN B 256 GLN B 329 GLN B 389 GLN B 481 ASN A 170 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN A1246 ASN A1590 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19162 Z= 0.244 Angle : 0.540 5.673 25997 Z= 0.289 Chirality : 0.042 0.194 2741 Planarity : 0.005 0.046 3260 Dihedral : 11.969 100.960 3004 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.66 % Allowed : 8.54 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2168 helix: 0.82 (0.18), residues: 775 sheet: 0.45 (0.26), residues: 379 loop : -0.09 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 474 HIS 0.006 0.001 HIS A 871 PHE 0.014 0.002 PHE A 757 TYR 0.012 0.002 TYR A 492 ARG 0.005 0.001 ARG A1358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 206 time to evaluate : 2.030 Fit side-chains revert: symmetry clash REVERT: B 16 LYS cc_start: 0.7209 (mmmt) cc_final: 0.6928 (mmmt) REVERT: B 24 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7000 (mmm) REVERT: B 32 LYS cc_start: 0.8000 (tttt) cc_final: 0.7795 (ttpp) REVERT: B 38 MET cc_start: 0.8106 (mtp) cc_final: 0.7861 (mtt) REVERT: B 62 GLN cc_start: 0.7580 (mt0) cc_final: 0.7373 (mt0) REVERT: B 94 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6597 (tttm) REVERT: B 198 TYR cc_start: 0.7295 (m-80) cc_final: 0.6974 (m-80) REVERT: B 362 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6363 (tm-30) REVERT: B 377 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6058 (mmt180) REVERT: B 389 GLN cc_start: 0.7940 (tt0) cc_final: 0.7472 (pt0) REVERT: B 400 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6778 (mtm-85) REVERT: B 483 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: A 3 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 97 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6937 (ptt90) REVERT: A 311 ASP cc_start: 0.6253 (t0) cc_final: 0.6033 (t0) REVERT: A 314 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8312 (tp) REVERT: A 387 ASP cc_start: 0.7678 (t0) cc_final: 0.7396 (m-30) REVERT: A 426 LYS cc_start: 0.7941 (mttt) cc_final: 0.7720 (mmtt) REVERT: A 559 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8046 (mmm) REVERT: A 605 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6771 (mm-30) REVERT: A 816 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7520 (tp40) REVERT: A 857 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: A 973 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7746 (ttmp) REVERT: A 1037 MET cc_start: 0.6227 (mpt) cc_final: 0.5952 (mmm) REVERT: A 1151 VAL cc_start: 0.4438 (OUTLIER) cc_final: 0.4230 (t) REVERT: A 1239 LYS cc_start: 0.7483 (tttt) cc_final: 0.7238 (tttp) REVERT: A 1501 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7164 (pt0) outliers start: 51 outliers final: 12 residues processed: 238 average time/residue: 1.6758 time to fit residues: 437.6668 Evaluate side-chains 212 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 973 LYS Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1501 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 276 ASN A 383 HIS A 619 ASN A 883 HIS A 942 GLN A1127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19162 Z= 0.368 Angle : 0.619 6.663 25997 Z= 0.328 Chirality : 0.046 0.222 2741 Planarity : 0.006 0.063 3260 Dihedral : 12.165 103.135 3004 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.12 % Allowed : 9.48 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2168 helix: 0.82 (0.18), residues: 778 sheet: 0.33 (0.26), residues: 363 loop : -0.32 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 474 HIS 0.007 0.001 HIS A 871 PHE 0.018 0.002 PHE A1361 TYR 0.015 0.002 TYR A 804 ARG 0.008 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 195 time to evaluate : 2.128 Fit side-chains REVERT: B 16 LYS cc_start: 0.7276 (mmmt) cc_final: 0.6990 (mmmt) REVERT: B 24 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6989 (mmm) REVERT: B 32 LYS cc_start: 0.8078 (tttt) cc_final: 0.7754 (ttpp) REVERT: B 38 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7860 (mtm) REVERT: B 78 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6882 (mtpp) REVERT: B 198 TYR cc_start: 0.7359 (m-80) cc_final: 0.7133 (m-80) REVERT: B 362 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6323 (tm-30) REVERT: B 368 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7710 (ttm110) REVERT: B 377 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6053 (mmt180) REVERT: B 400 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6747 (mtm-85) REVERT: B 453 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: B 483 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: B 500 MET cc_start: 0.8763 (mtt) cc_final: 0.8534 (mtt) REVERT: B 667 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5720 (tm-30) REVERT: A 3 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 93 GLU cc_start: 0.6707 (pm20) cc_final: 0.6271 (mp0) REVERT: A 97 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6945 (ptt90) REVERT: A 283 ARG cc_start: 0.7740 (tpt-90) cc_final: 0.6457 (ttp-110) REVERT: A 311 ASP cc_start: 0.6383 (t0) cc_final: 0.6092 (t0) REVERT: A 373 THR cc_start: 0.7849 (m) cc_final: 0.7553 (t) REVERT: A 559 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8153 (mmm) REVERT: A 605 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6779 (mm-30) REVERT: A 667 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: A 816 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7576 (tp40) REVERT: A 857 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: A 973 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7681 (ttmp) REVERT: A 1239 LYS cc_start: 0.7505 (tttt) cc_final: 0.7226 (tttp) REVERT: A 1250 GLN cc_start: 0.7270 (mt0) cc_final: 0.7021 (mt0) REVERT: A 1369 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: A 1457 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7555 (pp20) outliers start: 60 outliers final: 14 residues processed: 230 average time/residue: 1.7134 time to fit residues: 434.1808 Evaluate side-chains 221 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 973 LYS Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 589 ASN A 619 ASN A1127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19162 Z= 0.280 Angle : 0.553 5.822 25997 Z= 0.295 Chirality : 0.043 0.209 2741 Planarity : 0.005 0.048 3260 Dihedral : 12.079 102.102 3003 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.92 % Allowed : 10.36 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2168 helix: 1.03 (0.19), residues: 778 sheet: 0.35 (0.26), residues: 368 loop : -0.33 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 474 HIS 0.006 0.001 HIS A 871 PHE 0.017 0.002 PHE A 776 TYR 0.016 0.002 TYR B 31 ARG 0.006 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 190 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: B 16 LYS cc_start: 0.7276 (mmmt) cc_final: 0.6992 (mmmt) REVERT: B 32 LYS cc_start: 0.8010 (tttt) cc_final: 0.7710 (ttpp) REVERT: B 38 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7908 (mtm) REVERT: B 94 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6657 (tttm) REVERT: B 198 TYR cc_start: 0.7330 (m-80) cc_final: 0.7130 (m-80) REVERT: B 362 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: B 368 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7705 (ttm110) REVERT: B 377 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6112 (mmt180) REVERT: B 400 ARG cc_start: 0.7209 (mtp180) cc_final: 0.6759 (mtm-85) REVERT: B 453 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: B 483 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: B 545 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 3 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 93 GLU cc_start: 0.6736 (pm20) cc_final: 0.6317 (mp0) REVERT: A 97 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6943 (ptt90) REVERT: A 283 ARG cc_start: 0.7725 (tpt-90) cc_final: 0.6443 (ttp-110) REVERT: A 311 ASP cc_start: 0.6302 (t0) cc_final: 0.6000 (t0) REVERT: A 559 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8133 (mmm) REVERT: A 605 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6770 (mm-30) REVERT: A 667 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 786 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7225 (mm-30) REVERT: A 816 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7531 (tp40) REVERT: A 857 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: A 973 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7710 (ttmp) REVERT: A 1239 LYS cc_start: 0.7489 (tttt) cc_final: 0.7218 (tttp) REVERT: A 1369 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: A 1457 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7507 (pp20) outliers start: 56 outliers final: 18 residues processed: 225 average time/residue: 1.7824 time to fit residues: 440.9337 Evaluate side-chains 220 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 973 LYS Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 0.0060 chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 109 optimal weight: 0.0770 chunk 191 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 619 ASN A 626 HIS A1127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19162 Z= 0.134 Angle : 0.444 5.286 25997 Z= 0.239 Chirality : 0.039 0.187 2741 Planarity : 0.004 0.045 3260 Dihedral : 11.753 98.114 3003 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.19 % Allowed : 11.61 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2168 helix: 1.56 (0.19), residues: 778 sheet: 0.40 (0.26), residues: 382 loop : -0.15 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 474 HIS 0.005 0.001 HIS A1483 PHE 0.018 0.001 PHE A 776 TYR 0.012 0.001 TYR A 577 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 2.027 Fit side-chains REVERT: B 16 LYS cc_start: 0.7250 (mmmt) cc_final: 0.6979 (mmmt) REVERT: B 24 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6893 (mmm) REVERT: B 32 LYS cc_start: 0.8006 (tttt) cc_final: 0.7702 (ttpp) REVERT: B 362 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: B 377 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6054 (mmt180) REVERT: B 388 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7064 (mm-30) REVERT: B 400 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6725 (mtm-85) REVERT: B 545 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 3 THR cc_start: 0.8595 (m) cc_final: 0.8241 (p) REVERT: A 97 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7056 (ptt180) REVERT: A 283 ARG cc_start: 0.7681 (tpt-90) cc_final: 0.6309 (ttp-110) REVERT: A 311 ASP cc_start: 0.6259 (t0) cc_final: 0.5953 (t0) REVERT: A 559 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7959 (mmm) REVERT: A 605 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6718 (mm-30) REVERT: A 786 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 816 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7416 (tp40) REVERT: A 857 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: A 896 ARG cc_start: 0.7596 (mmm160) cc_final: 0.7337 (mmm160) REVERT: A 1239 LYS cc_start: 0.7454 (tttt) cc_final: 0.7188 (tttp) REVERT: A 1457 GLU cc_start: 0.7684 (pt0) cc_final: 0.7378 (pp20) REVERT: A 1525 LYS cc_start: 0.7777 (mttt) cc_final: 0.7079 (tttt) outliers start: 42 outliers final: 13 residues processed: 233 average time/residue: 1.6485 time to fit residues: 423.1136 Evaluate side-chains 208 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 0.0000 chunk 213 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 99 optimal weight: 0.0670 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 619 ASN A 942 GLN A1127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19162 Z= 0.132 Angle : 0.439 5.180 25997 Z= 0.235 Chirality : 0.039 0.183 2741 Planarity : 0.004 0.043 3260 Dihedral : 11.668 97.430 3003 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.29 % Allowed : 11.98 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2168 helix: 1.73 (0.19), residues: 778 sheet: 0.46 (0.26), residues: 381 loop : -0.07 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 474 HIS 0.004 0.001 HIS A1483 PHE 0.015 0.001 PHE A 776 TYR 0.018 0.001 TYR B 31 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 2.087 Fit side-chains REVERT: B 16 LYS cc_start: 0.7234 (mmmt) cc_final: 0.6935 (mmmt) REVERT: B 24 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6843 (mmm) REVERT: B 32 LYS cc_start: 0.7990 (tttt) cc_final: 0.7698 (ttpp) REVERT: B 362 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: B 377 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6060 (mmt180) REVERT: B 388 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7041 (mm-30) REVERT: B 400 ARG cc_start: 0.7119 (mtp180) cc_final: 0.6712 (mtm-85) REVERT: B 722 MET cc_start: 0.7566 (mtm) cc_final: 0.7139 (mpp) REVERT: A 283 ARG cc_start: 0.7680 (tpt-90) cc_final: 0.6277 (ttp-110) REVERT: A 311 ASP cc_start: 0.6260 (t0) cc_final: 0.5947 (t0) REVERT: A 361 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7478 (mp) REVERT: A 559 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: A 605 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6671 (mm-30) REVERT: A 786 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 816 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7416 (tp40) REVERT: A 896 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7122 (tpt170) REVERT: A 1037 MET cc_start: 0.6117 (mpt) cc_final: 0.5867 (ptp) REVERT: A 1457 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7309 (pp20) REVERT: A 1501 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: A 1525 LYS cc_start: 0.7768 (mttt) cc_final: 0.7087 (tttt) outliers start: 44 outliers final: 16 residues processed: 225 average time/residue: 1.7262 time to fit residues: 427.9953 Evaluate side-chains 215 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1443 ARG Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1501 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 0.0000 chunk 156 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 276 ASN A 619 ASN A 626 HIS A 942 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19162 Z= 0.180 Angle : 0.477 10.321 25997 Z= 0.253 Chirality : 0.040 0.186 2741 Planarity : 0.004 0.042 3260 Dihedral : 11.730 98.568 3003 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.24 % Allowed : 12.14 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2168 helix: 1.67 (0.19), residues: 778 sheet: 0.41 (0.25), residues: 388 loop : -0.07 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 474 HIS 0.004 0.001 HIS A1483 PHE 0.013 0.001 PHE A 776 TYR 0.016 0.001 TYR A 577 ARG 0.004 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 2.072 Fit side-chains REVERT: B 16 LYS cc_start: 0.7193 (mmmt) cc_final: 0.6934 (mmmt) REVERT: B 24 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6902 (mmm) REVERT: B 32 LYS cc_start: 0.8007 (tttt) cc_final: 0.7699 (ttpp) REVERT: B 362 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: B 368 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7709 (ttm110) REVERT: B 377 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.6032 (mmt180) REVERT: B 388 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7116 (mm-30) REVERT: B 389 GLN cc_start: 0.7938 (tt0) cc_final: 0.7536 (pt0) REVERT: B 400 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6704 (mtm-85) REVERT: B 453 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: A 1 MET cc_start: 0.6198 (tpp) cc_final: 0.5982 (tpp) REVERT: A 283 ARG cc_start: 0.7702 (tpt-90) cc_final: 0.6300 (ttp-110) REVERT: A 311 ASP cc_start: 0.6293 (t0) cc_final: 0.5943 (t0) REVERT: A 361 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7355 (mp) REVERT: A 559 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: A 601 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6221 (ptpp) REVERT: A 605 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6688 (mm-30) REVERT: A 816 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7415 (tp40) REVERT: A 1037 MET cc_start: 0.6304 (mpt) cc_final: 0.5907 (ptp) REVERT: A 1250 GLN cc_start: 0.7103 (mt0) cc_final: 0.6809 (mt0) REVERT: A 1457 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: A 1501 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7144 (pt0) REVERT: A 1525 LYS cc_start: 0.7787 (mttt) cc_final: 0.7039 (tttm) outliers start: 43 outliers final: 20 residues processed: 223 average time/residue: 1.6773 time to fit residues: 411.6789 Evaluate side-chains 220 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1501 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 276 ASN A 619 ASN A 942 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19162 Z= 0.166 Angle : 0.471 8.677 25997 Z= 0.249 Chirality : 0.040 0.183 2741 Planarity : 0.004 0.042 3260 Dihedral : 11.714 98.549 3003 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.93 % Allowed : 12.66 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2168 helix: 1.68 (0.19), residues: 778 sheet: 0.40 (0.25), residues: 388 loop : -0.05 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1509 HIS 0.004 0.001 HIS A1483 PHE 0.014 0.001 PHE A 776 TYR 0.016 0.001 TYR A 577 ARG 0.004 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 2.260 Fit side-chains REVERT: B 16 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6933 (mmmt) REVERT: B 24 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: B 32 LYS cc_start: 0.8002 (tttt) cc_final: 0.7695 (ttpp) REVERT: B 148 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6613 (mm-30) REVERT: B 362 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: B 377 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6046 (mmt180) REVERT: B 388 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7119 (mm-30) REVERT: B 389 GLN cc_start: 0.7937 (tt0) cc_final: 0.7535 (pt0) REVERT: B 400 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6699 (mtm-85) REVERT: A 283 ARG cc_start: 0.7703 (tpt-90) cc_final: 0.6299 (ttp-110) REVERT: A 311 ASP cc_start: 0.6291 (t0) cc_final: 0.5930 (t0) REVERT: A 361 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7351 (mp) REVERT: A 559 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8032 (mmm) REVERT: A 601 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6220 (ptpp) REVERT: A 605 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6665 (mm-30) REVERT: A 816 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7417 (tp40) REVERT: A 1037 MET cc_start: 0.6312 (mpt) cc_final: 0.5860 (ptp) REVERT: A 1250 GLN cc_start: 0.7117 (mt0) cc_final: 0.6830 (mt0) REVERT: A 1457 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7327 (pp20) REVERT: A 1525 LYS cc_start: 0.7778 (mttt) cc_final: 0.7034 (tttm) outliers start: 37 outliers final: 20 residues processed: 217 average time/residue: 1.7079 time to fit residues: 409.1529 Evaluate side-chains 217 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 276 ASN A 619 ASN A 942 GLN A1127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19162 Z= 0.270 Angle : 0.541 7.109 25997 Z= 0.286 Chirality : 0.043 0.201 2741 Planarity : 0.005 0.045 3260 Dihedral : 11.894 101.087 3003 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 12.81 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2168 helix: 1.42 (0.19), residues: 778 sheet: 0.35 (0.26), residues: 384 loop : -0.18 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1509 HIS 0.006 0.001 HIS A 871 PHE 0.015 0.002 PHE B 471 TYR 0.019 0.002 TYR A 577 ARG 0.005 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.937 Fit side-chains REVERT: B 16 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6961 (mmmt) REVERT: B 24 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6988 (mmm) REVERT: B 32 LYS cc_start: 0.8011 (tttt) cc_final: 0.7694 (ttpp) REVERT: B 148 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6713 (mm-30) REVERT: B 362 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: B 368 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7720 (ttm110) REVERT: B 377 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6067 (mmt180) REVERT: B 388 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7140 (mm-30) REVERT: B 400 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6714 (mtm-85) REVERT: A 93 GLU cc_start: 0.6656 (pm20) cc_final: 0.6248 (mp0) REVERT: A 283 ARG cc_start: 0.7742 (tpt-90) cc_final: 0.6380 (ttp-110) REVERT: A 311 ASP cc_start: 0.6288 (t0) cc_final: 0.5936 (t0) REVERT: A 361 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7382 (mp) REVERT: A 601 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6227 (ptpp) REVERT: A 605 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6728 (mm-30) REVERT: A 816 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7590 (tp40) REVERT: A 1250 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6838 (mt0) REVERT: A 1369 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6840 (mt-10) REVERT: A 1457 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: A 1501 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7153 (pt0) REVERT: A 1525 LYS cc_start: 0.7842 (mttt) cc_final: 0.7071 (tttt) outliers start: 37 outliers final: 18 residues processed: 213 average time/residue: 1.7026 time to fit residues: 399.0418 Evaluate side-chains 214 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Chi-restraints excluded: chain A residue 1501 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 276 ASN A 619 ASN A 942 GLN A1127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19162 Z= 0.200 Angle : 0.499 7.151 25997 Z= 0.265 Chirality : 0.041 0.191 2741 Planarity : 0.004 0.045 3260 Dihedral : 11.826 100.227 3003 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 13.07 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2168 helix: 1.48 (0.19), residues: 778 sheet: 0.33 (0.25), residues: 388 loop : -0.14 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1509 HIS 0.004 0.001 HIS A1483 PHE 0.015 0.002 PHE A 776 TYR 0.024 0.001 TYR B 31 ARG 0.004 0.000 ARG A 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 2.176 Fit side-chains REVERT: B 16 LYS cc_start: 0.7237 (mmmt) cc_final: 0.6966 (mmmt) REVERT: B 24 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6985 (mmm) REVERT: B 32 LYS cc_start: 0.7987 (tttt) cc_final: 0.7677 (ttpp) REVERT: B 38 MET cc_start: 0.8002 (mtm) cc_final: 0.7612 (mtm) REVERT: B 362 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: B 377 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6050 (mmt180) REVERT: B 388 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7104 (mm-30) REVERT: B 400 ARG cc_start: 0.7112 (mtp180) cc_final: 0.6728 (mtm-85) REVERT: A 93 GLU cc_start: 0.6654 (pm20) cc_final: 0.6272 (mp0) REVERT: A 283 ARG cc_start: 0.7737 (tpt-90) cc_final: 0.6338 (ttp-110) REVERT: A 311 ASP cc_start: 0.6259 (t0) cc_final: 0.5899 (t0) REVERT: A 361 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 559 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8068 (mmm) REVERT: A 601 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6272 (ptpp) REVERT: A 605 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6708 (mm-30) REVERT: A 816 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7509 (tp40) REVERT: A 857 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: A 1250 GLN cc_start: 0.7184 (mt0) cc_final: 0.6838 (mt0) REVERT: A 1457 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: A 1525 LYS cc_start: 0.7825 (mttt) cc_final: 0.7072 (tttt) outliers start: 31 outliers final: 19 residues processed: 208 average time/residue: 1.7175 time to fit residues: 392.3573 Evaluate side-chains 213 residues out of total 1920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 377 ARG Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 559 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1399 SER Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1499 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 7.9990 chunk 53 optimal weight: 0.0000 chunk 161 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 276 ASN A 619 ASN A 942 GLN A1127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.184013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138944 restraints weight = 16521.998| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.55 r_work: 0.3308 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19162 Z= 0.138 Angle : 0.452 7.170 25997 Z= 0.241 Chirality : 0.039 0.181 2741 Planarity : 0.004 0.043 3260 Dihedral : 11.662 97.823 3003 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.51 % Allowed : 13.33 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2168 helix: 1.69 (0.19), residues: 779 sheet: 0.40 (0.25), residues: 388 loop : -0.03 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1509 HIS 0.004 0.001 HIS A1483 PHE 0.015 0.001 PHE A 776 TYR 0.024 0.001 TYR B 31 ARG 0.003 0.000 ARG A 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7737.69 seconds wall clock time: 138 minutes 23.47 seconds (8303.47 seconds total)